Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
NPHP4	261734	broad.mit.edu	37	1	5993284	5993284	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:5993284G>A	uc001alq.1	-	10	1491	c.1225C>T	c.(1225-1227)CTG>TTG	p.L409L	NPHP4_uc001als.1_RNA|NPHP4_uc009vlt.1_RNA|NPHP4_uc001alt.1_RNA	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	409					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		CCACCCTGCAGAGGCAGGGTC	0.542													20	67	---	---	---	---	PASS
GPR153	387509	broad.mit.edu	37	1	6313942	6313942	+	Missense_Mutation	SNP	C	T	T	rs146978653	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:6313942C>T	uc001amp.1	-	3	882	c.622G>A	c.(622-624)GAC>AAC	p.D208N		NM_207370	NP_997253	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	208	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		GCGCGGCGGTCGGCCTGGCGC	0.701													4	19	---	---	---	---	PASS
CAMTA1	23261	broad.mit.edu	37	1	7792647	7792647	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:7792647G>C	uc001aoi.2	+	12	3261	c.3054G>C	c.(3052-3054)GGG>GGC	p.G1018G	CAMTA1_uc010nzv.1_Silent_p.G105G|CAMTA1_uc001aok.3_Silent_p.G61G	NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	1018					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GGAATGGAGGGAGCCAGGCAC	0.622													6	5	---	---	---	---	PASS
SLC45A1	50651	broad.mit.edu	37	1	8403861	8403861	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:8403861C>G	uc001apb.2	+	8	2035	c.2035C>G	c.(2035-2037)CTG>GTG	p.L679V	SLC45A1_uc001apc.2_Missense_Mutation_p.L377V	NM_001080397	NP_001073866	Q9Y2W3	S45A1_HUMAN	DNB5	679					carbohydrate transport	integral to membrane	symporter activity			central_nervous_system(2)|pancreas(1)|skin(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		GGACATCTCTCTGCTGAGCTG	0.652													18	57	---	---	---	---	PASS
VPS13D	55187	broad.mit.edu	37	1	12336242	12336242	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:12336242C>T	uc001atv.2	+	19	2738	c.2597C>T	c.(2596-2598)TCA>TTA	p.S866L	VPS13D_uc001atw.2_Missense_Mutation_p.S866L|VPS13D_uc001atx.2_Missense_Mutation_p.S54L	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	866					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ATTTATACTTCAGATCCCAAA	0.408											OREG0013110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	60	---	---	---	---	PASS
IGSF21	84966	broad.mit.edu	37	1	18691730	18691730	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:18691730G>C	uc001bau.1	+	6	937	c.554G>C	c.(553-555)CGA>CCA	p.R185P	IGSF21_uc001bav.1_Missense_Mutation_p.R6P	NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor	185						extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		TATTTCAAACGAGATGGGGAA	0.557													21	48	---	---	---	---	PASS
EPHA8	2046	broad.mit.edu	37	1	22902721	22902721	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:22902721C>T	uc001bfx.1	+	3	296	c.171C>T	c.(169-171)ATC>ATT	p.I57I	EPHA8_uc001bfw.2_Silent_p.I57I	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	57	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGGACTCCATCAACGAGGTGG	0.597													13	110	---	---	---	---	PASS
SRRM1	10250	broad.mit.edu	37	1	24995649	24995649	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:24995649C>G	uc001bjm.2	+	14	1999	c.1775C>G	c.(1774-1776)TCT>TGT	p.S592C	SRRM1_uc010oel.1_Missense_Mutation_p.S604C|SRRM1_uc009vrh.1_Missense_Mutation_p.S565C|SRRM1_uc009vri.1_Missense_Mutation_p.S521C	NM_005839	NP_005830	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	592	Pro-rich.|Necessary for speckles and matrix localization.|Arg-rich.|Ser-rich.				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck	DNA binding|protein binding|RNA binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CGCTCACCTTCTCCTAGAAGA	0.468													14	67	---	---	---	---	PASS
WDTC1	23038	broad.mit.edu	37	1	27618778	27618778	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:27618778G>T	uc009vst.2	+	7	1087	c.552G>T	c.(550-552)CTG>CTT	p.L184L	WDTC1_uc001bno.2_Silent_p.L184L|WDTC1_uc001bnp.1_RNA	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	184	WD 4.						protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		GTGGCCAGCTGGTGGAGGCCA	0.567													35	89	---	---	---	---	PASS
ZMYM6	9204	broad.mit.edu	37	1	35485050	35485050	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:35485050G>C	uc001byh.2	-	4	560	c.332C>G	c.(331-333)TCT>TGT	p.S111C	ZMYM6_uc001byf.1_Missense_Mutation_p.S111C|ZMYM6_uc010oht.1_Missense_Mutation_p.S14C|ZMYM6_uc009vup.2_Intron|ZMYM6_uc009vuq.1_Missense_Mutation_p.S111C|ZMYM6_uc009vur.1_Intron|ZMYM6_uc001byj.2_Missense_Mutation_p.S111C|ZMYM6_uc001byi.2_Missense_Mutation_p.S111C|ZMYM6_uc001byk.2_Missense_Mutation_p.S111C	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258	111					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				GAGCTGAGTAGATCCTGTCTT	0.448													50	92	---	---	---	---	PASS
MRPS15	64960	broad.mit.edu	37	1	36921956	36921956	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:36921956C>T	uc001cas.2	-	7	632	c.468G>A	c.(466-468)CTG>CTA	p.L156L		NM_031280	NP_112570	P82914	RT15_HUMAN	mitochondrial ribosomal protein S15 precursor	156					translation	mitochondrial small ribosomal subunit|nuclear membrane	structural constituent of ribosome			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TGCTCATTAGCAGATAGCGTT	0.383													22	89	---	---	---	---	PASS
IPO13	9670	broad.mit.edu	37	1	44422286	44422286	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:44422286G>C	uc001ckx.2	+	4	1812	c.1017G>C	c.(1015-1017)ATG>ATC	p.M339I		NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	339	HEAT 5.				protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TCGTCAACATGATTATGTTCT	0.537													17	179	---	---	---	---	PASS
RNF220	55182	broad.mit.edu	37	1	45110680	45110680	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:45110680G>A	uc001clv.1	+	10	1597	c.1237G>A	c.(1237-1239)GAT>AAT	p.D413N	RNF220_uc001clw.1_Missense_Mutation_p.D413N|RNF220_uc010oky.1_Missense_Mutation_p.D200N|RNF220_uc010okz.1_Missense_Mutation_p.D155N|RNF220_uc001clx.1_Missense_Mutation_p.D129N|RNF220_uc001cly.1_Missense_Mutation_p.D92N|RNF220_uc001clz.1_Missense_Mutation_p.D92N|RNF220_uc001cma.1_Missense_Mutation_p.D92N|TMEM53_uc001cmb.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220	413					protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						CACAGAGGCTGATGTCATCCC	0.587													9	36	---	---	---	---	PASS
TESK2	10420	broad.mit.edu	37	1	45887417	45887417	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:45887417G>A	uc001cns.1	-	3	727	c.324C>T	c.(322-324)CTC>CTT	p.L108L	TESK2_uc009vxr.1_Silent_p.L108L|TESK2_uc010olo.1_Silent_p.L25L|TESK2_uc009vxs.1_5'UTR|TESK2_uc010olp.1_Silent_p.L108L	NM_007170	NP_009101	Q96S53	TESK2_HUMAN	testis-specific protein kinase 2	108	Protein kinase.				actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)					TGGGATGGGAGAGTCTATTCA	0.428													11	182	---	---	---	---	PASS
TESK2	10420	broad.mit.edu	37	1	45887497	45887497	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:45887497G>A	uc001cns.1	-	3	647	c.244C>T	c.(244-246)CAG>TAG	p.Q82*	TESK2_uc009vxr.1_Nonsense_Mutation_p.Q82*|TESK2_uc010olo.1_5'UTR|TESK2_uc009vxs.1_5'UTR|TESK2_uc010olp.1_Nonsense_Mutation_p.Q82*	NM_007170	NP_009101	Q96S53	TESK2_HUMAN	testis-specific protein kinase 2	82	Protein kinase.				actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)					GCCATCACCTGACCAGAAGCT	0.418													6	136	---	---	---	---	PASS
ATPAF1	64756	broad.mit.edu	37	1	47123837	47123837	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:47123837C>G	uc001cqh.2	-	4	556	c.451G>C	c.(451-453)GAG>CAG	p.E151Q	ATPAF1_uc001cqg.2_5'UTR|ATPAF1_uc009vyk.2_5'UTR|ATPAF1_uc010omg.1_Missense_Mutation_p.E63Q|ATPAF1_uc001cqi.2_Missense_Mutation_p.E151Q	NM_022745	NP_073582	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly	151					protein complex assembly	mitochondrion	protein binding				0	Acute lymphoblastic leukemia(166;0.155)					TTTACCATCTCAATGTTAAAG	0.308													3	72	---	---	---	---	PASS
NRD1	4898	broad.mit.edu	37	1	52289374	52289374	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:52289374T>A	uc001ctc.3	-	9	1647	c.1325A>T	c.(1324-1326)TAC>TTC	p.Y442F	NRD1_uc009vzb.2_Missense_Mutation_p.Y137F|NRD1_uc001ctd.3_Missense_Mutation_p.Y374F|NRD1_uc001cte.2_Missense_Mutation_p.Y310F|NRD1_uc001ctf.2_Missense_Mutation_p.Y374F|NRD1_uc010ong.1_RNA|NRD1_uc009vzc.1_Missense_Mutation_p.Y242F	NM_002525	NP_002516	O43847	NRDC_HUMAN	nardilysin isoform a	373					cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0						ATGAGAAGAGTAGTAACGCAT	0.358													23	130	---	---	---	---	PASS
ZCCHC11	23318	broad.mit.edu	37	1	52991868	52991868	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:52991868T>C	uc001ctx.2	-	2	319	c.85A>G	c.(85-87)ATA>GTA	p.I29V	ZCCHC11_uc001cty.2_Missense_Mutation_p.I29V|ZCCHC11_uc001ctz.2_Missense_Mutation_p.I29V|ZCCHC11_uc009vze.1_Missense_Mutation_p.I29V|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Missense_Mutation_p.I29V|ZCCHC11_uc001cuc.2_RNA|ZCCHC11_uc001cud.2_Missense_Mutation_p.I29V	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	29					miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						TGATTACCTATAACTTGAACT	0.284													22	52	---	---	---	---	PASS
HOOK1	51361	broad.mit.edu	37	1	60312778	60312778	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:60312778G>A	uc009wad.2	+	11	952	c.850G>A	c.(850-852)GAA>AAA	p.E284K	HOOK1_uc001czo.2_Missense_Mutation_p.E284K|HOOK1_uc001czp.2_RNA|HOOK1_uc010oor.1_Missense_Mutation_p.E242K	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1	284	Potential.|Sufficient for interaction with microtubules.				early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)					GCAGCTAATCGAATTCCAGCA	0.348													24	152	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62503707	62503707	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:62503707C>G	uc001dab.2	+	30	4132	c.4018C>G	c.(4018-4020)CCA>GCA	p.P1340A	INADL_uc009waf.1_Missense_Mutation_p.P1340A|INADL_uc001daa.2_Missense_Mutation_p.P1340A|INADL_uc001dad.3_Missense_Mutation_p.P1037A|INADL_uc001dac.2_RNA|INADL_uc010oot.1_Missense_Mutation_p.P124A|INADL_uc009wag.2_Missense_Mutation_p.P124A|INADL_uc010oou.1_Missense_Mutation_p.P13A	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1340					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						ATCAAGTTCTCCATCTTCTAT	0.383													11	160	---	---	---	---	PASS
L1TD1	54596	broad.mit.edu	37	1	62672662	62672662	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:62672662G>A	uc001dae.3	+	3	664	c.362G>A	c.(361-363)GGA>GAA	p.G121E		NM_019079	NP_061952	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	121										ovary(1)|skin(1)	2						aaaatagaaggagaaaactct	0.050													24	127	---	---	---	---	PASS
SLC35D1	23169	broad.mit.edu	37	1	67486081	67486081	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:67486081G>C	uc001ddk.2	-	10	1231	c.847C>G	c.(847-849)CTT>GTT	p.L283V	SLC35D1_uc010oph.1_Missense_Mutation_p.L204V	NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic	283	Helical; (Potential).				chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	GTAGTTGTAAGAGCAGAATTA	0.328													12	140	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75112383	75112383	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:75112383G>T	uc001dgg.2	-	3	430	c.211C>A	c.(211-213)CAG>AAG	p.Q71K		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	71										ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						AAAATTGCCTGGGCTAAGCAT	0.294													3	10	---	---	---	---	PASS
AK5	26289	broad.mit.edu	37	1	77759537	77759537	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:77759537C>G	uc001dhn.2	+	3	564	c.307C>G	c.(307-309)CAA>GAA	p.Q103E	AK5_uc001dho.2_Missense_Mutation_p.Q77E|AK5_uc001dhm.1_Intron	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1	103					ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						TCCAATCCATCAATTCTCCAT	0.418													4	76	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103380302	103380302	+	Silent	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:103380302A>T	uc001dul.2	-	51	4200	c.3882T>A	c.(3880-3882)GGT>GGA	p.G1294G	COL11A1_uc001duk.2_Silent_p.G490G|COL11A1_uc001dum.2_Silent_p.G1306G|COL11A1_uc001dun.2_Silent_p.G1255G|COL11A1_uc009weh.2_Silent_p.G1178G	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	1294	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GCCCCTTGGCACCTGGAGGTC	0.493													5	44	---	---	---	---	PASS
SORT1	6272	broad.mit.edu	37	1	109883349	109883349	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:109883349C>T	uc001dxm.1	-	10	1310	c.1261G>A	c.(1261-1263)GAA>AAA	p.E421K	SORT1_uc010ovi.1_Missense_Mutation_p.E284K	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein	421	Extracellular (Potential).				endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		GACTCACCTTCGGAGAGCACG	0.552													9	87	---	---	---	---	PASS
PSMA5	5686	broad.mit.edu	37	1	109944647	109944647	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:109944647G>C	uc001dxn.2	-	9	799	c.714C>G	c.(712-714)ATC>ATG	p.I238M	PSMA5_uc010ovj.1_Missense_Mutation_p.I180M	NM_002790	NP_002781	P28066	PSA5_HUMAN	proteasome alpha 5 subunit	238					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	protein binding|threonine-type endopeptidase activity				0		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		AAATGTCCTTGATAACCTCTT	0.408													27	179	---	---	---	---	PASS
CTTNBP2NL	55917	broad.mit.edu	37	1	112958854	112958854	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:112958854G>A	uc001ebx.2	+	3	295	c.67G>A	c.(67-69)GAA>AAA	p.E23K		NM_018704	NP_061174	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	23						actin cytoskeleton	protein binding			central_nervous_system(2)|ovary(1)	3		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGAGAGCTTGAAGCAAGGGA	0.338													8	108	---	---	---	---	PASS
LRIG2	9860	broad.mit.edu	37	1	113657094	113657094	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:113657094G>C	uc001edf.1	+	15	2324	c.2126G>C	c.(2125-2127)CGA>CCA	p.R709P	LRIG2_uc009wgn.1_Missense_Mutation_p.R606P	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	709	Ig-like C2-type 3.|Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		ACAGTAACACGAGGTGAAACT	0.433													30	73	---	---	---	---	PASS
TTF2	8458	broad.mit.edu	37	1	117629135	117629135	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:117629135C>T	uc001egy.2	+	12	2171	c.2151C>T	c.(2149-2151)CTC>CTT	p.L717L		NM_003594	NP_003585	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase	717	Helicase ATP-binding.				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|termination of RNA polymerase II transcription	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		GTGCAAACCTCAATGTGGAGG	0.537													7	39	---	---	---	---	PASS
TRIM45	80263	broad.mit.edu	37	1	117654991	117654991	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:117654991G>T	uc001egz.2	-	6	2267	c.1679C>A	c.(1678-1680)TCT>TAT	p.S560Y	TRIM45_uc009whe.2_Missense_Mutation_p.S542Y|TRIM45_uc001eha.2_Missense_Mutation_p.S456Y	NM_025188	NP_079464	Q9H8W5	TRI45_HUMAN	tripartite motif-containing 45 isoform 1	560						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		TGTGCATTCAGATTTCTCATT	0.527													16	106	---	---	---	---	PASS
MAN1A2	10905	broad.mit.edu	37	1	118035835	118035835	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:118035835C>G	uc001ehd.1	+	9	1956	c.1235C>G	c.(1234-1236)TCA>TGA	p.S412*	MAN1A2_uc009whg.1_Nonsense_Mutation_p.S202*	NM_006699	NP_006690	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	412	Lumenal (Potential).				N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity				0	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		TGGTTGATGTCAGATAAAACA	0.368													5	70	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120468265	120468265	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:120468265G>A	uc001eik.2	-	25	4430	c.4174C>T	c.(4174-4176)CAG>TAG	p.Q1392*		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1392	Extracellular (Potential).|EGF-like 35.				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGCTGGCGCTGAGGGTGGCAG	0.682			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				7	40	---	---	---	---	PASS
SEC22B	9554	broad.mit.edu	37	1	145112515	145112515	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:145112515C>A	uc001eml.1	+	6	629	c.489C>A	c.(487-489)CTC>CTA	p.L163L	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron	NM_004892	NP_004883	O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B	163	v-SNARE coiled-coil homology.|Cytoplasmic (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome	protein binding				0						GAGAAGCACTCTCAGGTATCT	0.413													4	115	---	---	---	---	PASS
NOTCH2NL	388677	broad.mit.edu	37	1	145281550	145281550	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:145281550C>T	uc001emn.3	+	4	850	c.480C>T	c.(478-480)CTC>CTT	p.L160L	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_5'UTR|NOTCH2NL_uc001emm.3_Silent_p.L160L|NOTCH2NL_uc001emo.2_Silent_p.L160L|NOTCH2NL_uc010oyh.1_RNA	NM_203458	NP_982283	Q7Z3S9	NT2NL_HUMAN	Notch homolog 2 N-terminal like protein	160	EGF-like 5; calcium-binding (Potential).				cell differentiation|multicellular organismal development|Notch signaling pathway	cytoplasm|extracellular region	calcium ion binding			ovary(1)	1						GCACCTGCCTCAACCTGCCTG	0.562													12	249	---	---	---	---	PASS
HIST2H2BF	440689	broad.mit.edu	37	1	149783774	149783774	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:149783774C>T	uc001esr.2	-	1	155	c.105G>A	c.(103-105)AAG>AAA	p.K35K	HIST2H2BF_uc010pbj.1_Silent_p.K35K|HIST2H2BF_uc010pbk.1_Silent_p.K35K	NM_001024599	NP_001019770	Q5QNW6	H2B2F_HUMAN	histone cluster 2, H2bf isoform a	35					nucleosome assembly	nucleosome|nucleus	DNA binding				0	Breast(34;0.0124)|all_hematologic(923;0.127)					AGTAGCTCTCCTTGCGGCTGC	0.572													107	237	---	---	---	---	PASS
RPRD2	23248	broad.mit.edu	37	1	150429815	150429815	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:150429815C>T	uc009wlr.2	+	8	1123	c.922C>T	c.(922-924)CAA>TAA	p.Q308*	RPRD2_uc010pcc.1_Nonsense_Mutation_p.Q282*|RPRD2_uc001eup.3_Nonsense_Mutation_p.Q282*	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing	308							protein binding			ovary(1)	1						GAAGTTGGATCAATTGAAGTC	0.418													52	111	---	---	---	---	PASS
GOLPH3L	55204	broad.mit.edu	37	1	150620868	150620868	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:150620868C>T	uc001evj.2	-	5	1004	c.787G>A	c.(787-789)GAA>AAA	p.E263K	GOLPH3L_uc010pci.1_Missense_Mutation_p.E219K	NM_018178	NP_060648	Q9H4A5	GLP3L_HUMAN	Golgi phosphoprotein 3-like	263						Golgi cisterna membrane				ovary(1)	1	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			CCTTCCACTTCAGGGTCCAGT	0.488													25	127	---	---	---	---	PASS
S100A13	6284	broad.mit.edu	37	1	153591394	153591394	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:153591394C>G	uc001fcf.3	-	3	433	c.274G>C	c.(274-276)GAC>CAC	p.D92H	S100A14_uc001fce.2_5'Flank|S100A13_uc001fcg.2_Missense_Mutation_p.D92H|S100A13_uc009woh.2_Missense_Mutation_p.D92H|S100A13_uc001fch.2_Missense_Mutation_p.D92H|S100A13_uc001fci.2_Missense_Mutation_p.D92H|S100A13_uc001fcj.2_Missense_Mutation_p.D92H	NM_001024213	NP_001019384	Q99584	S10AD_HUMAN	S100 calcium binding protein A13	92					interleukin-1 alpha secretion|mast cell degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|extracellular space|nucleus|perinuclear region of cytoplasm	calcium ion binding|copper ion binding|fibroblast growth factor 1 binding|lipid binding|protein homodimerization activity|RAGE receptor binding|zinc ion binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		Amlexanox(DB01025)	ATCTTCAGGTCTTTCTTCTTC	0.517													33	242	---	---	---	---	PASS
NES	10763	broad.mit.edu	37	1	156641286	156641286	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:156641286C>T	uc001fpq.2	-	4	2827	c.2694G>A	c.(2692-2694)TGG>TGA	p.W898*		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	898	Tail.			QGAMNPLEKEIQEPLESVEVNQETFRLLEEENQESLRSLGA WNLENLRSPEE -> KSGGNESSRKGNSRTTGVCGSEPRDI QTPGRGESGIIEISGSMEPGEFEISRG (in Ref. 1; CAA46780).	brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCTCCAGGTTCCATGCTCCCA	0.468													11	93	---	---	---	---	PASS
CD1A	909	broad.mit.edu	37	1	158226844	158226844	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:158226844C>T	uc001frt.2	+	4	1406	c.873C>T	c.(871-873)GTC>GTT	p.V291V		NM_001763	NP_001754	P06126	CD1A_HUMAN	CD1A antigen precursor	291	Extracellular (Potential).|Ig-like.				antigen processing and presentation|immune response	endosome membrane|integral to plasma membrane|MHC class I protein complex				pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	AGGACATCGTCCTCTACTGGG	0.572													20	61	---	---	---	---	PASS
OR10R2	343406	broad.mit.edu	37	1	158449733	158449733	+	Missense_Mutation	SNP	G	T	T	rs146148080	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:158449733G>T	uc010pik.1	+	1	66	c.66G>T	c.(64-66)TTG>TTT	p.L22F	uc001fso.1_RNA	NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)					TGCAGATCTTGGCAGAAAACC	0.363													42	177	---	---	---	---	PASS
OR10R2	343406	broad.mit.edu	37	1	158449734	158449734	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:158449734G>T	uc010pik.1	+	1	67	c.67G>T	c.(67-69)GCA>TCA	p.A23S	uc001fso.1_RNA	NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	23	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)					GCAGATCTTGGCAGAAAACCT	0.363													42	176	---	---	---	---	PASS
NCSTN	23385	broad.mit.edu	37	1	160323932	160323932	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:160323932G>C	uc001fvx.2	+	11	1328	c.1204G>C	c.(1204-1206)GAG>CAG	p.E402Q	NCSTN_uc001fvy.2_Missense_Mutation_p.E382Q|NCSTN_uc010pjf.1_Missense_Mutation_p.E264Q|NCSTN_uc001fvz.2_Missense_Mutation_p.E182Q|NCSTN_uc010pjg.1_Missense_Mutation_p.E144Q	NM_015331	NP_056146	Q92542	NICA_HUMAN	nicastrin precursor	402	Extracellular (Potential).				amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane|melanosome	protein binding			ovary(1)|lung(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGCCACATTGGAGAAGAGTGG	0.567													7	54	---	---	---	---	PASS
B4GALT3	8703	broad.mit.edu	37	1	161141748	161141748	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:161141748C>T	uc001fyq.1	-	8	1302	c.1040G>A	c.(1039-1041)CGG>CAG	p.R347Q	PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron|B4GALT3_uc001fyo.1_Missense_Mutation_p.R127Q|B4GALT3_uc001fyp.1_RNA|B4GALT3_uc001fyr.1_Missense_Mutation_p.R347Q|B4GALT3_uc001fys.1_Missense_Mutation_p.R347Q	NM_003779	NP_003770	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	347	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|metal ion binding|N-acetyllactosamine synthase activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	CCGAGGACCCCGAGGGTCAGT	0.607													34	70	---	---	---	---	PASS
UHMK1	127933	broad.mit.edu	37	1	162469927	162469927	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:162469927C>T	uc001gcc.1	+	2	587	c.451C>T	c.(451-453)CAT>TAT	p.H151Y	UHMK1_uc001gcb.1_Missense_Mutation_p.H77Y|UHMK1_uc009wuu.1_Missense_Mutation_p.H151Y	NM_175866	NP_787062	Q8TAS1	UHMK1_HUMAN	kinase interacting stathmin	151	Protein kinase.				cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TTTTCTTCATCATGAGGGCTA	0.433													25	103	---	---	---	---	PASS
POGK	57645	broad.mit.edu	37	1	166818626	166818626	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:166818626C>G	uc001gdt.1	+	5	930	c.810C>G	c.(808-810)GTC>GTG	p.V270V	POGK_uc010ple.1_Silent_p.V185V|POGK_uc010plf.1_Silent_p.V152V	NM_017542	NP_060012	Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	270	HTH CENPB-type.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1						CCGAATATGTCAGATACATGC	0.572													11	77	---	---	---	---	PASS
C1orf9	51430	broad.mit.edu	37	1	172526451	172526451	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:172526451G>C	uc001giq.3	+	5	791	c.475G>C	c.(475-477)GCC>CCC	p.A159P	C1orf9_uc010pmm.1_Missense_Mutation_p.A159P|C1orf9_uc009wwd.2_Missense_Mutation_p.A122P|C1orf9_uc010pmn.1_Missense_Mutation_p.A122P|C1orf9_uc010pmo.1_RNA	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	159					multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)		TATTCCGATAGCCAAACCAAG	0.358													25	195	---	---	---	---	PASS
IVNS1ABP	10625	broad.mit.edu	37	1	185269418	185269418	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:185269418C>G	uc001grl.2	-	12	1923	c.1300G>C	c.(1300-1302)GAG>CAG	p.E434Q	IVNS1ABP_uc001gri.2_Missense_Mutation_p.E94Q|IVNS1ABP_uc001grj.2_Missense_Mutation_p.E94Q|IVNS1ABP_uc009wyj.2_Missense_Mutation_p.E216Q|IVNS1ABP_uc009wyk.2_RNA|IVNS1ABP_uc001grm.2_Missense_Mutation_p.E94Q	NM_006469	NP_006460	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	434	Kelch 2.				interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5						TCATACATCTCTCCACAACTC	0.413													5	49	---	---	---	---	PASS
IVNS1ABP	10625	broad.mit.edu	37	1	185270191	185270191	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:185270191C>T	uc001grl.2	-	10	1656	c.1033G>A	c.(1033-1035)GAG>AAG	p.E345K	IVNS1ABP_uc001gri.2_Missense_Mutation_p.E5K|IVNS1ABP_uc001grj.2_Missense_Mutation_p.E5K|IVNS1ABP_uc009wyj.2_Missense_Mutation_p.E127K|IVNS1ABP_uc009wyk.2_RNA|IVNS1ABP_uc001grm.2_Missense_Mutation_p.E5K	NM_006469	NP_006460	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	345	Sufficient for AHR interaction and signaling.				interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5						TCGATTAGCTCATCTTGTTGC	0.438													15	133	---	---	---	---	PASS
F13B	2165	broad.mit.edu	37	1	197019883	197019883	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:197019883C>A	uc001gtt.1	-	10	1726	c.1682G>T	c.(1681-1683)GGA>GTA	p.G561V		NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor	561	Sushi 9.				blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CTCCCTAGATCCTTCTAGGAA	0.353													23	71	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197390763	197390763	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:197390763A>T	uc001gtz.2	+	6	1940	c.1805A>T	c.(1804-1806)GAT>GTT	p.D602V	CRB1_uc010poz.1_Missense_Mutation_p.D533V|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Missense_Mutation_p.D490V|CRB1_uc010ppb.1_Missense_Mutation_p.D602V|CRB1_uc010ppc.1_Intron|CRB1_uc010ppd.1_Missense_Mutation_p.D83V|CRB1_uc001gub.1_Missense_Mutation_p.D251V	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	602	Extracellular (Potential).|Laminin G-like 1.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						CTTGAAAGTGATCAATCAATA	0.438													55	132	---	---	---	---	PASS
DENND1B	163486	broad.mit.edu	37	1	197479678	197479678	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:197479678T>C	uc010ppe.1	-	22	2518	c.2180A>G	c.(2179-2181)CAT>CGT	p.H727R	DENND1B_uc010ppf.1_RNA	NM_001142795	NP_001136267	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 1	Error:Variant_position_missing_in_Q6P3S1_after_alignment						clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0						CACTACTTCATGGAGCAGTCC	0.408													37	69	---	---	---	---	PASS
CAMSAP1L1	23271	broad.mit.edu	37	1	200822482	200822482	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:200822482C>T	uc001gvl.2	+	14	3985	c.3715C>T	c.(3715-3717)CGG>TGG	p.R1239W	CAMSAP1L1_uc001gvk.2_Missense_Mutation_p.R1228W|CAMSAP1L1_uc001gvm.2_Missense_Mutation_p.R1212W	NM_203459	NP_982284	Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein	1239						cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4						ATATATGAGGCGGAAACAACT	0.368													4	88	---	---	---	---	PASS
PPP1R12B	4660	broad.mit.edu	37	1	202464542	202464542	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:202464542C>T	uc001gya.1	+	16	2411	c.2267C>T	c.(2266-2268)TCA>TTA	p.S756L	PPP1R12B_uc001gxz.1_Missense_Mutation_p.S756L|PPP1R12B_uc001gyb.1_5'UTR|PPP1R12B_uc001gyc.1_5'UTR	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	756					regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			AATAGATTTTCAGTCCCTGAT	0.478													8	114	---	---	---	---	PASS
PPP1R12B	4660	broad.mit.edu	37	1	202464554	202464554	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:202464554C>A	uc001gya.1	+	16	2423	c.2279C>A	c.(2278-2280)TCT>TAT	p.S760Y	PPP1R12B_uc001gxz.1_Missense_Mutation_p.S760Y|PPP1R12B_uc001gyb.1_Translation_Start_Site|PPP1R12B_uc001gyc.1_Translation_Start_Site	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	760					regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			GTCCCTGATTCTGAGAGTTCA	0.468													9	101	---	---	---	---	PASS
SRGAP2	23380	broad.mit.edu	37	1	206566940	206566940	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:206566940C>G	uc001hdy.2	+	4	813	c.480C>G	c.(478-480)ATC>ATG	p.I160M	SRGAP2_uc009xbt.2_Missense_Mutation_p.I84M|SRGAP2_uc010prt.1_Missense_Mutation_p.I84M|SRGAP2_uc001hdx.2_Missense_Mutation_p.I160M|SRGAP2_uc010pru.1_Missense_Mutation_p.I84M|SRGAP2_uc010prv.1_Missense_Mutation_p.I84M	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	247					axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					TGAAGGCCATCAAAGCCCGGA	0.423													3	81	---	---	---	---	PASS
LAMB3	3914	broad.mit.edu	37	1	209791921	209791921	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:209791921G>A	uc001hhg.2	-	18	3175	c.2785C>T	c.(2785-2787)CTG>TTG	p.L929L	LAMB3_uc009xco.2_Silent_p.L929L|LAMB3_uc001hhh.2_Silent_p.L929L	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	929	Domain I.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|skin(2)|large_intestine(1)|ovary(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		ATCTTCTGCAGAACAGTAGCT	0.607													11	85	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215822039	215822039	+	Missense_Mutation	SNP	C	T	T	rs147532612	byFrequency	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:215822039C>T	uc001hku.1	-	66	14800	c.14413G>A	c.(14413-14415)GTA>ATA	p.V4805I		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4805	Fibronectin type-III 33.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAGGCCTCTACTCCAATAGAG	0.542										HNSCC(13;0.011)			30	56	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216373226	216373226	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:216373226G>T	uc001hku.1	-	17	3941	c.3554C>A	c.(3553-3555)TCC>TAC	p.S1185Y	USH2A_uc001hkv.2_Missense_Mutation_p.S1185Y	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1185	Extracellular (Potential).|Fibronectin type-III 2.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGGGGCACAGGACAAAATATA	0.428										HNSCC(13;0.011)			49	169	---	---	---	---	PASS
GPATCH2	55105	broad.mit.edu	37	1	217665061	217665061	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:217665061C>G	uc001hlf.1	-	8	1334	c.1238G>C	c.(1237-1239)AGA>ACA	p.R413T	GPATCH2_uc009xdq.1_RNA	NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	413						intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		CTTGTGTCCTCTTTCAGCTCG	0.313													18	97	---	---	---	---	PASS
MIA3	375056	broad.mit.edu	37	1	222802391	222802391	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:222802391C>T	uc001hnl.2	+	4	1838	c.1829C>T	c.(1828-1830)TCA>TTA	p.S610L	MIA3_uc009xea.1_Missense_Mutation_p.S446L	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	610	Extracellular (Potential).				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)		CACACGCTTTCAGTGGAGCAT	0.478													18	163	---	---	---	---	PASS
DISP1	84976	broad.mit.edu	37	1	223177892	223177892	+	Missense_Mutation	SNP	C	A	A	rs111796312	byFrequency	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:223177892C>A	uc001hnu.1	+	8	3300	c.3153C>A	c.(3151-3153)GAC>GAA	p.D1051E		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	1051	Helical; (Potential).				diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)		TGTCTGTAGACTTTGCCGTCC	0.542													63	128	---	---	---	---	PASS
DISP1	84976	broad.mit.edu	37	1	223177893	223177893	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:223177893T>G	uc001hnu.1	+	8	3301	c.3154T>G	c.(3154-3156)TTT>GTT	p.F1052V		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	1052	Helical; (Potential).				diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)		GTCTGTAGACTTTGCCGTCCA	0.537													62	129	---	---	---	---	PASS
LBR	3930	broad.mit.edu	37	1	225600282	225600282	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:225600282G>A	uc001hoy.2	-	8	1101	c.958C>T	c.(958-960)CAT>TAT	p.H320Y	LBR_uc001hoz.2_Missense_Mutation_p.H320Y|LBR_uc001hpa.1_Missense_Mutation_p.H320Y	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	320					cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		TACACGTAATGAAACTCTACG	0.408													15	84	---	---	---	---	PASS
C1orf55	163859	broad.mit.edu	37	1	226175869	226175869	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:226175869C>G	uc001hpu.3	-	6	915	c.862G>C	c.(862-864)GAC>CAC	p.D288H	C1orf55_uc001hpv.2_Missense_Mutation_p.D288H	NM_152608	NP_689821	Q6IQ49	CA055_HUMAN	hypothetical protein LOC163859	288										lung(1)	1	Breast(184;0.197)					CTCCCAGAGTCAGTCACCGGG	0.507													24	211	---	---	---	---	PASS
MRPL55	128308	broad.mit.edu	37	1	228295503	228295503	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:228295503G>A	uc001hry.2	-	2	838	c.94C>T	c.(94-96)CGA>TGA	p.R32*	MRPL55_uc001hrz.3_Nonsense_Mutation_p.R68*|MRPL55_uc009xex.2_Nonsense_Mutation_p.R32*|MRPL55_uc001hsa.3_Nonsense_Mutation_p.R32*|MRPL55_uc001hsb.3_Nonsense_Mutation_p.R32*|MRPL55_uc001hsc.3_Nonsense_Mutation_p.R32*|MRPL55_uc001hsd.3_Nonsense_Mutation_p.R32*|MRPL55_uc001hse.3_Nonsense_Mutation_p.R32*|MRPL55_uc001hsf.3_Nonsense_Mutation_p.R32*|MRPL55_uc001hsg.3_Nonsense_Mutation_p.R32*	NM_181465	NP_852130	Q7Z7F7	RM55_HUMAN	mitochondrial ribosomal protein L55 isoform a	32					translation	mitochondrial large ribosomal subunit	structural constituent of ribosome			central_nervous_system(1)	1		Prostate(94;0.0405)				CTGTCAGCTCGCCAGGAGGAT	0.627													17	65	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228400408	228400408	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:228400408C>G	uc009xez.1	+	2	968	c.924C>G	c.(922-924)CTC>CTG	p.L308L	OBSCN_uc001hsn.2_Silent_p.L308L|uc001hsm.1_RNA	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	308	Ig-like 3.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				ACCGCGGCCTCTACACCTGCA	0.682													4	38	---	---	---	---	PASS
ACTA1	58	broad.mit.edu	37	1	229567525	229567525	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:229567525G>A	uc001htm.2	-	6	1038	c.933C>T	c.(931-933)ATC>ATT	p.I311I		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	311					muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)	TGCGGTCAGCGATCCCAGGGT	0.602													14	114	---	---	---	---	PASS
COG2	22796	broad.mit.edu	37	1	230795272	230795272	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:230795272G>A	uc001htw.2	+	2	286	c.135G>A	c.(133-135)CTG>CTA	p.L45L	COG2_uc001htx.2_Silent_p.L45L|COG2_uc010pwc.1_5'UTR	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	45					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				TGGAAGAACTGAGAGATGACC	0.383													11	148	---	---	---	---	PASS
SIPA1L2	57568	broad.mit.edu	37	1	232551265	232551265	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:232551265G>C	uc001hvg.2	-	17	4895	c.4737C>G	c.(4735-4737)CTC>CTG	p.L1579L	SIPA1L2_uc001hvf.2_Silent_p.L653L	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1579					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CAGCATCCACGAGGTGGGTCC	0.582													21	96	---	---	---	---	PASS
TARBP1	6894	broad.mit.edu	37	1	234569206	234569206	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:234569206G>C	uc001hwd.2	-	14	2344	c.2344C>G	c.(2344-2346)CTT>GTT	p.L782V		NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1	782					regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TTTTTCAAAAGAGAAATAACT	0.398													17	110	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237806719	237806719	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:237806719C>G	uc001hyl.1	+	48	7434	c.7314C>G	c.(7312-7314)ATC>ATG	p.I2438M		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2438	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTATCAGCATCGCTTTTCAGA	0.438													27	130	---	---	---	---	PASS
CNST	163882	broad.mit.edu	37	1	246811316	246811316	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:246811316G>C	uc001ibp.2	+	9	2191	c.1813G>C	c.(1813-1815)GCC>CCC	p.A605P	CNST_uc001ibo.3_Missense_Mutation_p.A605P	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	605					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0						TGATGATCTTGCCAAAAGGAT	0.368													7	160	---	---	---	---	PASS
OR2B11	127623	broad.mit.edu	37	1	247615256	247615256	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:247615256C>A	uc010pyx.1	-	1	29	c.29G>T	c.(28-30)GGG>GTG	p.G10V		NM_001004492	NP_001004492	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B,	10	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			upper_aerodigestive_tract(1)	1	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			AGGGGAGTCCCCTAAGAAGCT	0.483													39	81	---	---	---	---	PASS
C1orf150	148823	broad.mit.edu	37	1	247737523	247737523	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:247737523A>G	uc001idf.2	+	5	292	c.247A>G	c.(247-249)AGC>GGC	p.S83G	C1orf150_uc009xgw.2_RNA|C1orf150_uc001ida.3_RNA|C1orf150_uc001idb.3_RNA|C1orf150_uc009xgx.2_RNA	NM_145278	NP_660321	Q5JQS6	CA150_HUMAN	hypothetical protein LOC148823	83											0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0241)			ATCCTCCCTGAGCTCCAATGA	0.453													19	113	---	---	---	---	PASS
OR11L1	391189	broad.mit.edu	37	1	248004481	248004481	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:248004481T>A	uc001idn.1	-	1	718	c.718A>T	c.(718-720)ACA>TCA	p.T240S		NM_001001959	NP_001001959	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L,	240	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GAGCCACATGTGGAAAAGGTC	0.493													27	67	---	---	---	---	PASS
TRIM58	25893	broad.mit.edu	37	1	248039238	248039238	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:248039238G>T	uc001ido.2	+	6	956	c.908G>T	c.(907-909)AGT>ATT	p.S303I	OR2W3_uc001idp.1_5'UTR	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	303	B30.2/SPRY.					intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GCGCACCCGAGTCTGCTCTTG	0.562													14	67	---	---	---	---	PASS
SH3BP5L	80851	broad.mit.edu	37	1	249106336	249106336	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr1:249106336C>A	uc001iew.1	-	7	1497	c.945G>T	c.(943-945)GGG>GGT	p.G315G	SH3BP5L_uc010pzp.1_Silent_p.G208G|SH3BP5L_uc010pzq.1_Silent_p.G283G|SH3BP5L_uc001iev.1_Silent_p.G196G	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	315											0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CCTCCTCCAGCCCCGCACCCT	0.736													5	13	---	---	---	---	PASS
CPSF3	51692	broad.mit.edu	37	2	9588382	9588382	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:9588382G>A	uc002qzo.1	+	11	1333	c.1298G>A	c.(1297-1299)CGA>CAA	p.R433Q	CPSF3_uc010ewx.1_Missense_Mutation_p.R384Q|CPSF3_uc002qzp.1_Missense_Mutation_p.R396Q|CPSF3_uc002qzq.1_Missense_Mutation_p.R10Q	NM_016207	NP_057291	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3,	433					histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GCACTGATTCGAGAATATGAA	0.358													15	40	---	---	---	---	PASS
TAF1B	9014	broad.mit.edu	37	2	9991696	9991696	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:9991696G>A	uc002qzz.2	+	4	332	c.232G>A	c.(232-234)GAA>AAA	p.E78K	TAF1B_uc010exc.2_Missense_Mutation_p.E78K|TAF1B_uc002qzy.3_Missense_Mutation_p.E78K|TAF1B_uc010yja.1_5'UTR|TAF1B_uc010exd.2_5'UTR	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B	78					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GTATGTGTGTGAAGGTTTCCA	0.343													27	127	---	---	---	---	PASS
TAF1B	9014	broad.mit.edu	37	2	9991740	9991740	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:9991740G>C	uc002qzz.2	+	4	376	c.276G>C	c.(274-276)AAG>AAC	p.K92N	TAF1B_uc010exc.2_Missense_Mutation_p.K92N|TAF1B_uc002qzy.3_Missense_Mutation_p.K92N|TAF1B_uc010yja.1_5'UTR|TAF1B_uc010exd.2_5'UTR	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B	92					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AAGCCTTAAAGAACCTTGGAG	0.343													23	115	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11706686	11706686	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:11706686G>A	uc002rbk.1	+	4	658	c.358G>A	c.(358-360)GTG>ATG	p.V120M	GREB1_uc002rbl.2_Missense_Mutation_p.V120M|GREB1_uc002rbm.2_Missense_Mutation_p.V10M|GREB1_uc002rbn.1_Missense_Mutation_p.V120M	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	120						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CTTTCTCCTCGTGGGGGTCAA	0.597													39	114	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15415908	15415908	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:15415908C>G	uc002rcc.1	-	44	5450	c.5424G>C	c.(5422-5424)ATG>ATC	p.M1808I	NBAS_uc010exl.1_Missense_Mutation_p.M880I|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1808										ovary(2)|liver(1)|skin(1)	4						CAAGAGGACTCATGTTTTCAT	0.353													27	89	---	---	---	---	PASS
ITSN2	50618	broad.mit.edu	37	2	24484607	24484607	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:24484607T>A	uc002rfe.2	-	21	2618	c.2360A>T	c.(2359-2361)GAT>GTT	p.D787V	ITSN2_uc002rff.2_Missense_Mutation_p.D760V|ITSN2_uc002rfg.2_Missense_Mutation_p.D787V	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1	787	SH3 1.				endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTTTTTTCATCAACCTACGG	0.333													5	47	---	---	---	---	PASS
TRMT61B	55006	broad.mit.edu	37	2	29092700	29092700	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:29092700C>T	uc002rmm.2	-	1	476	c.444G>A	c.(442-444)GAG>GAA	p.E148E	TRMT61B_uc002rmn.2_Silent_p.E148E|TRMT61B_uc010ezk.2_RNA	NM_017910	NP_060380	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B	148							tRNA (adenine-N1-)-methyltransferase activity				0						GAAAGGGTCTCTCTCTGGAAG	0.493													12	57	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	30987131	30987131	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:30987131T>C	uc002rnn.2	-	6	742	c.566A>G	c.(565-567)GAG>GGG	p.E189G	CAPN13_uc002rnp.1_Missense_Mutation_p.E189G	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	189	Calpain catalytic.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					CAGGGCATCCTCGAGGAAGCC	0.587													9	23	---	---	---	---	PASS
CDKL4	344387	broad.mit.edu	37	2	39411779	39411779	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:39411779C>G	uc002rrm.2	-	7	745	c.745G>C	c.(745-747)GAG>CAG	p.E249Q	CDKL4_uc010fal.1_Missense_Mutation_p.E249Q	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	249	Protein kinase.					cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)				AACTTTTCCTCAAGAGTTTCC	0.239													6	38	---	---	---	---	PASS
EML4	27436	broad.mit.edu	37	2	42483655	42483655	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:42483655C>T	uc002rsi.2	+	3	485	c.223C>T	c.(223-225)CGA>TGA	p.R75*	EML4_uc002rsh.3_Nonsense_Mutation_p.R75*|EML4_uc010fap.2_Nonsense_Mutation_p.R75*	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	75					microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						ACCAAGCCCTCGAGCAGTTAT	0.343			T	ALK	NSCLC								23	56	---	---	---	---	PASS
MSH6	2956	broad.mit.edu	37	2	48026133	48026133	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:48026133G>A	uc002rwd.3	+	4	1163	c.1011G>A	c.(1009-1011)TTG>TTA	p.L337L	MSH6_uc002rwc.2_Silent_p.L337L|MSH6_uc010fbj.2_Silent_p.L35L|MSH6_uc010yoi.1_Silent_p.L207L|MSH6_uc010yoj.1_Silent_p.L35L	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	337					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGAATACTTTGAGAGCTTTCT	0.448			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				77	333	---	---	---	---	PASS
KLRAQ1	129285	broad.mit.edu	37	2	48688336	48688336	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:48688336C>G	uc002rwm.2	+	7	844	c.659C>G	c.(658-660)TCA>TGA	p.S220*	KLRAQ1_uc002rwi.1_Nonsense_Mutation_p.S220*|KLRAQ1_uc002rwj.2_Nonsense_Mutation_p.S220*|KLRAQ1_uc002rwl.2_Nonsense_Mutation_p.S174*|KLRAQ1_uc002rwk.2_Nonsense_Mutation_p.S220*|KLRAQ1_uc010yok.1_Nonsense_Mutation_p.S220*	NM_001135629	NP_001129101	Q6ZMI0	KLRAQ_HUMAN	KLRAQ motif containing 1 isoform 1	220										ovary(1)	1						GAATCCTTATCAATCATCAAT	0.294													45	146	---	---	---	---	PASS
SPTBN1	6711	broad.mit.edu	37	2	54856492	54856492	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:54856492G>C	uc002rxu.2	+	14	2470	c.2221G>C	c.(2221-2223)GAG>CAG	p.E741Q	SPTBN1_uc002rxv.1_Missense_Mutation_p.E741Q|SPTBN1_uc002rxx.2_Missense_Mutation_p.E728Q	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	741	Spectrin 5.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			GAAGCGCCTGGAGGAGGCCTC	0.587													9	256	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55561844	55561844	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:55561844C>T	uc002ryv.2	-	15	2955	c.2113G>A	c.(2113-2115)GAA>AAA	p.E705K	CCDC88A_uc010yoz.1_Missense_Mutation_p.E705K|CCDC88A_uc010ypa.1_Missense_Mutation_p.E705K|CCDC88A_uc010ypb.1_Missense_Mutation_p.E607K|CCDC88A_uc002ryu.2_5'UTR|CCDC88A_uc002ryw.2_5'UTR	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	705	Potential.				activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						CTTCGCAGTTCTAAGTTTTCC	0.333													25	228	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55576656	55576656	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:55576656C>T	uc002ryv.2	-	9	1722	c.880G>A	c.(880-882)GAG>AAG	p.E294K	CCDC88A_uc010yoz.1_Missense_Mutation_p.E294K|CCDC88A_uc010ypa.1_Missense_Mutation_p.E294K|CCDC88A_uc010ypb.1_Missense_Mutation_p.E196K	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	294	Potential.				activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						GTACAAACCTCTTGTTGCAGC	0.328													5	236	---	---	---	---	PASS
SMEK2	57223	broad.mit.edu	37	2	55806830	55806830	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:55806830C>G	uc002rzc.2	-	9	1828	c.1453G>C	c.(1453-1455)GAC>CAC	p.D485H	SMEK2_uc002rzb.2_Missense_Mutation_p.D485H|SMEK2_uc002rzd.2_Missense_Mutation_p.D485H|SMEK2_uc002rza.2_Missense_Mutation_p.D361H	NM_001122964	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 isoform 1	485						microtubule organizing center|nucleus	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TCACATTTGTCTTCTGAAGTA	0.318													15	199	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61558465	61558465	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:61558465T>C	uc002sbe.2	-	20	2898	c.2876A>G	c.(2875-2877)GAT>GGT	p.D959G		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	959					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TACCAAATTATCAAAGAAAAG	0.343													131	71	---	---	---	---	PASS
PLEK	5341	broad.mit.edu	37	2	68608007	68608007	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:68608007C>G	uc002sen.3	+	3	513	c.351C>G	c.(349-351)TCC>TCG	p.S117S	PLEK_uc010fde.2_Silent_p.S117S	NM_002664	NP_002655	P08567	PLEK_HUMAN	pleckstrin	117					actin cytoskeleton reorganization|cortical actin cytoskeleton organization|hemopoietic progenitor cell differentiation|inhibition of phospholipase C activity involved in G-protein coupled receptor signaling pathway|integrin-mediated signaling pathway|negative regulation of calcium-mediated signaling|negative regulation of inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|platelet aggregation|positive regulation of actin filament bundle assembly|positive regulation of actin filament depolymerization|positive regulation of inositol-polyphosphate 5-phosphatase activity|positive regulation of integrin activation|positive regulation of platelet activation|protein kinase C signaling cascade|protein secretion by platelet|regulation of cell diameter|ruffle organization|thrombin receptor signaling pathway|vesicle docking involved in exocytosis	cytosol|extracellular region|membrane fraction|ruffle membrane|soluble fraction	phosphatidylinositol-3,4-bisphosphate binding|protein homodimerization activity|protein kinase C binding			ovary(1)	1		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		CCAGGAGGTCCATTCGACTGC	0.458													84	217	---	---	---	---	PASS
AAK1	22848	broad.mit.edu	37	2	69704048	69704048	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:69704048C>A	uc002sfp.2	-	21	3260	c.2755G>T	c.(2755-2757)GAC>TAC	p.D919Y		NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	919						coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						GGAATAGGGTCAAACTCATCT	0.428													24	53	---	---	---	---	PASS
C2orf7	84279	broad.mit.edu	37	2	73456011	73456011	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:73456011C>T	uc002siy.2	-	4	426	c.358G>A	c.(358-360)GAC>AAC	p.D120N		NM_032319	NP_115695	Q9BSG0	PADC1_HUMAN	chromosome 2 open reading frame 7 precursor	120	PA.					extracellular region					0						CTGTCATTGTCAACTGCGTTG	0.612													12	32	---	---	---	---	PASS
ALMS1	7840	broad.mit.edu	37	2	73826595	73826595	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:73826595C>G	uc002sje.1	+	19	11729	c.11618C>G	c.(11617-11619)TCT>TGT	p.S3873C	ALMS1_uc002sjf.1_Missense_Mutation_p.S3829C|ALMS1_uc002sjh.1_Missense_Mutation_p.S3259C	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3871					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						AGCTCAAACTCTACTTTTTGC	0.303													27	378	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	76976038	76976038	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:76976038G>T	uc002snr.2	-	4	1971	c.1556C>A	c.(1555-1557)CCA>CAA	p.P519Q	LRRTM4_uc002snq.2_Missense_Mutation_p.P519Q	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	519	Cytoplasmic (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		CATGTGGTGTGGCATCTGGAT	0.458													18	35	---	---	---	---	PASS
REG1A	5967	broad.mit.edu	37	2	79348017	79348017	+	Silent	SNP	G	A	A	rs113485193	byFrequency	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:79348017G>A	uc002snz.2	+	2	133	c.30G>A	c.(28-30)CTG>CTA	p.L10L	REG1A_uc010ffx.1_Silent_p.L10L|REG1A_uc010ysd.1_Silent_p.L10L	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor	10					positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						ACTTCATGCTGATCTCCTGCC	0.463													16	126	---	---	---	---	PASS
TCF7L1	83439	broad.mit.edu	37	2	85361184	85361184	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:85361184C>A	uc002soy.2	+	2	369	c.295C>A	c.(295-297)CGG>AGG	p.R99R		NM_031283	NP_112573	Q9HCS4	TF7L1_HUMAN	HMG-box transcription factor TCF-3	99					chromatin organization|regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)|central_nervous_system(1)	3						CCAGAAGCCGCGGGACTATTT	0.706													14	41	---	---	---	---	PASS
KDM3A	55818	broad.mit.edu	37	2	86719209	86719209	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:86719209G>A	uc002sri.3	+	26	4260	c.3933G>A	c.(3931-3933)CTG>CTA	p.L1311L	KDM3A_uc010ytj.1_Silent_p.L1311L|KDM3A_uc010ytk.1_Silent_p.L1259L	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	1311					androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5						TTGCTATGCTGAAAGCCAGTG	0.393													13	76	---	---	---	---	PASS
ACOXL	55289	broad.mit.edu	37	2	111542385	111542385	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:111542385G>A	uc002tgr.3	+	3	376	c.152G>A	c.(151-153)GGA>GAA	p.G51E	ACOXL_uc010fkc.2_Missense_Mutation_p.G51E|ACOXL_uc010yxk.1_Missense_Mutation_p.G51E	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2	51					fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						ATGGCCACAGGAGTGAAGGTG	0.493													22	86	---	---	---	---	PASS
TTL	150465	broad.mit.edu	37	2	113258796	113258796	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:113258796C>G	uc002thu.2	+	4	662	c.483C>G	c.(481-483)CTC>CTG	p.L161L	TTL_uc010fkm.1_5'Flank	NM_153712	NP_714923	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	161	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity				0		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		AAGGCATTCTCATCTCCTCAG	0.443			T	ETV6	ALL								13	94	---	---	---	---	PASS
MARCO	8685	broad.mit.edu	37	2	119732103	119732103	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:119732103C>G	uc002tln.1	+	6	707	c.575C>G	c.(574-576)TCG>TGG	p.S192W	MARCO_uc010yyf.1_Missense_Mutation_p.S114W	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	192	Collagen-like.|Extracellular (Potential).				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|skin(2)|central_nervous_system(1)	6						CCAGGCCCCTCGGGACCCCAA	0.537													7	31	---	---	---	---	PASS
PCDP1	200373	broad.mit.edu	37	2	120362833	120362833	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:120362833C>G	uc002tmb.2	+	12	1335	c.243C>G	c.(241-243)GAC>GAG	p.D81E	PCDP1_uc010yyq.1_Missense_Mutation_p.D211E	NM_001029996	NP_001025167	Q4G0U5	PCDP1_HUMAN	primary ciliary dyskinesia protein 1	367				D -> G (in Ref. 2; BAG57111).		cilium	calmodulin binding				0	Colorectal(110;0.196)					TCAGACAGGACATTCACGAAG	0.373													36	56	---	---	---	---	PASS
FAM123C	205147	broad.mit.edu	37	2	131520757	131520757	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:131520757C>A	uc002trw.2	+	2	1302	c.1112C>A	c.(1111-1113)ACC>AAC	p.T371N	FAM123C_uc010fmv.2_Missense_Mutation_p.T371N|FAM123C_uc010fms.1_Missense_Mutation_p.T371N|FAM123C_uc010fmt.1_Missense_Mutation_p.T371N|FAM123C_uc010fmu.1_Missense_Mutation_p.T371N	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	371										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)		GACACAGGCACCCCCAAGAGC	0.627													39	39	---	---	---	---	PASS
ACMSD	130013	broad.mit.edu	37	2	135630170	135630170	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:135630170G>A	uc002ttz.2	+	8	875	c.808G>A	c.(808-810)GAT>AAT	p.D270N	ACMSD_uc002tua.2_Missense_Mutation_p.D212N|uc010zbe.1_Intron	NM_138326	NP_612199	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	270					quinolinate metabolic process|tryptophan catabolic process	cytosol	aminocarboxymuconate-semialdehyde decarboxylase activity|metal ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.115)		TTTGGTTCATGATCCTCTGTC	0.507													44	57	---	---	---	---	PASS
ZEB2	9839	broad.mit.edu	37	2	145156514	145156514	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:145156514A>T	uc002tvu.2	-	8	2720	c.2240T>A	c.(2239-2241)CTC>CAC	p.L747H	ZEB2_uc002tvv.2_Missense_Mutation_p.L741H|ZEB2_uc010zbm.1_Missense_Mutation_p.L718H|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Missense_Mutation_p.L776H	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	747						cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		ACTGTTGTGGAGTTCTGCTAT	0.428													130	183	---	---	---	---	PASS
KCNH7	90134	broad.mit.edu	37	2	163256909	163256909	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:163256909G>C	uc002uch.1	-	10	2409	c.2197C>G	c.(2197-2199)CTA>GTA	p.L733V		NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	733	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	TTGAGATGTAGACAAATGTCT	0.443													23	136	---	---	---	---	PASS
ITGA6	3655	broad.mit.edu	37	2	173355770	173355770	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:173355770A>G	uc002uhp.1	+	21	2901	c.2698A>G	c.(2698-2700)AAG>GAG	p.K900E	ITGA6_uc010zdy.1_Missense_Mutation_p.K781E|ITGA6_uc002uho.1_Missense_Mutation_p.K900E|ITGA6_uc010fqm.1_Missense_Mutation_p.K531E	NM_001079818	NP_001073286	P23229	ITA6_HUMAN	integrin alpha chain, alpha 6 isoform a	939	Extracellular (Potential).				blood coagulation|cell adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter	integrin complex	protein binding|receptor activity			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			CAACTCAAGAAAGAAACGGGA	0.313													102	107	---	---	---	---	PASS
OLA1	29789	broad.mit.edu	37	2	174987919	174987919	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:174987919C>T	uc002uih.2	-	7	903	c.717G>A	c.(715-717)AAG>AAA	p.K239K	OLA1_uc002uii.2_Silent_p.K81K|OLA1_uc010fqq.2_Silent_p.K239K|OLA1_uc002uij.2_Silent_p.K81K|OLA1_uc002uik.2_Silent_p.K209K|OLA1_uc010fqr.2_Silent_p.K239K	NM_013341	NP_037473	Q9NTK5	OLA1_HUMAN	Obg-like ATPase 1 isoform 1	239					ATP catabolic process	cytoplasm	ATP binding|GTP binding|hydrolase activity|protein binding			ovary(1)|breast(1)	2						ATTTGTTTTTCTTTCTAATGT	0.343													11	44	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179506971	179506971	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:179506971C>G	uc010zfg.1	-	168	33071	c.32847G>C	c.(32845-32847)CTG>CTC	p.L10949L	TTN_uc010zfh.1_Silent_p.L4644L|TTN_uc010zfi.1_Silent_p.L4577L|TTN_uc010zfj.1_Silent_p.L4452L|TTN_uc010fre.1_Silent_p.L827L|TTN_uc002umw.1_Intron|TTN_uc002umx.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	11876							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACCGCTTTTCAGAACAACTT	0.328													2	8	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179588843	179588843	+	Missense_Mutation	SNP	C	A	A	rs148072021	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:179588843C>A	uc010zfg.1	-	70	17635	c.17411G>T	c.(17410-17412)CGA>CTA	p.R5804L	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.R2465L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6731							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCAGTCTTCGTGTGAAAGA	0.418													25	27	---	---	---	---	PASS
CCDC141	285025	broad.mit.edu	37	2	179730515	179730515	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:179730515G>T	uc002unf.1	-	7	1035	c.978C>A	c.(976-978)GCC>GCA	p.A326A		NM_173648	NP_775919	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	326	Potential.						protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			CGTCTCTCATGGCGCAGTACT	0.522													181	222	---	---	---	---	PASS
SGOL2	151246	broad.mit.edu	37	2	201436108	201436108	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:201436108C>G	uc002uvw.2	+	7	1152	c.1039C>G	c.(1039-1041)CAA>GAA	p.Q347E	SGOL2_uc010zhd.1_Missense_Mutation_p.Q347E|SGOL2_uc010zhe.1_Missense_Mutation_p.Q347E	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2 isoform 1	347					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)|skin(2)	4						GTGCATGAATCAAATTGAGGA	0.368													19	39	---	---	---	---	PASS
AOX1	316	broad.mit.edu	37	2	201533380	201533380	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:201533380G>A	uc002uvx.2	+	33	3753	c.3652G>A	c.(3652-3654)GAG>AAG	p.E1218K	AOX1_uc010zhf.1_Missense_Mutation_p.E774K|AOX1_uc010fsu.2_Missense_Mutation_p.E584K	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	1218					inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TTATACAATAGAGGAACTGAA	0.428													65	144	---	---	---	---	PASS
C2orf62	375307	broad.mit.edu	37	2	219232573	219232573	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:219232573C>T	uc002vhr.2	+	10	1079	c.1050C>T	c.(1048-1050)TTC>TTT	p.F350F	C2orf62_uc002vhs.2_RNA|uc002vht.2_5'Flank	NM_198559	NP_940961	Q7Z7H3	CB062_HUMAN	hypothetical protein LOC375307	350											0		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGCCGAGTTCTTCGGCCCCT	0.701													30	29	---	---	---	---	PASS
RQCD1	9125	broad.mit.edu	37	2	219457065	219457065	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:219457065C>T	uc010zkh.1	+	6	579	c.579C>T	c.(577-579)GAC>GAT	p.D193D	RQCD1_uc002vih.1_Silent_p.D193D|RQCD1_uc010zki.1_Silent_p.D225D	NM_005444	NP_005435	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog	193					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|sex differentiation|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(1)|skin(1)	2		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGTTAGATGACACTGGTTTGG	0.378													74	141	---	---	---	---	PASS
NDUFA10	4705	broad.mit.edu	37	2	240900568	240900568	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:240900568G>A	uc002vyn.2	-	10	1115	c.1035C>T	c.(1033-1035)ACC>ACT	p.T345T		NM_004544	NP_004535	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	345					mitochondrial electron transport, NADH to ubiquinone|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transport	mitochondrial matrix|mitochondrial respiratory chain complex I	ATP binding|NADH dehydrogenase (ubiquinone) activity|phosphotransferase activity, alcohol group as acceptor			central_nervous_system(1)	1		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)	NADH(DB00157)	CTCCCACCTCGGTGTTGTACC	0.562													4	54	---	---	---	---	PASS
NUP210	23225	broad.mit.edu	37	3	13372064	13372064	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:13372064C>T	uc003bxv.1	-	30	4089	c.4006G>A	c.(4006-4008)GAG>AAG	p.E1336K		NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor	1336	Lumenal (Probable).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)					AAGCCTTTCTCATCAACATGC	0.493													30	147	---	---	---	---	PASS
NUP210	23225	broad.mit.edu	37	3	13372096	13372096	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:13372096C>T	uc003bxv.1	-	30	4057	c.3974G>A	c.(3973-3975)GGA>GAA	p.G1325E		NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor	1325	Lumenal (Probable).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)					CTTTTCGGGTCCATCCAGGAC	0.512													24	113	---	---	---	---	PASS
NR2C2	7182	broad.mit.edu	37	3	15062303	15062303	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:15062303C>G	uc003bzj.3	+	5	637	c.420C>G	c.(418-420)TTC>TTG	p.F140L	NR2C2_uc003bzi.2_Missense_Mutation_p.F159L	NM_003298	NP_003289	P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	140	Nuclear receptor.				cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0						GCAAAGGTTTCTTCAAAAGGA	0.443													19	86	---	---	---	---	PASS
GPD1L	23171	broad.mit.edu	37	3	32180216	32180216	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:32180216C>G	uc003cew.2	+	3	423	c.363C>G	c.(361-363)ATC>ATG	p.I121M		NM_015141	NP_055956	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	121					glycerol-3-phosphate catabolic process	glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|NAD binding|protein homodimerization activity				0						TCACCCTCATCAAGGTAACTC	0.488													28	42	---	---	---	---	PASS
SUSD5	26032	broad.mit.edu	37	3	33195066	33195066	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:33195066T>A	uc003cfo.1	-	5	1476	c.1058A>T	c.(1057-1059)AAG>ATG	p.K353M		NM_015551	NP_056366	O60279	SUSD5_HUMAN	sushi domain containing 5 precursor	353	Extracellular (Potential).				cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2						GCTGTCATTCTTGCCCACAAA	0.547													16	41	---	---	---	---	PASS
GOLGA4	2803	broad.mit.edu	37	3	37367039	37367039	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:37367039G>T	uc003cgv.2	+	14	3966	c.3662G>T	c.(3661-3663)TGT>TTT	p.C1221F	GOLGA4_uc010hgr.1_Missense_Mutation_p.C782F|GOLGA4_uc003cgw.2_Missense_Mutation_p.C1243F|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Missense_Mutation_p.C1102F	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	1221	Potential.|Glu-rich.				Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						GATATTTGCTGTAAGAAAACC	0.338													38	50	---	---	---	---	PASS
ITGA9	3680	broad.mit.edu	37	3	37514854	37514854	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:37514854G>A	uc003chd.2	+	3	376	c.323G>A	c.(322-324)CGG>CAG	p.R108Q	ITGA9_uc003chc.2_Missense_Mutation_p.R108Q	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor	108	Extracellular (Potential).				axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GGGAAGAATCGGGGCACGTCC	0.567													24	32	---	---	---	---	PASS
ITGA9	3680	broad.mit.edu	37	3	37514855	37514855	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:37514855G>T	uc003chd.2	+	3	377	c.324G>T	c.(322-324)CGG>CGT	p.R108R	ITGA9_uc003chc.2_Silent_p.R108R	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor	108	Extracellular (Potential).				axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GGAAGAATCGGGGCACGTCCT	0.567													24	32	---	---	---	---	PASS
KBTBD5	131377	broad.mit.edu	37	3	42730526	42730526	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:42730526G>T	uc003clv.1	+	4	1687	c.1587G>T	c.(1585-1587)GTG>GTT	p.V529V		NM_152393	NP_689606	Q2TBA0	KBTB5_HUMAN	kelch repeat and BTB (POZ) domain containing 5	529	Kelch 4.									ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTGCCGAAGTGTACAGCATCA	0.582													18	34	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48682912	48682912	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:48682912G>A	uc003cul.2	-	24	8042	c.7761C>T	c.(7759-7761)CTC>CTT	p.L2587L	CELSR3_uc003cuf.1_Silent_p.L2657L|CELSR3_uc010hkf.2_5'Flank|CELSR3_uc010hkg.2_Silent_p.L570L	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	2587	Helical; Name=2; (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GCAGGAAGAGGAGCTCTGCCA	0.632													9	80	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48682972	48682972	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:48682972G>C	uc003cul.2	-	24	7982	c.7701C>G	c.(7699-7701)CTC>CTG	p.L2567L	CELSR3_uc003cuf.1_Silent_p.L2637L|CELSR3_uc010hkf.2_5'Flank|CELSR3_uc010hkg.2_Silent_p.L550L	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	2567	Cytoplasmic (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CATTGGACTTGAGGCTGCGCA	0.637													4	56	---	---	---	---	PASS
BSN	8927	broad.mit.edu	37	3	49694176	49694176	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:49694176G>A	uc003cxe.3	+	5	7301	c.7187G>A	c.(7186-7188)CGG>CAG	p.R2396Q		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	2396	Potential.				synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GAGCTAGAGCGGGAACGTGTG	0.627													4	8	---	---	---	---	PASS
SEMA3B	7869	broad.mit.edu	37	3	50310865	50310865	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:50310865G>A	uc003cyu.2	+	9	1043	c.801G>A	c.(799-801)CAG>CAA	p.Q267Q	SEMA3B_uc010hlh.1_RNA|SEMA3B_uc003cyt.2_Silent_p.Q267Q|SEMA3B_uc003cyv.2_Silent_p.Q154Q|SEMA3B_uc003cyw.2_5'UTR|SEMA3B_uc010hli.2_Silent_p.Q154Q|SEMA3B_uc003cyx.2_Silent_p.Q154Q|SEMA3B_uc003cyy.2_5'UTR|SEMA3B_uc011bdo.1_Intron	NM_004636	NP_004627	Q13214	SEM3B_HUMAN	semaphorin 3B isoform 1 precursor	267	Sema.				axon guidance|cell-cell signaling	endoplasmic reticulum|extracellular region|membrane	receptor activity			lung(2)|central_nervous_system(2)|kidney(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCGTTGGCCAGATCTGCCGGG	0.662											OREG0015583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	70	---	---	---	---	PASS
SEMA3G	56920	broad.mit.edu	37	3	52476875	52476875	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:52476875G>C	uc003dea.1	-	2	164	c.164C>G	c.(163-165)TCC>TGC	p.S55C		NM_020163	NP_064548	Q9NS98	SEM3G_HUMAN	semaphorin sem2 precursor	55	Sema.				multicellular organismal development	extracellular region|membrane	receptor activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		GAGGTTCAGGGAGCCCTGGGG	0.622													4	27	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52692308	52692308	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:52692308C>G	uc003des.2	-	5	564	c.552G>C	c.(550-552)GAG>GAC	p.E184D	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.E184D|PBRM1_uc003der.2_Missense_Mutation_p.E184D|PBRM1_uc003det.2_Missense_Mutation_p.E184D|PBRM1_uc003deu.2_Missense_Mutation_p.E184D|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.E184D|PBRM1_uc010hmk.1_Missense_Mutation_p.E184D|PBRM1_uc003dey.2_Missense_Mutation_p.E184D|PBRM1_uc003dez.1_Missense_Mutation_p.E184D|PBRM1_uc003dfb.1_Missense_Mutation_p.E82D	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	184					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GCTCCAGGATCTCCTTCAAGT	0.373			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								7	59	---	---	---	---	PASS
CCDC66	285331	broad.mit.edu	37	3	56627033	56627033	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:56627033G>C	uc003dhz.2	+	8	1059	c.972G>C	c.(970-972)GTG>GTC	p.V324V	CCDC66_uc003dhy.2_5'UTR|CCDC66_uc003dhu.2_Silent_p.V290V|CCDC66_uc003dhx.2_RNA	NM_001141947	NP_001135419	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66 isoform 1	324										breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		TCAGTGCTGTGAAACAAGAAC	0.338													35	144	---	---	---	---	PASS
FHIT	2272	broad.mit.edu	37	3	60522645	60522645	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:60522645G>C	uc003dkx.3	-	5	422	c.51C>G	c.(49-51)CTC>CTG	p.L17L	FHIT_uc003dky.2_Silent_p.L17L|FHIT_uc010hnn.1_Silent_p.L17L	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene	17	HIT.				nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		GTTCTGTTTTGAGAAACACTA	0.383			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				20	31	---	---	---	---	PASS
TMF1	7110	broad.mit.edu	37	3	69075232	69075232	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:69075232G>T	uc003dnn.2	-	14	3021	c.2774C>A	c.(2773-2775)TCT>TAT	p.S925Y	TMF1_uc011bfx.1_Missense_Mutation_p.S928Y	NM_007114	NP_009045	P82094	TMF1_HUMAN	TATA element modulatory factor 1	925					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi membrane|nucleus	DNA binding|protein binding|transcription cofactor activity				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		GCTAGAAACAGAAAATGGCTT	0.383													7	58	---	---	---	---	PASS
FOXP1	27086	broad.mit.edu	37	3	71008498	71008498	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:71008498G>T	uc003dol.2	-	17	2257	c.1934C>A	c.(1933-1935)GCT>GAT	p.A645D	FOXP1_uc003dom.2_Missense_Mutation_p.A569D|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Missense_Mutation_p.A644D|FOXP1_uc003dop.2_Missense_Mutation_p.A645D|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_Missense_Mutation_p.A545D|FOXP1_uc003doj.2_Missense_Mutation_p.A545D|FOXP1_uc003dok.2_Missense_Mutation_p.A458D	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1	645					cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GGGCCCTTCAGCTTCCTCTGG	0.502			T	PAX5	ALL								47	63	---	---	---	---	PASS
GXYLT2	727936	broad.mit.edu	37	3	72957687	72957687	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:72957687C>G	uc003dpg.2	+	2	445	c.445C>G	c.(445-447)CTG>GTG	p.L149V		NM_001080393	NP_001073862	A0PJZ3	GXLT2_HUMAN	glycosyltransferase 8 domain containing 4	149	Lumenal (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0						TGAAGACTCTCTGAAGCCCGA	0.443													16	20	---	---	---	---	PASS
ROBO1	6091	broad.mit.edu	37	3	78795913	78795913	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:78795913C>T	uc003dqe.2	-	5	845	c.637G>A	c.(637-639)GAT>AAT	p.D213N	ROBO1_uc003dqb.2_Missense_Mutation_p.D174N|ROBO1_uc003dqc.2_Missense_Mutation_p.D174N|ROBO1_uc003dqd.2_Missense_Mutation_p.D174N	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	213	Extracellular (Potential).|Ig-like C2-type 2.				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TCATCTTTATCATCCAGTGGA	0.418													20	140	---	---	---	---	PASS
OR5H14	403273	broad.mit.edu	37	3	97868721	97868721	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:97868721C>G	uc003dsg.1	+	1	492	c.492C>G	c.(490-492)TTC>TTG	p.F164L		NM_001005514	NP_001005514	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H,	164	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GATTTTTATTCAGACTAACCT	0.338													33	205	---	---	---	---	PASS
OR5K1	26339	broad.mit.edu	37	3	98189077	98189077	+	Silent	SNP	C	G	G	rs74372753	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:98189077C>G	uc003dsm.2	+	1	657	c.657C>G	c.(655-657)CTC>CTG	p.L219L		NM_001004736	NP_001004736	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)	1						TATCTTATCTCTATATTCTTC	0.348													10	164	---	---	---	---	PASS
KIAA1524	57650	broad.mit.edu	37	3	108298180	108298180	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:108298180C>T	uc003dxb.3	-	7	1035	c.766G>A	c.(766-768)GAC>AAC	p.D256N	KIAA1524_uc003dxc.1_Missense_Mutation_p.D97N|KIAA1524_uc010hpw.1_Missense_Mutation_p.D97N	NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	256						cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						ATCAGTAGGTCAACTGAATAC	0.328													30	173	---	---	---	---	PASS
PVRL3	25945	broad.mit.edu	37	3	110831075	110831075	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:110831075G>C	uc003dxt.1	+	2	359	c.359G>C	c.(358-360)AGA>ACA	p.R120T	PVRL3_uc003dxu.1_Missense_Mutation_p.R97T	NM_015480	NP_056295	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3 precursor	120	Extracellular (Potential).|Ig-like V-type.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane	cell adhesion molecule binding|protein homodimerization activity			upper_aerodigestive_tract(2)	2						TATCAGGGAAGAGTCTTGTTT	0.373													14	113	---	---	---	---	PASS
ATP6V1A	523	broad.mit.edu	37	3	113528274	113528274	+	Nonstop_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:113528274G>C	uc003eao.2	+	15	1920	c.1854G>C	c.(1852-1854)TAG>TAC	p.*618Y	ATP6V1A_uc011bik.1_Nonstop_Mutation_p.*585Y	NM_001690	NP_001681	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal V1 subunit A	618					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(2)|skin(1)	3						TTGAAGATTAGAAGCCTTGAA	0.393													9	79	---	---	---	---	PASS
KIAA1407	57577	broad.mit.edu	37	3	113761652	113761652	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:113761652G>C	uc003eax.2	-	4	460	c.313C>G	c.(313-315)CAA>GAA	p.Q105E	KIAA1407_uc011bin.1_RNA|KIAA1407_uc011bio.1_Missense_Mutation_p.Q83E|KIAA1407_uc011bip.1_Missense_Mutation_p.Q92E	NM_020817	NP_065868	Q8NCU4	K1407_HUMAN	hypothetical protein LOC57577	105										ovary(2)	2						GCTAATTCTTGCTTAAGTTTG	0.363													42	128	---	---	---	---	PASS
GSK3B	2932	broad.mit.edu	37	3	119562180	119562180	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:119562180G>A	uc003edo.2	-	10	2100	c.1117C>T	c.(1117-1119)CTG>TTG	p.L373L	GSK3B_uc003edn.2_Silent_p.L386L|GSK3B_uc003edm.2_Intron	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2	373					axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ATGGTAGCCAGAGGTGGATTA	0.413													6	77	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121207343	121207343	+	Missense_Mutation	SNP	G	A	A	rs149344067		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:121207343G>A	uc003eee.3	-	16	4564	c.4435C>T	c.(4435-4437)CCT>TCT	p.P1479S	POLQ_uc003eed.2_Missense_Mutation_p.P651S	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1479					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		CTTGTTTCAGGAACTGGAAGA	0.353								DNA_polymerases_(catalytic_subunits)					13	139	---	---	---	---	PASS
EAF2	55840	broad.mit.edu	37	3	121591497	121591497	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:121591497G>A	uc003een.2	+	5	697	c.598G>A	c.(598-600)GAA>AAA	p.E200K	EAF2_uc003eeo.2_Missense_Mutation_p.E70K	NM_018456	NP_060926	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	200	Ser-rich.|Necessary for transactivation activity.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	protein binding				0				GBM - Glioblastoma multiforme(114;0.0972)		CTCAGAAGATGAAGATTGCAA	0.398													17	169	---	---	---	---	PASS
PARP9	83666	broad.mit.edu	37	3	122255105	122255105	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:122255105C>G	uc010hri.2	-	10	2240	c.2095G>C	c.(2095-2097)GTG>CTG	p.V699L	PARP9_uc003eff.3_Missense_Mutation_p.V664L|PARP9_uc011bjs.1_Missense_Mutation_p.V664L|PARP9_uc003efg.2_Missense_Mutation_p.V244L|PARP9_uc003efi.2_Missense_Mutation_p.V664L|PARP9_uc003efh.2_Missense_Mutation_p.V699L|PARP9_uc003efj.2_Missense_Mutation_p.V664L	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	699	PARP catalytic.				cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)|prostate(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0519)		CTATGGCTCACAGGTTGCCTG	0.443													42	125	---	---	---	---	PASS
PARP9	83666	broad.mit.edu	37	3	122274371	122274371	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:122274371C>T	uc010hri.2	-	4	897	c.752G>A	c.(751-753)TGT>TAT	p.C251Y	PARP9_uc003eff.3_Missense_Mutation_p.C216Y|PARP9_uc011bjs.1_Missense_Mutation_p.C216Y|PARP9_uc003efg.2_Intron|PARP9_uc003efi.2_Missense_Mutation_p.C216Y|PARP9_uc003efh.2_Missense_Mutation_p.C251Y|PARP9_uc003efj.2_Missense_Mutation_p.C216Y	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	251	Macro 1.				cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)|prostate(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0519)		AGTCTTTGTACACAAATTCAG	0.383													11	179	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122411176	122411176	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:122411176C>G	uc003efq.3	+	4	443	c.384C>G	c.(382-384)CTC>CTG	p.L128L		NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	128					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		ATACAAAACTCCCTCTTGATG	0.368													21	102	---	---	---	---	PASS
HEG1	57493	broad.mit.edu	37	3	124748078	124748078	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:124748078C>T	uc003ehs.3	-	2	639	c.571G>A	c.(571-573)GAG>AAG	p.E191K	HEG1_uc011bke.1_Missense_Mutation_p.E191K	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor	191	Extracellular (Potential).					extracellular region|integral to membrane	calcium ion binding	p.E191E(1)		ovary(2)	2						GTTGCTATCTCCAGTGAGTAC	0.478													6	45	---	---	---	---	PASS
OSBPL11	114885	broad.mit.edu	37	3	125257330	125257330	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:125257330C>T	uc003eic.2	-	11	2726	c.1989G>A	c.(1987-1989)GTG>GTA	p.V663V		NM_022776	NP_073613	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	663					lipid transport		lipid binding			ovary(3)|breast(1)|kidney(1)	5						CCAGAGGTCTCACTCTTTTCT	0.353													12	394	---	---	---	---	PASS
ZXDC	79364	broad.mit.edu	37	3	126180755	126180755	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:126180755G>A	uc003eiv.2	-	6	1804	c.1750C>T	c.(1750-1752)CTC>TTC	p.L584F	ZXDC_uc010hsh.2_RNA|ZXDC_uc003eix.2_Missense_Mutation_p.L584F	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	584	Required for transcriptional activation.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)		GCTGTCCCGAGAACCAGAGGG	0.597													14	163	---	---	---	---	PASS
MCM2	4171	broad.mit.edu	37	3	127327758	127327758	+	Silent	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:127327758A>G	uc003ejp.2	+	8	1377	c.1320A>G	c.(1318-1320)CTA>CTG	p.L440L	MCM2_uc011bkm.1_Silent_p.L310L|MCM2_uc010hsl.2_RNA|MCM2_uc011bkn.1_Silent_p.L324L	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	440					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4						CTGTCATCCTAGCCAACCACG	0.527													66	167	---	---	---	---	PASS
PLXND1	23129	broad.mit.edu	37	3	129286443	129286443	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:129286443G>A	uc003emx.2	-	22	4078	c.3978C>T	c.(3976-3978)TTC>TTT	p.F1326F	PLXND1_uc011blb.1_5'UTR	NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor	1326	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1						GCAGCTCAGCGAAGCCTGGCG	0.622													3	55	---	---	---	---	PASS
TMCC1	23023	broad.mit.edu	37	3	129389306	129389306	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:129389306C>G	uc003emz.3	-	5	1879	c.1378G>C	c.(1378-1380)GAT>CAT	p.D460H	TMCC1_uc003emy.3_Missense_Mutation_p.D136H|TMCC1_uc011blc.1_Missense_Mutation_p.D281H|TMCC1_uc010htg.2_Missense_Mutation_p.D346H	NM_001017395	NP_001017395	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	460	Potential.					integral to membrane				skin(1)	1						AGTAGTGCATCAAATCCTGAG	0.517													20	199	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130293257	130293257	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:130293257C>T	uc010htl.2	+	7	3466	c.3435C>T	c.(3433-3435)CTC>CTT	p.L1145L		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1145	Nonhelical region.|VWFA 6.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						ACCAGCAGCTCATTCAGATCA	0.532													7	99	---	---	---	---	PASS
ACAD11	84129	broad.mit.edu	37	3	132324026	132324026	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:132324026G>A	uc003eov.3	-	12	1818	c.1438C>T	c.(1438-1440)CAC>TAC	p.H480Y	ACAD11_uc011blr.1_Missense_Mutation_p.H91Y	NM_032169	NP_115545	Q709F0	ACD11_HUMAN	putative acyl-CoA dehydrogenase	480						peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|transferase activity, transferring phosphorus-containing groups			ovary(1)	1						CCATACAGGTGCAGAACCTCC	0.393													32	104	---	---	---	---	PASS
SRPRB	58477	broad.mit.edu	37	3	133525544	133525544	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:133525544C>T	uc003epx.1	+	2	262	c.246C>T	c.(244-246)GTC>GTT	p.V82V		NM_021203	NP_067026	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, beta	82						endoplasmic reticulum membrane|integral to membrane	GTP binding|protein binding|receptor activity			ovary(1)	1						TGCTCTTTGTCAGGGTAAATG	0.408													16	129	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136117636	136117636	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:136117636C>T	uc003era.1	-	22	2524	c.2232G>A	c.(2230-2232)TCG>TCA	p.S744S	STAG1_uc003erb.1_Silent_p.S744S|STAG1_uc003erc.1_Silent_p.S518S	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	744					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						GCCAAAGAATCGAATAATGGG	0.328													4	97	---	---	---	---	PASS
ARMC8	25852	broad.mit.edu	37	3	138009477	138009477	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:138009477G>A	uc003esa.1	+	22	2309	c.1942G>A	c.(1942-1944)GAC>AAC	p.D648N	TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Missense_Mutation_p.D631N|ARMC8_uc011bmg.1_Missense_Mutation_p.D595N|ARMC8_uc011bmh.1_Missense_Mutation_p.D589N|ARMC8_uc003esb.1_Missense_Mutation_p.D620N|ARMC8_uc003esc.1_Missense_Mutation_p.D420N|ARMC8_uc003esf.1_Missense_Mutation_p.D231N	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2	662	ARM 14.						binding				0						AAACCTTTGTGACAAGTGAGT	0.393													3	16	---	---	---	---	PASS
MRAS	22808	broad.mit.edu	37	3	138117390	138117390	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:138117390G>C	uc003esh.3	+	4	988	c.427G>C	c.(427-429)GAA>CAA	p.E143Q	MRAS_uc011bmi.1_Missense_Mutation_p.E67Q|MRAS_uc003esi.3_Missense_Mutation_p.E143Q|MRAS_uc011bmj.1_Missense_Mutation_p.E67Q	NM_012219	NP_036351	O14807	RASM_HUMAN	muscle RAS oncogene homolog precursor	143					actin cytoskeleton organization|muscle organ development|Ras protein signal transduction	intracellular|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4						GCAAGGAAAAGAAATGGCGAC	0.507													30	127	---	---	---	---	PASS
PIK3CB	5291	broad.mit.edu	37	3	138433508	138433508	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:138433508G>A	uc011bmq.1	-	7	1104	c.1104C>T	c.(1102-1104)ATC>ATT	p.I368I	PIK3CB_uc011bmo.1_5'UTR|PIK3CB_uc011bmp.1_5'UTR	NM_006219	NP_006210	P42338	PK3CB_HUMAN	catalytic phosphatidylinositol 3-kinase beta	368	C2 PI3K-type.				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5						CTGAGCTTACGATGGTTTTAC	0.373													32	296	---	---	---	---	PASS
GK5	256356	broad.mit.edu	37	3	141900354	141900354	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:141900354C>A	uc003euq.1	-	11	1128	c.997G>T	c.(997-999)GAA>TAA	p.E333*	GK5_uc003eup.1_Nonsense_Mutation_p.E54*|GK5_uc010hus.1_RNA	NM_001039547	NP_001034636	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	333					glycerol metabolic process		ATP binding|glycerol kinase activity				0						GCATTGCTTTCAGCTAAGCAT	0.378													14	156	---	---	---	---	PASS
PCOLCE2	26577	broad.mit.edu	37	3	142542385	142542385	+	Nonsense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:142542385G>C	uc003evd.2	-	7	1134	c.938C>G	c.(937-939)TCA>TGA	p.S313*		NM_013363	NP_037495	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	313	NTR.					extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3						AAAGTCACTTGAACAATAATT	0.393													20	185	---	---	---	---	PASS
SR140	23350	broad.mit.edu	37	3	142735215	142735215	+	Splice_Site	SNP	T	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:142735215T>G	uc003evh.1	+	5	535	c.436_splice	c.e5+2	p.E146_splice	SR140_uc003evi.1_Splice_Site|SR140_uc011bnj.1_Splice_Site_p.E146_splice|SR140_uc003evj.1_Splice_Site|SR140_uc003evk.1_Splice_Site_p.E146_splice	NM_001080415	NP_001073884	O15042	SR140_HUMAN	U2-associated SR140 protein						RNA processing	nucleus	nucleotide binding|RNA binding				0						CAGCTAAAGGTAAGTTTATAA	0.373													12	162	---	---	---	---	PASS
TM4SF1	4071	broad.mit.edu	37	3	149089577	149089577	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:149089577G>C	uc003exb.1	-	4	725	c.491C>G	c.(490-492)TCT>TGT	p.S164C	TM4SF1_uc003exc.1_Missense_Mutation_p.S75C	NM_014220	NP_055035	P30408	T4S1_HUMAN	transmembrane 4 superfamily member 1	164	Helical; (Probable).					integral to plasma membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CAAGAGGATAGAAAACAGAGA	0.433													6	202	---	---	---	---	PASS
GPR87	53836	broad.mit.edu	37	3	151012303	151012303	+	Nonsense_Mutation	SNP	G	C	C	rs79475431		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:151012303G>C	uc003eyt.2	-	3	1092	c.731C>G	c.(730-732)TCA>TGA	p.S244*	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_023915	NP_076404	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	244	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CTTTCGGCTTGACTGACTTAT	0.433													7	139	---	---	---	---	PASS
P2RY12	64805	broad.mit.edu	37	3	151056472	151056472	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:151056472C>G	uc003eyw.1	-	2	378	c.162G>C	c.(160-162)CGG>CGC	p.R54R	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron|P2RY12_uc011boa.1_Silent_p.R54R|P2RY12_uc003eyx.1_Silent_p.R54R	NM_176876	NP_795345	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y12	54	Cytoplasmic (Potential).				platelet activation	integral to membrane|plasma membrane	guanyl-nucleotide exchange factor activity			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Ticlopidine(DB00208)|Treprostinil(DB00374)	TTGATTTACTCCGGATTTGAA	0.378													13	84	---	---	---	---	PASS
AADACL2	344752	broad.mit.edu	37	3	151458563	151458563	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:151458563C>G	uc003ezc.2	+	2	388	c.268C>G	c.(268-270)CCA>GCA	p.P90A	AADACL2_uc010hvn.2_Intron	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2 precursor	90						extracellular region|integral to membrane	carboxylesterase activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			TGTTGACATTCCAGTACGATT	0.378													13	189	---	---	---	---	PASS
SGEF	26084	broad.mit.edu	37	3	153943771	153943771	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:153943771G>A	uc011bog.1	+	11	2273	c.2062G>A	c.(2062-2064)GAT>AAT	p.D688N	SGEF_uc011boh.1_Missense_Mutation_p.D688N|SGEF_uc011boi.1_5'UTR	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine	688	PH.				regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TCTCTTTAACGATGTGCTCAT	0.398													7	110	---	---	---	---	PASS
MME	4311	broad.mit.edu	37	3	154834285	154834285	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:154834285A>G	uc010hvr.1	+	5	587	c.376A>G	c.(376-378)AAA>GAA	p.K126E	MME_uc003fab.1_Missense_Mutation_p.K126E|MME_uc003fac.1_Missense_Mutation_p.K126E|MME_uc003fad.1_Missense_Mutation_p.K126E|MME_uc003fae.1_Missense_Mutation_p.K126E	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase	126	Extracellular (Potential).				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)	TCAAGAACCCAAAACTGAAGA	0.318													20	94	---	---	---	---	PASS
CCNL1	57018	broad.mit.edu	37	3	156867907	156867907	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:156867907C>T	uc003fbf.2	-	7	1425	c.826G>A	c.(826-828)GAG>AAG	p.E276K	CCNL1_uc003fbd.1_Missense_Mutation_p.E276K|CCNL1_uc003fbe.2_Missense_Mutation_p.E70K|CCNL1_uc003fbg.2_RNA|CCNL1_uc011bor.1_RNA|CCNL1_uc003fbi.1_Missense_Mutation_p.E121K	NM_020307	NP_064703	Q9UK58	CCNL1_HUMAN	cyclin L1	276	Cyclin-like 2.				regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nuclear speck	protein kinase binding			lung(3)|breast(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			TGGATTTCCTCTTCTGTAGTA	0.358													6	148	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906446	164906446	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:164906446G>C	uc003fej.3	-	2	2617	c.2173C>G	c.(2173-2175)CCA>GCA	p.P725A	SLITRK3_uc003fek.2_Missense_Mutation_p.P725A	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	725	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						GAAAGAGTTGGTCGaccacca	0.453										HNSCC(40;0.11)			60	69	---	---	---	---	PASS
FNDC3B	64778	broad.mit.edu	37	3	172098776	172098776	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:172098776G>A	uc003fhy.2	+	25	3368	c.3196G>A	c.(3196-3198)GAA>AAA	p.E1066K	FNDC3B_uc003fhz.3_Missense_Mutation_p.E1066K	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1066	Fibronectin type-III 9.					endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AACACAGTTAGAAGGAAATTC	0.373													8	310	---	---	---	---	PASS
FXR1	8087	broad.mit.edu	37	3	180671549	180671549	+	Splice_Site	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:180671549G>A	uc003fkq.2	+	9	824	c.802_splice	c.e9-1	p.S268_splice	FXR1_uc003fkp.2_Splice_Site_p.S183_splice|FXR1_uc003fkr.2_Splice_Site_p.S268_splice|FXR1_uc011bqj.1_Splice_Site_p.S182_splice|FXR1_uc003fks.2_Splice_Site_p.S182_splice|FXR1_uc011bqk.1_Splice_Site_p.S219_splice|FXR1_uc011bql.1_Splice_Site_p.S255_splice	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1						apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			CTCATCTACAGAGTGCTGATG	0.363													16	382	---	---	---	---	PASS
HTR3C	170572	broad.mit.edu	37	3	183778074	183778074	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:183778074C>T	uc003fmk.2	+	9	1312	c.1278C>T	c.(1276-1278)CTC>CTT	p.L426L		NM_130770	NP_570126	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine receptor 3 subunit C	426	Helical; Name=4; (Potential).					integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			ACACCCTGCTCTTCCGCCTCT	0.577													20	497	---	---	---	---	PASS
EIF4G1	1981	broad.mit.edu	37	3	184039636	184039636	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:184039636G>C	uc003fnp.2	+	10	1462	c.1264G>C	c.(1264-1266)GAG>CAG	p.E422Q	EIF4G1_uc003fno.1_Missense_Mutation_p.E363Q|EIF4G1_uc010hxw.1_Missense_Mutation_p.E258Q|EIF4G1_uc003fnt.2_Missense_Mutation_p.E133Q|EIF4G1_uc003fnq.2_Missense_Mutation_p.E335Q|EIF4G1_uc003fnr.2_Missense_Mutation_p.E258Q|EIF4G1_uc010hxx.2_Missense_Mutation_p.E429Q|EIF4G1_uc003fns.2_Missense_Mutation_p.E382Q|EIF4G1_uc010hxy.2_Missense_Mutation_p.E429Q|EIF4G1_uc003fnv.3_Missense_Mutation_p.E422Q|EIF4G1_uc003fnu.3_Missense_Mutation_p.E422Q|EIF4G1_uc003fnw.2_Missense_Mutation_p.E429Q|EIF4G1_uc003fnx.2_Missense_Mutation_p.E226Q|EIF4G1_uc003fny.3_Missense_Mutation_p.E226Q	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	422					insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CAGTGAGCCAGAGGAGCAGGC	0.617													10	745	---	---	---	---	PASS
RFC4	5984	broad.mit.edu	37	3	186512450	186512450	+	Nonsense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:186512450G>C	uc003fqz.2	-	5	630	c.407C>G	c.(406-408)TCA>TGA	p.S136*	RFC4_uc011bsc.1_Nonsense_Mutation_p.S136*|RFC4_uc011bsd.1_Nonsense_Mutation_p.S136*	NM_002916	NP_002907	P35249	RFC4_HUMAN	replication factor C 4	136					cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1)	5	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		TACTTACTCTGAGCGACTTCC	0.294													10	208	---	---	---	---	PASS
ST6GAL1	6480	broad.mit.edu	37	3	186760494	186760494	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:186760494G>A	uc003frb.2	+	4	435	c.3G>A	c.(1-3)ATG>ATA	p.M1I	ST6GAL1_uc003frc.2_Intron|ST6GAL1_uc003frd.2_Missense_Mutation_p.M1I	NM_173216	NP_775323	P15907	SIAT1_HUMAN	ST6 beta-galactosamide	1	Cytoplasmic.				humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		TCTTCATTATGATTCACACCA	0.398													97	616	---	---	---	---	PASS
BCL6	604	broad.mit.edu	37	3	187449664	187449664	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:187449664G>A	uc003frp.3	-	4	673	c.216C>T	c.(214-216)ATC>ATT	p.I72I	BCL6_uc011bsf.1_Silent_p.I72I|BCL6_uc010hza.2_Intron|BCL6_uc003frq.1_Silent_p.I72I	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1	72	BTB.				negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		GATCTAGATTGATCACACTAA	0.443			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								6	183	---	---	---	---	PASS
TP63	8626	broad.mit.edu	37	3	189526204	189526204	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:189526204C>T	uc003fry.2	+	4	557	c.468C>T	c.(466-468)TTC>TTT	p.F156F	TP63_uc003frx.2_Silent_p.F156F|TP63_uc003frz.2_Silent_p.F156F|TP63_uc010hzc.1_Silent_p.F156F|TP63_uc003fsa.2_Silent_p.F62F|TP63_uc003fsb.2_Silent_p.F62F|TP63_uc003fsc.2_Silent_p.F62F|TP63_uc003fsd.2_Silent_p.F62F|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Silent_p.F37F	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	156					anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		GCTCCACCTTCGATGCTCTCT	0.627									Hay-Wells_syndrome	HNSCC(45;0.13)			13	217	---	---	---	---	PASS
TP63	8626	broad.mit.edu	37	3	189590662	189590662	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:189590662G>C	uc003fry.2	+	10	1316	c.1227G>C	c.(1225-1227)GAG>GAC	p.E409D	TP63_uc003frx.2_Missense_Mutation_p.E409D|TP63_uc003frz.2_Missense_Mutation_p.E409D|TP63_uc010hzc.1_Missense_Mutation_p.E409D|TP63_uc003fsa.2_Missense_Mutation_p.E315D|TP63_uc003fsb.2_Missense_Mutation_p.E315D|TP63_uc003fsc.2_Missense_Mutation_p.E315D|TP63_uc003fsd.2_Missense_Mutation_p.E315D|TP63_uc010hzd.1_Missense_Mutation_p.E230D	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	409	Oligomerization.				anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		GGGGCCGTGAGACTTATGAAA	0.408									Hay-Wells_syndrome	HNSCC(45;0.13)			8	194	---	---	---	---	PASS
LEPREL1	55214	broad.mit.edu	37	3	189700892	189700892	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:189700892G>A	uc011bsk.1	-	8	1655	c.1267C>T	c.(1267-1269)CAT>TAT	p.H423Y	LEPREL1_uc003fsg.2_Missense_Mutation_p.H242Y	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a	423					collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GAGAATCCATGAACTTCTGCT	0.423													23	500	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193159353	193159353	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:193159353C>A	uc003ftd.2	-	20	2449	c.2341G>T	c.(2341-2343)GAA>TAA	p.E781*	ATP13A4_uc003fte.1_Nonsense_Mutation_p.E781*|ATP13A4_uc011bsr.1_Nonsense_Mutation_p.E252*|ATP13A4_uc010hzi.2_RNA	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	781	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TCAGAGACTTCATCCCTGATG	0.378													21	298	---	---	---	---	PASS
MFI2	4241	broad.mit.edu	37	3	196733571	196733571	+	Nonsense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr3:196733571G>C	uc003fxk.3	-	14	1900	c.1787C>G	c.(1786-1788)TCA>TGA	p.S596*		NM_005929	NP_005920	P08582	TRFM_HUMAN	melanoma-associated antigen p97 isoform 1	596	Transferrin-like 2.				cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		ATAGTCCTCTGACCTGAGCTC	0.612													10	113	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3418748	3418748	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:3418748C>T	uc003ggw.2	+	8	3440	c.2536C>T	c.(2536-2538)CAG>TAG	p.Q846*	RGS12_uc010ics.1_Nonsense_Mutation_p.Q45*|RGS12_uc003ggv.2_Nonsense_Mutation_p.Q846*|RGS12_uc003ggy.1_Nonsense_Mutation_p.Q244*|RGS12_uc010ict.1_Nonsense_Mutation_p.Q198*|RGS12_uc003ggz.2_Nonsense_Mutation_p.Q198*|RGS12_uc010icu.1_Nonsense_Mutation_p.Q45*|RGS12_uc011bvs.1_Nonsense_Mutation_p.Q188*|RGS12_uc003gha.2_Nonsense_Mutation_p.Q188*|RGS12_uc010icv.2_Nonsense_Mutation_p.Q45*|RGS12_uc003ghb.2_Nonsense_Mutation_p.Q45*	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	846						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGACTCGCAGCAGGTCCCCAG	0.612													30	41	---	---	---	---	PASS
MAN2B2	23324	broad.mit.edu	37	4	6598903	6598903	+	Missense_Mutation	SNP	G	A	A	rs144033191	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:6598903G>A	uc003gjf.1	+	8	1157	c.1121G>A	c.(1120-1122)CGA>CAA	p.R374Q	MAN2B2_uc003gje.1_Missense_Mutation_p.R374Q|MAN2B2_uc011bwf.1_Missense_Mutation_p.R323Q	NM_015274	NP_056089	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	374					mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2						CTGGCCCGGCGAGCCAGCGCC	0.657													11	116	---	---	---	---	PASS
SH3TC1	54436	broad.mit.edu	37	4	8229027	8229027	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:8229027G>T	uc003gkv.3	+	12	1707	c.1606G>T	c.(1606-1608)GAG>TAG	p.E536*	SH3TC1_uc003gkw.3_Nonsense_Mutation_p.E460*|SH3TC1_uc003gkx.3_RNA|SH3TC1_uc003gky.2_5'Flank	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	536							binding			large_intestine(2)|pancreas(1)	3						CTTCAGCGACGAGGAGGAGCT	0.687													6	20	---	---	---	---	PASS
CPEB2	132864	broad.mit.edu	37	4	15060838	15060838	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:15060838G>C	uc003gni.1	+	9	1360	c.1273G>C	c.(1273-1275)GAT>CAT	p.D425H	CPEB2_uc003gnj.1_Missense_Mutation_p.D395H|CPEB2_uc003gnk.1_Missense_Mutation_p.D433H|CPEB2_uc003gnl.1_Missense_Mutation_p.D406H|CPEB2_uc003gnm.1_Missense_Mutation_p.D403H|CPEB2_uc003gnn.1_Missense_Mutation_p.D398H	NM_182485	NP_872291	Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding	425					regulation of translation	cytoplasm	nucleotide binding|RNA binding			skin(1)	1						GAATTTAAGTGATAGTGATTT	0.373													17	100	---	---	---	---	PASS
KLHL5	51088	broad.mit.edu	37	4	39122658	39122658	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:39122658G>A	uc003gts.2	+	11	2315	c.2240G>A	c.(2239-2241)GGA>GAA	p.G747E	KLHL5_uc003gtp.2_Missense_Mutation_p.G701E|KLHL5_uc003gtq.2_Missense_Mutation_p.G560E|KLHL5_uc003gtt.2_Missense_Mutation_p.G686E	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN	kelch-like 5 isoform 1	747	Kelch 6.					cytoplasm|cytoskeleton	actin binding			ovary(1)	1						GGAAGAGCTGGAGCTTGTGTT	0.358													17	81	---	---	---	---	PASS
KCTD8	386617	broad.mit.edu	37	4	44449797	44449797	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:44449797G>A	uc003gwu.2	-	1	1028	c.744C>T	c.(742-744)TTC>TTT	p.F248F		NM_198353	NP_938167	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerisation domain	248						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(2)|ovary(1)	3						GCGTGTCCCCGAAGACCTCCT	0.647										HNSCC(17;0.042)			10	18	---	---	---	---	PASS
LRRC66	339977	broad.mit.edu	37	4	52883607	52883607	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:52883607A>G	uc003gzi.2	-	1	186	c.173T>C	c.(172-174)ATA>ACA	p.I58T		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	58						integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3						TGTCTGTGATATGTCCACAGG	0.343													13	111	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	55161433	55161433	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:55161433C>T	uc003han.3	+	23	3595	c.3264C>T	c.(3262-3264)TTC>TTT	p.F1088F	PDGFRA_uc003haa.2_Silent_p.F848F	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	1088	Cytoplasmic (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	AAGACAGCTTCCTGTAACTGG	0.512			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			13	156	---	---	---	---	PASS
ENAM	10117	broad.mit.edu	37	4	71508450	71508450	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:71508450C>G	uc011caw.1	+	9	1588	c.1307C>G	c.(1306-1308)CCA>CGA	p.P436R		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	436					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)			ATCCAAAATCCAAAGGAGAAG	0.448													12	88	---	---	---	---	PASS
SCARB2	950	broad.mit.edu	37	4	77084496	77084496	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:77084496G>C	uc003hju.1	-	11	1619	c.1280C>G	c.(1279-1281)TCT>TGT	p.S427C	SCARB2_uc011cbu.1_Missense_Mutation_p.S284C	NM_005506	NP_005497	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	427	Lumenal (Potential).				cell adhesion|protein targeting to lysosome	integral to plasma membrane|lysosomal lumen|lysosomal membrane|membrane fraction	enzyme binding|receptor activity				0			Lung(101;0.196)			GTTAATCATAGACTTCAGTCG	0.408													29	116	---	---	---	---	PASS
SHROOM3	57619	broad.mit.edu	37	4	77662404	77662404	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:77662404G>A	uc011cbx.1	+	5	4031	c.3078G>A	c.(3076-3078)ATG>ATA	p.M1026I	SHROOM3_uc011cbz.1_Missense_Mutation_p.M850I|SHROOM3_uc003hkf.1_Missense_Mutation_p.M901I|SHROOM3_uc003hkg.2_Missense_Mutation_p.M804I	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein	1026	ASD1.				apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			CCGAGAAGATGAACGAGGTGG	0.711													4	21	---	---	---	---	PASS
BMP2K	55589	broad.mit.edu	37	4	79832756	79832756	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:79832756C>T	uc003hlk.2	+	16	3221	c.3055C>T	c.(3055-3057)CGC>TGC	p.R1019C	PAQR3_uc003hlm.2_Intron|PAQR3_uc003hln.2_Intron|uc010ijm.1_5'Flank	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	1019						nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						AGAGAGGGCTCGCAGGCACAA	0.478													10	107	---	---	---	---	PASS
HELQ	113510	broad.mit.edu	37	4	84376570	84376570	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:84376570C>T	uc003hom.2	-	1	456	c.277G>A	c.(277-279)GAC>AAC	p.D93N	HELQ_uc010ikb.2_Missense_Mutation_p.D93N|HELQ_uc003hol.3_RNA|HELQ_uc010ikc.2_RNA|HELQ_uc003hon.1_5'UTR|HELQ_uc003hoo.1_Intron|HELQ_uc003hop.1_5'UTR|HELQ_uc003hoq.1_Missense_Mutation_p.D93N|MRPS18C_uc003hor.3_5'Flank|MRPS18C_uc011ccu.1_5'Flank	NM_133636	NP_598375	Q8TDG4	HELQ_HUMAN	DNA helicase HEL308	93							ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|breast(1)|skin(1)	3						ACCCCTCTGTCAGTGGGCATG	0.532								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					21	187	---	---	---	---	PASS
WDFY3	23001	broad.mit.edu	37	4	85664938	85664938	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:85664938C>T	uc003hpd.2	-	37	6396	c.5988G>A	c.(5986-5988)AGG>AGA	p.R1996R		NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	1996						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TTCTTGTAGACCTTTCAGGGG	0.323													12	90	---	---	---	---	PASS
PKD2	5311	broad.mit.edu	37	4	88979148	88979148	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:88979148C>T	uc003hre.2	+	9	1978	c.1912C>T	c.(1912-1914)CGT>TGT	p.R638C	PKD2_uc011cdf.1_Missense_Mutation_p.R56C|PKD2_uc011cdg.1_Intron|PKD2_uc011cdh.1_Intron	NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	638	Extracellular (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity			skin(1)	1		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		CACTCAATTCCGTATCATTTT	0.313													9	71	---	---	---	---	PASS
MTTP	4547	broad.mit.edu	37	4	100510802	100510802	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:100510802C>G	uc003hvc.3	+	5	652	c.396C>G	c.(394-396)GTC>GTG	p.V132V	MTTP_uc011cej.1_Silent_p.V159V	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large	132	Vitellogenin.				lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)	CCCACCAGGTCAAAGAGTTCT	0.408													6	43	---	---	---	---	PASS
MANBA	4126	broad.mit.edu	37	4	103553402	103553402	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:103553402C>G	uc003hwg.2	-	17	2552	c.2452G>C	c.(2452-2454)GAC>CAC	p.D818H	MANBA_uc011ces.1_Missense_Mutation_p.D761H	NM_005908	NP_005899	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal precursor	818					carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GTCTCCAGGTCAAAAACAAAT	0.418													11	108	---	---	---	---	PASS
LARP1B	55132	broad.mit.edu	37	4	129035746	129035746	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:129035746G>C	uc003iga.2	+	10	1141	c.1010G>C	c.(1009-1011)AGA>ACA	p.R337T	LARP1B_uc003ifz.1_Missense_Mutation_p.R337T|LARP1B_uc003igb.1_Missense_Mutation_p.R52T	NM_018078	NP_060548	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family member 2	337							RNA binding				0						AATTCTCCAAGAATTGGAAGC	0.343													16	44	---	---	---	---	PASS
RBM46	166863	broad.mit.edu	37	4	155720158	155720158	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:155720158G>A	uc003ioo.2	+	4	1017	c.844G>A	c.(844-846)GAA>AAA	p.E282K	RBM46_uc011cim.1_Missense_Mutation_p.E282K|RBM46_uc003iop.1_Missense_Mutation_p.E282K	NM_144979	NP_659416	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	282	RRM 3.						nucleotide binding|RNA binding			central_nervous_system(1)|skin(1)	2	all_hematologic(180;0.24)	Renal(120;0.0854)				TTTCAACCGAGAAGATGCAGT	0.363													7	33	---	---	---	---	PASS
NAF1	92345	broad.mit.edu	37	4	164050300	164050300	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:164050300G>A	uc003iqj.2	-	8	1428	c.1234C>T	c.(1234-1236)CAG>TAG	p.Q412*	NAF1_uc010iqw.1_Intron	NM_138386	NP_612395	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 homolog isoform a	412					rRNA processing|snRNA pseudouridine synthesis	cytoplasm|nucleus|small nucleolar ribonucleoprotein complex	protein binding|snoRNA binding			ovary(2)	2	all_hematologic(180;0.166)	Prostate(90;0.109)				TTTTGTCTCTGAGAAGGAAAT	0.413													14	101	---	---	---	---	PASS
NPY1R	4886	broad.mit.edu	37	4	164247167	164247167	+	Silent	SNP	A	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:164247167A>C	uc003iqm.1	-	2	806	c.540T>G	c.(538-540)ACT>ACG	p.T180T	NPY1R_uc011cjj.1_Intron	NM_000909	NP_000900	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	180	Extracellular (Potential).				inhibition of adenylate cyclase activity by G-protein signaling pathway|outflow tract morphogenesis	integral to plasma membrane	protein binding			lung(1)|pancreas(1)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				ACGGCTCATCAGTCATTACTT	0.418													63	67	---	---	---	---	PASS
ANP32C	23520	broad.mit.edu	37	4	165118229	165118229	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr4:165118229T>C	uc011cjk.1	-	1	635	c.635A>G	c.(634-636)GAT>GGT	p.D212G	MARCH1_uc003iqs.1_Intron	NM_012403	NP_036535	O43423	AN32C_HUMAN	acidic nuclear phosphoprotein 32C	212	Asp/Glu-rich (highly acidic).										0	all_hematologic(180;0.203)	Prostate(90;0.0138)|Melanoma(52;0.18)|all_neural(102;0.223)		KIRC - Kidney renal clear cell carcinoma(143;0.242)		tacctctccatcgttataacc	0.030													29	19	---	---	---	---	PASS
CCDC127	133957	broad.mit.edu	37	5	205636	205636	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:205636C>G	uc003jam.1	-	3	659	c.559G>C	c.(559-561)GAG>CAG	p.E187Q		NM_145265	NP_660308	Q96BQ5	CC127_HUMAN	coiled-coil domain containing 127	187											0			all cancers(22;0.0236)|Lung(60;0.113)			AAGCTCTTCTCTATCTCCAGC	0.517													10	195	---	---	---	---	PASS
BRD9	65980	broad.mit.edu	37	5	865589	865589	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:865589G>A	uc003jbq.2	-	15	1800	c.1633C>T	c.(1633-1635)CGG>TGG	p.R545W	BRD9_uc003jbl.2_Missense_Mutation_p.R429W|BRD9_uc003jbm.2_RNA|BRD9_uc003jbn.2_RNA|BRD9_uc011cmb.1_Missense_Mutation_p.R492W|BRD9_uc003jbo.2_Missense_Mutation_p.R449W	NM_023924	NP_076413	Q9H8M2	BRD9_HUMAN	bromodomain containing 9 isoform 1	545							nucleic acid binding				0			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			GACGACGGCCGAGAGCCGCCG	0.652													9	176	---	---	---	---	PASS
SLC12A7	10723	broad.mit.edu	37	5	1075584	1075584	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:1075584C>G	uc003jbu.2	-	15	1935	c.1869G>C	c.(1867-1869)ATG>ATC	p.M623I		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	623	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GGCACAGGCTCATACCCAGAA	0.642													12	66	---	---	---	---	PASS
TERT	7015	broad.mit.edu	37	5	1264696	1264696	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:1264696C>T	uc003jcb.1	-	11	2724	c.2666G>A	c.(2665-2667)CGA>CAA	p.R889Q	TERT_uc003jbz.1_Missense_Mutation_p.R85Q|TERT_uc003jca.1_Missense_Mutation_p.R877Q|TERT_uc003jcc.1_Intron|TERT_uc003jcd.1_Intron|TERT_uc003jce.1_Intron	NM_198253	NP_937983	O14746	TERT_HUMAN	telomerase reverse transcriptase isoform 1	889	Reverse transcriptase.				anti-apoptosis|DNA strand elongation|replicative senescence|telomere formation via telomerase|telomere maintenance via telomerase	cytoplasm|nucleolus|PML body|telomerase holoenzyme complex	protein homodimerization activity|telomeric DNA binding|telomeric RNA binding|telomeric template RNA reverse transcriptase activity			lung(7)|ovary(2)|central_nervous_system(2)|skin(1)	12	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AGGGACACCTCGGACCAGGGT	0.577									TERT_Mutation-Associated_Haematological_Disorders|Congenital_Dyskeratosis|Pulmonary_Fibrosis_Idiopathic				10	243	---	---	---	---	PASS
KIAA0947	23379	broad.mit.edu	37	5	5463329	5463329	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:5463329G>C	uc003jdm.3	+	13	4104	c.3882G>C	c.(3880-3882)ATG>ATC	p.M1294I		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	1294										ovary(1)|central_nervous_system(1)	2						ATAACAACATGACCACTGAGA	0.408													13	51	---	---	---	---	PASS
CTNND2	1501	broad.mit.edu	37	5	11384923	11384923	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:11384923G>C	uc003jfa.1	-	7	1176	c.1031C>G	c.(1030-1032)TCG>TGG	p.S344W	CTNND2_uc010itt.2_Missense_Mutation_p.S253W|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_5'UTR	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	344					multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						GTGGATGGGCGAGGAGGAGAT	0.672													6	46	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14488200	14488200	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:14488200C>G	uc003jff.2	+	48	7469	c.7463C>G	c.(7462-7464)TCC>TGC	p.S2488C	TRIO_uc003jfg.2_Intron|TRIO_uc003jfh.1_Missense_Mutation_p.S2137C	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2488					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					TTCTGGAGCTCCATCCCCGCC	0.731													5	30	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24505332	24505332	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:24505332G>A	uc003jgr.1	-	8	1614	c.1282C>T	c.(1282-1284)CTT>TTT	p.L428F	CDH10_uc011cnu.1_Intron	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	428	Cadherin 4.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		ATTCTGTCAAGGTCAGTATGG	0.363										HNSCC(23;0.051)			65	74	---	---	---	---	PASS
CDH9	1007	broad.mit.edu	37	5	26916023	26916023	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:26916023C>G	uc003jgs.1	-	3	407	c.238G>C	c.(238-240)GAC>CAC	p.D80H	CDH9_uc010iug.2_Missense_Mutation_p.D80H	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	80	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9						TTATCTTGGTCAGTGTGAAGC	0.338													123	109	---	---	---	---	PASS
OSMR	9180	broad.mit.edu	37	5	38932055	38932055	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:38932055G>A	uc003jln.1	+	16	2650	c.2283G>A	c.(2281-2283)TTG>TTA	p.L761L	OSMR_uc011cpj.1_Intron	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor	761	Helical; (Potential).				cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)					TGTGCTACTTGAAAAGTCAGT	0.388													20	225	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45353208	45353208	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:45353208C>T	uc003jok.2	-	5	1396	c.1371G>A	c.(1369-1371)CTG>CTA	p.L457L		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	457	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						TTACCTCTCTCAGAGGATCAT	0.343													15	170	---	---	---	---	PASS
ITGA2	3673	broad.mit.edu	37	5	52374695	52374695	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:52374695C>T	uc003joy.2	+	24	3062	c.2919C>T	c.(2917-2919)TTC>TTT	p.F973F	ITGA2_uc011cqa.1_RNA|ITGA2_uc011cqb.1_RNA|ITGA2_uc011cqc.1_Silent_p.F897F|ITGA2_uc011cqd.1_Intron|ITGA2_uc011cqe.1_RNA	NM_002203	NP_002194	P17301	ITA2_HUMAN	integrin alpha 2 precursor	973	Extracellular (Potential).				axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				AATTCATCTTCTCCCTGAAGG	0.368													12	75	---	---	---	---	PASS
PPAP2A	8611	broad.mit.edu	37	5	54721826	54721826	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:54721826G>C	uc003jqa.2	-	5	1007	c.591C>G	c.(589-591)CTC>CTG	p.L197L	PPAP2A_uc003jpz.2_Silent_p.L198L|PPAP2A_uc003jqb.2_RNA	NM_003711	NP_003702	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A isoform 1	197	Cytoplasmic (Potential).				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|androgen receptor signaling pathway|germ cell migration|negative regulation of cell proliferation|phospholipid dephosphorylation|regulation of lipid metabolic process|sphingolipid metabolic process	integral to plasma membrane|membrane fraction	phosphatidate phosphatase activity|sphingosine-1-phosphate phosphatase activity			ovary(2)	2		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				TGGGGCGTAAGAGTCTTGCCC	0.383													15	100	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75591689	75591689	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:75591689G>A	uc003kei.1	+	9	1558	c.1424G>A	c.(1423-1425)AGA>AAA	p.R475K		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	475	Extracellular (Potential).				neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		AATGTGGAGAGAGATAAATAT	0.358													20	113	---	---	---	---	PASS
LYSMD3	116068	broad.mit.edu	37	5	89815272	89815272	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:89815272G>A	uc003kjr.2	-	3	433	c.285C>T	c.(283-285)CTC>CTT	p.L95L	LYSMD3_uc010jaz.1_Intron|LYSMD3_uc003kjs.1_Intron	NM_198273	NP_938014	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain	95	Extracellular (Potential).|LysM.				cell wall macromolecule catabolic process	integral to membrane					0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		GATCACTGATGAGATTGTTAA	0.373													11	85	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89933761	89933761	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:89933761G>C	uc003kju.2	+	11	2332	c.2236G>C	c.(2236-2238)GAC>CAC	p.D746H	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	746	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ACTTTCTCTAGACAGGTAATA	0.294													8	57	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89981778	89981778	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:89981778G>A	uc003kju.2	+	29	6552	c.6456G>A	c.(6454-6456)GTG>GTA	p.V2152V	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2152	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATGTCTCTGTGAAGTTTAAAG	0.428													7	26	---	---	---	---	PASS
SNCAIP	9627	broad.mit.edu	37	5	121785556	121785556	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:121785556G>C	uc003ksw.1	+	9	1815	c.1609G>C	c.(1609-1611)GTC>CTC	p.V537L	SNCAIP_uc011cwl.1_Missense_Mutation_p.V95L|SNCAIP_uc003ksx.1_Missense_Mutation_p.V584L|SNCAIP_uc003ksy.1_Missense_Mutation_p.V171L|SNCAIP_uc003ksz.1_Missense_Mutation_p.V171L|SNCAIP_uc010jcu.2_Missense_Mutation_p.V133L|SNCAIP_uc011cwm.1_Missense_Mutation_p.V171L|SNCAIP_uc003kta.1_Missense_Mutation_p.V169L|SNCAIP_uc010jcv.1_RNA|SNCAIP_uc010jcw.1_Missense_Mutation_p.V231L|SNCAIP_uc010jcx.1_Missense_Mutation_p.V477L|uc003ktb.1_Intron|SNCAIP_uc003ktc.1_Missense_Mutation_p.V53L	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein	537	Potential.				cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		AGTAGAACGTGTCACGCTGCA	0.403													89	123	---	---	---	---	PASS
P4HA2	8974	broad.mit.edu	37	5	131552898	131552898	+	Nonsense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:131552898G>C	uc003kwh.2	-	4	887	c.323C>G	c.(322-324)TCA>TGA	p.S108*	P4HA2_uc003kwg.2_Nonsense_Mutation_p.S108*|P4HA2_uc003kwi.2_Nonsense_Mutation_p.S108*|P4HA2_uc003kwk.2_Nonsense_Mutation_p.S108*|P4HA2_uc003kwl.2_Nonsense_Mutation_p.S108*|P4HA2_uc003kwj.2_Nonsense_Mutation_p.S108*	NM_004199	NP_004190	O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha II subunit isoform 1	108						endoplasmic reticulum lumen	electron carrier activity|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity|protein binding				0		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	ACCTGCAGCTGAGTCCTGCAG	0.577													15	141	---	---	---	---	PASS
EGR1	1958	broad.mit.edu	37	5	137803577	137803577	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:137803577C>T	uc003ldb.1	+	2	1709	c.1439C>T	c.(1438-1440)TCG>TTG	p.S480L	EGR1_uc011cyu.1_Intron	NM_001964	NP_001955	P18146	EGR1_HUMAN	early growth response 1	480					cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|interleukin-1-mediated signaling pathway|positive regulation of glomerular metanephric mesangial cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of protein sumoylation|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytoplasm|nucleus	histone acetyltransferase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			cccggctcctcgacctaccca	0.279													14	111	---	---	---	---	PASS
CTNNA1	1495	broad.mit.edu	37	5	138268336	138268336	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:138268336C>T	uc003ldh.2	+	17	2463	c.2368C>T	c.(2368-2370)CTG>TTG	p.L790L	CTNNA1_uc011cyx.1_Silent_p.L687L|CTNNA1_uc011cyy.1_Silent_p.L667L|CTNNA1_uc003ldi.2_Silent_p.L488L|CTNNA1_uc003ldj.2_Silent_p.L790L|CTNNA1_uc003ldl.2_Silent_p.L420L	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1	790					adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTGCCACCAGCTGAACATCTG	0.572													5	57	---	---	---	---	PASS
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139918523	139918523	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:139918523A>G	uc003lfs.1	+	33	7548	c.7424A>G	c.(7423-7425)TAT>TGT	p.Y2475C	ANKHD1_uc003lfr.2_Missense_Mutation_p.Y2475C|ANKHD1-EIF4EBP3_uc011czh.1_Missense_Mutation_p.Y1231C|ANKHD1_uc003lfw.2_Missense_Mutation_p.Y1130C|ANKHD1_uc010jfl.2_Missense_Mutation_p.Y851C|ANKHD1-EIF4EBP3_uc003lfx.1_Missense_Mutation_p.Y620C	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	2475						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTTCCATGTATGGAGGCACC	0.368													30	51	---	---	---	---	PASS
PCDHA7	56141	broad.mit.edu	37	5	140215333	140215333	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:140215333C>G	uc003lhq.2	+	1	1365	c.1365C>G	c.(1363-1365)TTC>TTG	p.F455L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.F455L	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	455	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCCGGCGTTCGCGCAGCCCG	0.677													48	64	---	---	---	---	PASS
PCDHA10	56139	broad.mit.edu	37	5	140237240	140237240	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:140237240C>T	uc003lhx.2	+	1	1607	c.1607C>T	c.(1606-1608)GCG>GTG	p.A536V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc011dad.1_Missense_Mutation_p.A536V	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	536	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGTGAGCGCGCGCGATGGG	0.677													37	66	---	---	---	---	PASS
DIAPH1	1729	broad.mit.edu	37	5	140953218	140953218	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:140953218G>A	uc003llb.3	-	16	2340	c.2199C>T	c.(2197-2199)CCC>CCT	p.P733P	DIAPH1_uc003llc.3_Silent_p.P724P|DIAPH1_uc010jgc.1_Silent_p.P172P	NM_005219	NP_005210	O60610	DIAP1_HUMAN	diaphanous 1 isoform 1	733	FH1.				regulation of microtubule-based process|sensory perception of sound	cytoplasm|cytoskeleton|ruffle membrane	actin binding|receptor binding|Rho GTPase binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGGCCTCCGGGAAATGGAG	0.612													7	28	---	---	---	---	PASS
PDGFRB	5159	broad.mit.edu	37	5	149515421	149515421	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:149515421G>A	uc003lro.2	-	3	530	c.61C>T	c.(61-63)CTC>TTC	p.L21F	PDGFRB_uc010jhd.2_5'UTR|PDGFRB_uc011dcg.1_Missense_Mutation_p.L21F	NM_002609	NP_002600	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor beta	21					aorta morphogenesis|cardiac myofibril assembly|hemopoiesis|metanephric glomerular capillary formation|metanephric glomerular mesangial cell proliferation involved in metanephros development|peptidyl-tyrosine phosphorylation|positive regulation of calcium ion import|positive regulation of chemotaxis|positive regulation of DNA biosynthetic process|positive regulation of ERK1 and ERK2 cascade|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|protein autophosphorylation|regulation of actin cytoskeleton organization|retina vasculature development in camera-type eye|smooth muscle cell chemotaxis	apical plasma membrane|cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|vascular endothelial growth factor receptor activity			central_nervous_system(4)|lung(4)|breast(3)|stomach(2)|prostate(2)|large_intestine(1)|ovary(1)	17		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGTAACAGGAGAGACAGCAAC	0.592			T	ETV6|TRIP11|HIP1|RAB5EP|H4|NIN|HCMOGT-1|PDE4DIP	MPD|AML|CMML|CML								8	33	---	---	---	---	PASS
FAT2	2196	broad.mit.edu	37	5	150946710	150946710	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:150946710G>A	uc003lue.3	-	1	1796	c.1783C>T	c.(1783-1785)CAG>TAG	p.Q595*	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Nonsense_Mutation_p.Q595*	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	595	Extracellular (Potential).|Cadherin 5.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTAGGTTCTGAAGCTCATCC	0.413													15	112	---	---	---	---	PASS
GRIA1	2890	broad.mit.edu	37	5	153030008	153030008	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:153030008G>A	uc003lva.3	+	4	944	c.579G>A	c.(577-579)GAG>GAA	p.E193E	GRIA1_uc003luy.3_Silent_p.E193E|GRIA1_uc003luz.3_Silent_p.E98E|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Silent_p.E113E|GRIA1_uc011dcx.1_Silent_p.E124E|GRIA1_uc011dcy.1_Silent_p.E203E|GRIA1_uc011dcz.1_Silent_p.E203E|GRIA1_uc010jia.1_Silent_p.E173E	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	193	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AGGACCTGGAGAAGAAAAAGG	0.537													7	74	---	---	---	---	PASS
SGCD	6444	broad.mit.edu	37	5	155935666	155935666	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:155935666C>A	uc003lwd.3	+	3	721	c.245C>A	c.(244-246)TCT>TAT	p.S82Y	SGCD_uc003lwa.1_Missense_Mutation_p.S83Y|SGCD_uc003lwb.2_Missense_Mutation_p.S83Y|SGCD_uc003lwc.3_Missense_Mutation_p.S83Y	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3	82	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAAGGAGACTCTGAATTCTTA	0.408													3	37	---	---	---	---	PASS
LCP2	3937	broad.mit.edu	37	5	169697832	169697832	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:169697832G>T	uc003man.1	-	7	621	c.414C>A	c.(412-414)CCC>CCA	p.P138P	LCP2_uc011det.1_5'UTR|LCP2_uc010jjo.1_5'Flank	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	138					immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		CATCTTCCACGGGTGCCTCTT	0.547													22	32	---	---	---	---	PASS
UNC5A	90249	broad.mit.edu	37	5	176300995	176300995	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr5:176300995C>A	uc003mey.2	+	7	1105	c.913C>A	c.(913-915)CTC>ATC	p.L305I	UNC5A_uc010jkg.1_Missense_Mutation_p.L265I	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor	305	Extracellular (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGACGTGGCCCTCTATGTGGG	0.627													18	42	---	---	---	---	PASS
CAGE1	285782	broad.mit.edu	37	6	7355299	7355299	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:7355299C>G	uc003mxi.2	-	8	2471	c.1750G>C	c.(1750-1752)GCA>CCA	p.A584P	CAGE1_uc003mxh.2_RNA|CAGE1_uc003mxj.2_Missense_Mutation_p.A537P|CAGE1_uc003mxk.1_Missense_Mutation_p.A502P	NM_205864	NP_995586	Q8TC20	CAGE1_HUMAN	cancer antigen 1	720											0	Ovarian(93;0.0418)					TGGGATATTGCAAGCCTTTGG	0.279													15	81	---	---	---	---	PASS
DSP	1832	broad.mit.edu	37	6	7569565	7569565	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:7569565C>T	uc003mxp.1	+	12	1845	c.1566C>T	c.(1564-1566)CTC>CTT	p.L522L	DSP_uc003mxq.1_Silent_p.L522L	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	522	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CCGTGGACCTCTCTTGCAAGT	0.567													23	102	---	---	---	---	PASS
LRRC16A	55604	broad.mit.edu	37	6	25492188	25492188	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:25492188C>A	uc011djw.1	+	15	1532	c.1156C>A	c.(1156-1158)CTT>ATT	p.L386I	LRRC16A_uc010jpx.2_Missense_Mutation_p.L386I|LRRC16A_uc010jpy.2_Missense_Mutation_p.L386I	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	386					actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						CTGTGGAGCTCTTCTCCGTGG	0.413													11	60	---	---	---	---	PASS
HIST1H1B	3009	broad.mit.edu	37	6	27835170	27835170	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:27835170C>G	uc003njx.2	-	1	190	c.138G>C	c.(136-138)CTG>CTC	p.L46L		NM_005322	NP_005313	P16401	H15_HUMAN	histone cluster 1, H1b	46	H15.				nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(2)|lung(1)	3						CCTTGGTGATCAGCTCTGAGA	0.602													35	108	---	---	---	---	PASS
ZNF323	64288	broad.mit.edu	37	6	28297319	28297319	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:28297319G>A	uc003nla.2	-	2	542	c.142C>T	c.(142-144)CAA>TAA	p.Q48*	ZNF323_uc003nld.2_Nonsense_Mutation_p.Q48*|ZNF323_uc010jra.2_Nonsense_Mutation_p.Q48*|ZNF323_uc003nlb.2_Intron|ZNF323_uc010jrb.2_Intron|ZNF323_uc003nlc.2_Nonsense_Mutation_p.Q48*	NM_001135216	NP_001128688	Q96LW9	ZN323_HUMAN	zinc finger protein 323	48	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						GGAGTCTCTTGGTAACAAAAC	0.517													9	257	---	---	---	---	PASS
GABBR1	2550	broad.mit.edu	37	6	29572676	29572676	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:29572676G>C	uc003nmt.3	-	21	2865	c.2529C>G	c.(2527-2529)TTC>TTG	p.F843L	GABBR1_uc003nmp.3_Missense_Mutation_p.F726L|GABBR1_uc003nms.3_Missense_Mutation_p.F726L|GABBR1_uc003nmu.3_Missense_Mutation_p.F781L|GABBR1_uc011dlr.1_Missense_Mutation_p.F666L	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1	843	Helical; Name=7; (Potential).				gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)	TATAGGAGGAGAAAACTATGG	0.512													14	80	---	---	---	---	PASS
MDC1	9656	broad.mit.edu	37	6	30672587	30672587	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:30672587G>T	uc003nrg.3	-	10	4813	c.4373C>A	c.(4372-4374)TCC>TAC	p.S1458Y	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Missense_Mutation_p.S1065Y	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1458	Pro-rich.|Interaction with the PRKDC complex.				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4						TGTGGAGGTGGAAGGCTGGAG	0.567								Other_conserved_DNA_damage_response_genes					21	238	---	---	---	---	PASS
MDC1	9656	broad.mit.edu	37	6	30673549	30673549	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:30673549G>C	uc003nrg.3	-	10	3851	c.3411C>G	c.(3409-3411)GTC>GTG	p.V1137V	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Silent_p.V744V	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1137	Pro-rich.			Missing (in Ref. 2; CAH18685).	cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4						GCTTGGGAGTGACTGGCTGGG	0.577								Other_conserved_DNA_damage_response_genes					33	253	---	---	---	---	PASS
CDSN	1041	broad.mit.edu	37	6	31083910	31083910	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:31083910G>T	uc003nsm.1	-	2	1509	c.1482C>A	c.(1480-1482)ATC>ATA	p.I494I	PSORS1C1_uc003nsl.1_Intron|PSORS1C1_uc010jsj.1_Intron	NM_001264	NP_001255	Q15517	CDSN_HUMAN	corneodesmosin precursor	494					cell-cell adhesion|keratinocyte differentiation|skin morphogenesis	cornified envelope|desmosome|extracellular region	protein homodimerization activity			ovary(1)|pancreas(1)	2						AGCGGCAGGGGATCTTTCCAG	0.607													16	65	---	---	---	---	PASS
BAT3	7917	broad.mit.edu	37	6	31607333	31607333	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:31607333C>T	uc003nvg.3	-	24	3561	c.3247G>A	c.(3247-3249)GAG>AAG	p.E1083K	BAT3_uc003nvf.3_Missense_Mutation_p.E1077K|BAT3_uc003nvh.3_Missense_Mutation_p.E1077K|BAT3_uc003nvi.3_Missense_Mutation_p.E1077K|BAT3_uc011dnw.1_Intron|BAT3_uc011dnx.1_Intron	NM_004639	NP_004630	P46379	BAG6_HUMAN	HLA-B associated transcript-3 isoform a	1083					apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process	BAT3 complex|nucleus	polyubiquitin binding|proteasome binding|ribosome binding				0						CTCAGGCTCTCGGGGCTCGTC	0.652													11	104	---	---	---	---	PASS
BTNL2	56244	broad.mit.edu	37	6	32374847	32374847	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:32374847G>A	uc003obg.1	-	1	54	c.54C>T	c.(52-54)TTC>TTT	p.F18F	BTNL2_uc010jty.1_5'UTR|BTNL2_uc010jtz.1_RNA|BTNL2_uc010jua.1_Silent_p.F18F	NM_019602	NP_062548	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2	18	Helical; Signal-anchor for type II membrane protein; (Potential).					integral to membrane				central_nervous_system(1)	1						TCAGCAGGATGAATAGGAAGG	0.493													19	156	---	---	---	---	PASS
COL11A2	1302	broad.mit.edu	37	6	33133405	33133405	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:33133405C>T	uc003ocx.1	-	63	4899	c.4671G>A	c.(4669-4671)ATG>ATA	p.M1557I	COL11A2_uc010jul.1_Missense_Mutation_p.M127I|COL11A2_uc003ocy.1_Missense_Mutation_p.M1471I|COL11A2_uc003ocz.1_Missense_Mutation_p.M1450I	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1557	Fibrillar collagen NC1.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						TTGGCCGCCTCATCTGCTCGA	0.657													21	125	---	---	---	---	PASS
RING1	6015	broad.mit.edu	37	6	33179274	33179274	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:33179274G>C	uc003odk.2	+	5	989	c.795G>C	c.(793-795)GTG>GTC	p.V265V	RING1_uc011dqx.1_Silent_p.V265V|RING1_uc003odl.2_Silent_p.V236V	NM_002931	NP_002922	Q06587	RING1_HUMAN	ring finger protein 1	265	Necessary for interaction with CBX2 (By similarity).				histone H2A monoubiquitination|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear speck|PcG protein complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2						TTGAGCTCGTGTTCCGGCCCC	0.652													5	30	---	---	---	---	PASS
DAXX	1616	broad.mit.edu	37	6	33289247	33289247	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:33289247G>A	uc003oec.2	-	3	509	c.305C>T	c.(304-306)TCG>TTG	p.S102L	DAXX_uc011drd.1_Missense_Mutation_p.S27L|DAXX_uc011dre.1_Missense_Mutation_p.S114L|DAXX_uc003oed.2_Missense_Mutation_p.S102L|DAXX_uc010juw.2_Missense_Mutation_p.S27L	NM_001350	NP_001341	Q9UER7	DAXX_HUMAN	death-domain associated protein isoform a	102	Necessary for interaction with USP7.				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23						GAACTCCGCCGAGGCCAAAAA	0.547			Mis|F|N		Pancreatic neuroendocrine tumors								23	156	---	---	---	---	PASS
USP49	25862	broad.mit.edu	37	6	41774221	41774221	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:41774221C>T	uc003ori.2	-	4	723	c.501G>A	c.(499-501)GCG>GCA	p.A167A		NM_018561	NP_061031	Q70CQ1	UBP49_HUMAN	ubiquitin thioesterase 49	167					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCTCCAGCTTCGCCTGGCCCC	0.716													4	14	---	---	---	---	PASS
ZNF318	24149	broad.mit.edu	37	6	43305564	43305564	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:43305564C>A	uc003oux.2	-	10	6250	c.6172G>T	c.(6172-6174)GAT>TAT	p.D2058Y	ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2058					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TCAGCGGGATCGGAGGAATTA	0.468													17	89	---	---	---	---	PASS
SNAP91	9892	broad.mit.edu	37	6	84290168	84290168	+	Splice_Site	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:84290168C>T	uc011dze.1	-	23	2616	c.2299_splice	c.e23+1	p.N767_splice	SNAP91_uc011dzd.1_Splice_Site_p.N265_splice|SNAP91_uc003pkb.2_Splice_Site_p.N676_splice|SNAP91_uc003pkc.2_Splice_Site_p.N737_splice|SNAP91_uc003pkd.2_Splice_Site_p.N460_splice|SNAP91_uc003pka.2_Splice_Site_p.N765_splice	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		AGATTACTCACTGCCTACTAA	0.358													19	84	---	---	---	---	PASS
TBX18	9096	broad.mit.edu	37	6	85446736	85446736	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:85446736C>A	uc003pkl.1	-	8	1491	c.1491G>T	c.(1489-1491)CAG>CAT	p.Q497H	TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	497					multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		GCATGATATACTGGAGCTGGG	0.522													41	180	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90382074	90382074	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:90382074C>G	uc003pnn.1	-	82	13755	c.13639G>C	c.(13639-13641)GAG>CAG	p.E4547Q		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	4547					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TGCAGTCTCTCAAAGCCTGCT	0.393													13	104	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90513082	90513082	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:90513082C>T	uc003pnn.1	-	2	410	c.294G>A	c.(292-294)ATG>ATA	p.M98I	MDN1_uc003pnp.1_Missense_Mutation_p.M98I	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	98					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TGAGTTTGCTCATCGACACAC	0.468													38	266	---	---	---	---	PASS
LIN28B	389421	broad.mit.edu	37	6	105526314	105526314	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:105526314C>A	uc003pqv.1	+	4	612	c.409C>A	c.(409-411)CAT>AAT	p.H137N	LIN28B_uc010kda.1_3'UTR	NM_001004317	NP_001004317	Q6ZN17	LN28B_HUMAN	lin-28 homolog B	137	CCHC-type 1.	Zinc 1 (By similarity).			miRNA catabolic process|pre-miRNA processing|regulation of transcription, DNA-dependent|RNA 3'-end processing	cytoplasm|nucleus	DNA binding|protein binding|RNA binding|zinc ion binding				0		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)				TGGCCTTGATCATCATGCTAA	0.403													33	112	---	---	---	---	PASS
FOXO3	2309	broad.mit.edu	37	6	108985121	108985121	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:108985121G>T	uc003psk.2	+	3	1401	c.1085G>T	c.(1084-1086)TGC>TTC	p.C362F	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Missense_Mutation_p.C362F|FOXO3_uc011ean.1_Missense_Mutation_p.C142F|FOXO3_uc010kdj.1_Missense_Mutation_p.C142F	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	362					antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		AGCAAGCCGTGCACGGTGGAA	0.552													5	34	---	---	---	---	PASS
REV3L	5980	broad.mit.edu	37	6	111709286	111709286	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:111709286G>C	uc003puy.3	-	8	1188	c.865C>G	c.(865-867)CAC>GAC	p.H289D	REV3L_uc003pux.3_Missense_Mutation_p.H211D|REV3L_uc003puz.3_Missense_Mutation_p.H211D	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	289					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		ACAAACCTGTGATCTTTGAAT	0.299								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					20	93	---	---	---	---	PASS
REV3L	5980	broad.mit.edu	37	6	111732738	111732738	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:111732738C>G	uc003puy.3	-	3	672	c.349G>C	c.(349-351)GAG>CAG	p.E117Q	REV3L_uc003pux.3_Missense_Mutation_p.E39Q|REV3L_uc003puz.3_Missense_Mutation_p.E39Q	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	117					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTTTCCTTCTCATGATAACCA	0.269								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					7	31	---	---	---	---	PASS
VGLL2	245806	broad.mit.edu	37	6	117589561	117589561	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:117589561G>T	uc003pxn.2	+	2	488	c.298G>T	c.(298-300)GAT>TAT	p.D100Y	VGLL2_uc003pxo.2_Missense_Mutation_p.D100Y	NM_182645	NP_872586	Q8N8G2	VGLL2_HUMAN	vestigial-like 2 isoform 1	100					transcription, DNA-dependent	nucleus				central_nervous_system(1)	1				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		CTCCGTGGTGGATGAACATTT	0.582													24	80	---	---	---	---	PASS
HEBP2	23593	broad.mit.edu	37	6	138727245	138727245	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:138727245G>C	uc003qhw.1	+	3	673	c.376G>C	c.(376-378)GAT>CAT	p.D126H		NM_014320	NP_055135	Q9Y5Z4	HEBP2_HUMAN	heme binding protein 2	126						mitochondrion					0	Breast(32;0.0933)			GBM - Glioblastoma multiforme(68;0.000732)|OV - Ovarian serous cystadenocarcinoma(155;0.00171)		TTTAGAGTCAGATGTCTTCAT	0.438													57	240	---	---	---	---	PASS
T	6862	broad.mit.edu	37	6	166580150	166580150	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:166580150G>C	uc003quu.1	-	3	894	c.401C>G	c.(400-402)GCC>GGC	p.A134G	T_uc003qut.1_Missense_Mutation_p.A134G|T_uc003quv.1_Missense_Mutation_p.A134G	NM_003181	NP_003172	O15178	BRAC_HUMAN	transcription factor T	134	T-box.				anterior/posterior axis specification, embryo|mesoderm development|primitive streak formation	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		CATCCAGTGGGCCCCGAAGTT	0.657									Chordoma_Familial_Clustering_of				15	78	---	---	---	---	PASS
TCP10	6953	broad.mit.edu	37	6	167786830	167786830	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:167786830G>T	uc003qvv.1	-	8	1020	c.808C>A	c.(808-810)CCA>ACA	p.P270T	TCP10_uc003qvu.2_Intron	NM_004610	NP_004601	Q12799	TCP10_HUMAN	t-complex 10	297						cytosol				breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		AGGGAAGATGGTGGGTTTACA	0.488													22	149	---	---	---	---	PASS
THBS2	7058	broad.mit.edu	37	6	169622523	169622523	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:169622523G>C	uc003qwt.2	-	20	3290	c.3042C>G	c.(3040-3042)TTC>TTG	p.F1014L		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	1014	TSP C-terminal.				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		TGTTTACGTAGAATGTGCCAC	0.468													11	172	---	---	---	---	PASS
THBS2	7058	broad.mit.edu	37	6	169628356	169628356	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:169628356G>C	uc003qwt.2	-	16	2528	c.2280C>G	c.(2278-2280)TTC>TTG	p.F760L		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	760	TSP type-3 2.				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GGCGGGGATTGAAGAGGAGCT	0.498													5	47	---	---	---	---	PASS
C6orf120	387263	broad.mit.edu	37	6	170103065	170103065	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr6:170103065G>T	uc003qxb.2	+	1	809	c.510G>T	c.(508-510)GAG>GAT	p.E170D	WDR27_uc010kkw.1_5'Flank|WDR27_uc003qwx.2_5'Flank|WDR27_uc003qwy.2_5'Flank|WDR27_uc011egw.1_5'Flank|WDR27_uc010kkx.2_5'Flank|C6orf120_uc011egx.1_Missense_Mutation_p.E189D	NM_001029863	NP_001025034	Q7Z4R8	CF120_HUMAN	hypothetical protein LOC387263 precursor	170						extracellular region					0		Breast(66;0.000338)		OV - Ovarian serous cystadenocarcinoma(33;9.65e-22)|BRCA - Breast invasive adenocarcinoma(81;1.29e-07)|GBM - Glioblastoma multiforme(31;0.0015)		CCTCGCAAGAGGAGGAATCTG	0.562													4	25	---	---	---	---	PASS
MAD1L1	8379	broad.mit.edu	37	7	1997351	1997351	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:1997351C>A	uc003slh.1	-	16	1775	c.1509G>T	c.(1507-1509)TTG>TTT	p.L503F	MAD1L1_uc003sle.1_Missense_Mutation_p.L232F|MAD1L1_uc003slf.1_Missense_Mutation_p.L503F|MAD1L1_uc003slg.1_Missense_Mutation_p.L503F|MAD1L1_uc010ksh.1_Missense_Mutation_p.L503F|MAD1L1_uc003sli.1_Missense_Mutation_p.L411F|MAD1L1_uc010ksi.1_Missense_Mutation_p.L456F|MAD1L1_uc010ksj.2_Missense_Mutation_p.L503F	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein	503	Necessary for interaction with NEK2.|Potential.				cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		CCTCGACCTTCAACCTGCAAG	0.632													11	72	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5355647	5355647	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:5355647C>A	uc003soi.3	-	25	7151	c.6802G>T	c.(6802-6804)GAC>TAC	p.D2268Y		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2268							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CTGCCCGTGTCTCCGTCGTCA	0.607													6	68	---	---	---	---	PASS
PMS2	5395	broad.mit.edu	37	7	6045587	6045587	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:6045587C>T	uc003spl.2	-	2	186	c.99G>A	c.(97-99)CTG>CTA	p.L33L	PMS2_uc003spj.2_5'Flank|PMS2_uc003spk.2_5'UTR|PMS2_uc011jwl.1_Intron|PMS2_uc010ktg.2_5'UTR|PMS2_uc010kte.2_Silent_p.L33L|PMS2_uc010ktf.1_Silent_p.L33L	NM_000535	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 isoform	33					mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TGCTTAGACTCAGTACCACCT	0.428			Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				44	393	---	---	---	---	PASS
DGKB	1607	broad.mit.edu	37	7	14758225	14758225	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:14758225C>T	uc003ssz.2	-	5	595	c.408G>A	c.(406-408)AAG>AAA	p.K136K	DGKB_uc011jxt.1_Silent_p.K129K|DGKB_uc003sta.2_Silent_p.K136K|DGKB_uc011jxu.1_Silent_p.K136K|DGKB_uc011jxv.1_Silent_p.K136K	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1	136					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)	AGACAATGTCCTTCAGATGGA	0.438													15	53	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21750313	21750313	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:21750313G>C	uc003svc.2	+	42	6878	c.6847G>C	c.(6847-6849)GAT>CAT	p.D2283H		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2283	AAA 2 (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						TGTAATGGATGATAACAAGGT	0.368									Kartagener_syndrome				4	37	---	---	---	---	PASS
PKD1L1	168507	broad.mit.edu	37	7	47886498	47886498	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:47886498G>A	uc003tny.1	-	32	5132	c.5132C>T	c.(5131-5133)TCT>TTT	p.S1711F		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	1711	Extracellular (Potential).|GPS.				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						TTTTTCAGGAGAAGTCCCTGG	0.433													9	136	---	---	---	---	PASS
UPP1	7378	broad.mit.edu	37	7	48139316	48139316	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:48139316G>A	uc003toj.2	+	5	623	c.94G>A	c.(94-96)GAT>AAT	p.D32N	UPP1_uc003tok.2_Missense_Mutation_p.D32N|UPP1_uc003tol.2_Missense_Mutation_p.D32N|UPP1_uc011kcg.1_Missense_Mutation_p.D32N|UPP1_uc011kch.1_Intron|UPP1_uc003ton.2_Intron|UPP1_uc003too.2_Intron	NM_181597	NP_853628	Q16831	UPP1_HUMAN	uridine phosphorylase 1	32					nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage	cytosol	uridine phosphorylase activity				0						AATGAAAGAAGATATTCTCTA	0.403													18	188	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77762213	77762213	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:77762213C>T	uc003ugx.2	-	18	3450	c.3196G>A	c.(3196-3198)GAA>AAA	p.E1066K	MAGI2_uc003ugy.2_Missense_Mutation_p.E1052K|MAGI2_uc010ldx.1_Missense_Mutation_p.E659K	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	1066	Pro-rich.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TACCTATTTTCGTGTCCTTGC	0.567													63	468	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82581599	82581599	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:82581599C>A	uc003uhx.2	-	5	8959	c.8670G>T	c.(8668-8670)CAG>CAT	p.Q2890H	PCLO_uc003uhv.2_Missense_Mutation_p.Q2890H|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2821					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						CAGTGATTCCCTGGGATACGG	0.453													68	182	---	---	---	---	PASS
ADAM22	53616	broad.mit.edu	37	7	87760697	87760697	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:87760697G>C	uc003ujn.2	+	11	1018	c.939G>C	c.(937-939)ATG>ATC	p.M313I	ADAM22_uc003ujj.1_Missense_Mutation_p.M313I|ADAM22_uc003ujk.1_Missense_Mutation_p.M313I|ADAM22_uc003ujl.1_Missense_Mutation_p.M313I|ADAM22_uc003ujm.2_Missense_Mutation_p.M313I|ADAM22_uc003ujo.2_Missense_Mutation_p.M313I|ADAM22_uc003ujp.1_Missense_Mutation_p.M365I	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1	313	Peptidase M12B.|Extracellular (Potential).				cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			GTGAGTTTATGAAATACAGGA	0.363													12	131	---	---	---	---	PASS
KRIT1	889	broad.mit.edu	37	7	91830051	91830051	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:91830051C>T	uc003ulq.1	-	17	2381	c.2210G>A	c.(2209-2211)TGA>TAA	p.*737*	KRIT1_uc010lev.1_Silent_p.*494*|KRIT1_uc003ulr.1_Silent_p.*737*|KRIT1_uc003uls.1_Silent_p.*737*|KRIT1_uc003ult.1_Silent_p.*689*|KRIT1_uc003ulu.1_Silent_p.*737*|KRIT1_uc003ulv.1_Silent_p.*737*	NM_194456	NP_919438	O00522	KRIT1_HUMAN	krev interaction trapped 1 isoform 1	737					angiogenesis|cell redox homeostasis|negative regulation of angiogenesis|negative regulation of endothelial cell apoptosis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|regulation of establishment of cell polarity|small GTPase mediated signal transduction	cell-cell junction|cytoskeleton	protein binding|small GTPase regulator activity			ovary(2)|lung(1)	3	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACTTCTCTTTCATGAATTTCT	0.289									Familial_Cerebral_Cavernous_Angioma				6	50	---	---	---	---	PASS
PEX1	5189	broad.mit.edu	37	7	92146731	92146731	+	Missense_Mutation	SNP	A	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:92146731A>C	uc003uly.2	-	5	1194	c.1098T>G	c.(1096-1098)GAT>GAG	p.D366E	PEX1_uc011khr.1_Missense_Mutation_p.D158E|PEX1_uc010ley.2_Missense_Mutation_p.D366E|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	366					microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTTTTTTTTGATCTAGTGGCT	0.363													27	230	---	---	---	---	PASS
ARPC1A	10552	broad.mit.edu	37	7	98951667	98951667	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:98951667C>A	uc003upx.1	+	6	783	c.636C>A	c.(634-636)TTC>TTA	p.F212L	ARPC1A_uc010lfu.1_RNA|ARPC1A_uc003upy.1_Missense_Mutation_p.F198L|ARPC1A_uc011kit.1_RNA	NM_006409	NP_006400	Q92747	ARC1A_HUMAN	actin related protein 2/3 complex subunit 1A	212	WD 4.				actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)			GGGTAAGCTTCTCTGCCAGTG	0.592													9	86	---	---	---	---	PASS
CPSF4	10898	broad.mit.edu	37	7	99042437	99042437	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:99042437C>G	uc003uqj.2	+	2	272	c.129C>G	c.(127-129)TTC>TTG	p.F43L	PTCD1_uc011kiw.1_Intron|CPSF4_uc003uqi.2_Missense_Mutation_p.F43L|CPSF4_uc003uqk.2_Missense_Mutation_p.F43L|CPSF4_uc011kix.1_5'UTR	NM_006693	NP_006684	O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4,	43	C3H1-type 1.				modification by virus of host mRNA processing|mRNA processing|viral infectious cycle	mRNA cleavage and polyadenylation specificity factor complex	RNA binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					TCTGTGAATTCTTTTTGAAAG	0.542													53	328	---	---	---	---	PASS
LRCH4	4034	broad.mit.edu	37	7	100174907	100174907	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:100174907C>T	uc003uvj.2	-	11	1337	c.1284G>A	c.(1282-1284)CCG>CCA	p.P428P	LRCH4_uc010lgz.2_RNA|LRCH4_uc003uvi.2_RNA|LRCH4_uc011kjw.1_5'UTR|LRCH4_uc011kjx.1_RNA	NM_002319	NP_002310	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH)	428					nervous system development	PML body	protein binding			large_intestine(1)|ovary(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TATCCTTCCTCGGGGCCCCCC	0.736													7	14	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100366312	100366312	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:100366312C>A	uc003uwj.2	+	27	5286	c.5121C>A	c.(5119-5121)GCC>GCA	p.A1707A	ZAN_uc003uwk.2_Silent_p.A1707A|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA|ZAN_uc011kkd.1_Silent_p.A284A	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	1707	Extracellular (Potential).|VWFD 2.				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			AGCTGGGGGCCGCCTGGAAGT	0.612													5	22	---	---	---	---	PASS
SLC26A5	375611	broad.mit.edu	37	7	103051974	103051974	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:103051974C>T	uc003vbz.2	-	6	699	c.463G>A	c.(463-465)GAT>AAT	p.D155N	SLC26A5_uc003vbt.1_Missense_Mutation_p.D155N|SLC26A5_uc003vbu.1_Missense_Mutation_p.D155N|SLC26A5_uc003vbv.1_Missense_Mutation_p.D155N|SLC26A5_uc003vbw.2_RNA|SLC26A5_uc003vbx.2_Missense_Mutation_p.D155N|SLC26A5_uc003vby.2_RNA|SLC26A5_uc010liy.2_RNA	NM_198999	NP_945350	P58743	S26A5_HUMAN	prestin isoform a	155	Extracellular (Potential).				regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1						ATGACTATATCATCTGGTACT	0.443													37	96	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103143678	103143678	+	Splice_Site	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:103143678C>G	uc003vca.2	-	52	8435	c.8275_splice	c.e52-1	p.I2759_splice	RELN_uc010liz.2_Splice_Site_p.I2759_splice	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CAACTGAGATCTAATAAACAG	0.368													8	100	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103202380	103202380	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:103202380C>G	uc003vca.2	-	35	5391	c.5231G>C	c.(5230-5232)AGA>ACA	p.R1744T	RELN_uc010liz.2_Missense_Mutation_p.R1744T	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1744					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CTGAATCCATCTGAACCGGGT	0.453													5	46	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103214687	103214687	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:103214687C>G	uc003vca.2	-	30	4523	c.4363G>C	c.(4363-4365)GAG>CAG	p.E1455Q	RELN_uc010liz.2_Missense_Mutation_p.E1455Q	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1455					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AGCTTCCCCTCAAACCTATCG	0.468													25	135	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103234130	103234130	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:103234130T>G	uc003vca.2	-	27	4071	c.3911A>C	c.(3910-3912)AAG>ACG	p.K1304T	RELN_uc010liz.2_Missense_Mutation_p.K1304T	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1304					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CATAAATACCTTGAACTGTAG	0.383													43	114	---	---	---	---	PASS
MLL5	55904	broad.mit.edu	37	7	104752848	104752848	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:104752848C>T	uc003vcm.2	+	27	5179	c.4645C>T	c.(4645-4647)CCT>TCT	p.P1549S	MLL5_uc010ljc.2_Missense_Mutation_p.P1549S|MLL5_uc010ljf.1_Intron|MLL5_uc010ljg.2_Missense_Mutation_p.P283S	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1549	Pro-rich.				cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						CCCTCCACCTCCTCCACCTCC	0.443													8	126	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116381073	116381073	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:116381073C>G	uc003vij.2	+	5	1882	c.1695C>G	c.(1693-1695)ATC>ATG	p.I565M	MET_uc010lkh.2_Missense_Mutation_p.I565M|MET_uc011knc.1_Missense_Mutation_p.I565M|MET_uc011knd.1_Missense_Mutation_p.I565M|MET_uc011kne.1_Missense_Mutation_p.I537M|MET_uc011knf.1_Missense_Mutation_p.I565M|MET_uc011kng.1_Missense_Mutation_p.I565M|MET_uc011knh.1_Missense_Mutation_p.I565M|MET_uc011kni.1_Missense_Mutation_p.I565M|MET_uc011knj.1_Missense_Mutation_p.I135M|MET_uc011knb.1_Missense_Mutation_p.I565M	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	565	Extracellular (Potential).|IPT/TIG 1.				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TGCCTGCAATCTACAAGGTAG	0.368			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				16	170	---	---	---	---	PASS
POT1	25913	broad.mit.edu	37	7	124499073	124499073	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:124499073G>A	uc003vlm.2	-	9	1241	c.640C>T	c.(640-642)CAA>TAA	p.Q214*	POT1_uc011koe.1_RNA|POT1_uc003vlk.2_RNA|POT1_uc003vll.2_RNA|POT1_uc003vlo.2_Nonsense_Mutation_p.Q83*|POT1_uc003vln.2_RNA	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	214					DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						GTCAGATTTTGTAGCCGATGG	0.378													23	73	---	---	---	---	PASS
MIR129-1	406917	broad.mit.edu	37	7	127847965	127847965	+	RNA	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:127847965T>C	hsa-mir-129-1|MI0000252	+			c.41T>C			uc011koi.1_RNA																	0						CTCTCAACAGTAGTCAGGAAG	0.597													10	18	---	---	---	---	PASS
FLNC	2318	broad.mit.edu	37	7	128489458	128489458	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:128489458G>T	uc003vnz.3	+	30	5234	c.5025G>T	c.(5023-5025)GAG>GAT	p.E1675D	FLNC_uc003voa.3_Missense_Mutation_p.E1675D	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1675	Filamin 15.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12						CAGCCGGTGAGGGGAAGGTGA	0.612													31	66	---	---	---	---	PASS
TNPO3	23534	broad.mit.edu	37	7	128622324	128622324	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:128622324C>G	uc003vol.1	-	14	2211	c.1837G>C	c.(1837-1839)GAT>CAT	p.D613H	TNPO3_uc010llx.1_Missense_Mutation_p.D24H|TNPO3_uc003vom.1_Missense_Mutation_p.D547H|TNPO3_uc010lly.1_Missense_Mutation_p.D647H|TNPO3_uc010llz.1_Missense_Mutation_p.D549H	NM_012470	NP_036602	Q9Y5L0	TNPO3_HUMAN	transportin 3	613					splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5						GCAAGGCGATCTAAGAACACT	0.408													8	69	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131864622	131864622	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:131864622G>T	uc003vra.3	-	20	3927	c.3698C>A	c.(3697-3699)CCG>CAG	p.P1233Q		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1233	Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						CAGGCTGAGCGGGCTGTCCGG	0.647													4	25	---	---	---	---	PASS
LRGUK	136332	broad.mit.edu	37	7	133821796	133821796	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:133821796G>C	uc003vrm.1	+	2	334	c.318G>C	c.(316-318)CTG>CTC	p.L106L		NM_144648	NP_653249	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain	106							ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5						ATGGGGTCCTGAGAGAGGAGG	0.438													7	30	---	---	---	---	PASS
SVOPL	136306	broad.mit.edu	37	7	138329559	138329559	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:138329559G>A	uc011kqh.1	-	8	692	c.692C>T	c.(691-693)TCC>TTC	p.S231F	SVOPL_uc003vue.2_Missense_Mutation_p.S79F	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1	231						integral to membrane	transmembrane transporter activity				0						GTTCCCAGTGGAGACATTGAA	0.562													10	149	---	---	---	---	PASS
BRAF	673	broad.mit.edu	37	7	140481417	140481417	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:140481417C>A	uc003vwc.3	-	11	1452	c.1391G>T	c.(1390-1392)GGA>GTA	p.G464V		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	464	ATP (By similarity).|Protein kinase.		G -> E (in colorectal cancer).|G -> V (in a colorectal cancer cell line; elevated kinase activity; efficiently induces cell transformation).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.G464E(7)|p.G464V(7)|p.G464R(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TGATCCAGATCCAATTCTTTG	0.388		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				13	193	---	---	---	---	PASS
OR9A4	130075	broad.mit.edu	37	7	141619217	141619217	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:141619217G>A	uc003vwu.1	+	1	542	c.542G>A	c.(541-543)CGA>CAA	p.R181Q		NM_001001656	NP_001001656	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	Melanoma(164;0.0171)					TTTTGTGACCGAGGGCAATTG	0.383													29	274	---	---	---	---	PASS
PRSS1	5644	broad.mit.edu	37	7	142459707	142459707	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:142459707C>T	uc003wak.2	+	3	300	c.283C>T	c.(283-285)CGC>TGC	p.R95C	uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron|PRSS1_uc011ksm.1_3'UTR|PRSS1_uc003wam.2_Missense_Mutation_p.R35C	NM_002769	NP_002760	P07477	TRY1_HUMAN	protease, serine, 1 preproprotein	95	Peptidase S1.				digestion|proteolysis	extracellular space	metal ion binding|protein binding|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)			CAAGATCATCCGCCACCCCCA	0.542									Hereditary_Pancreatitis				6	268	---	---	---	---	PASS
PRSS1	5644	broad.mit.edu	37	7	142460325	142460325	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:142460325G>A	uc003wak.2	+	4	515	c.498G>A	c.(496-498)CTG>CTA	p.L166L	uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron|PRSS1_uc003wam.2_Silent_p.L106L	NM_002769	NP_002760	P07477	TRY1_HUMAN	protease, serine, 1 preproprotein	166	Peptidase S1.				digestion|proteolysis	extracellular space	metal ion binding|protein binding|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)			CTCCTGTGCTGAGCCAGGCTA	0.527									Hereditary_Pancreatitis				26	697	---	---	---	---	PASS
EZH2	2146	broad.mit.edu	37	7	148516729	148516729	+	Silent	SNP	G	A	A	rs6954744		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:148516729G>A	uc003wfd.1	-	9	1109	c.943C>T	c.(943-945)CTA>TTA	p.L315L	EZH2_uc011kug.1_Silent_p.L306L|EZH2_uc003wfb.1_Silent_p.L320L|EZH2_uc003wfc.1_Silent_p.L276L|EZH2_uc011kuh.1_Silent_p.L306L|EZH2_uc011kui.1_Silent_p.L315L|EZH2_uc011kuj.1_RNA	NM_004456	NP_004447	Q15910	EZH2_HUMAN	enhancer of zeste 2 isoform a	315	Interaction with DNMT1, DNMT3A and DNMT3B.				negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			TTGTTGTCTAGAGCTGTTTCT	0.378			Mis		DLBCL								20	106	---	---	---	---	PASS
TMEM176B	28959	broad.mit.edu	37	7	150490335	150490335	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:150490335C>A	uc003wht.3	-	5	607	c.441G>T	c.(439-441)GTG>GTT	p.V147V	TMEM176B_uc003whu.3_Silent_p.V147V|TMEM176B_uc003whv.3_Silent_p.V110V|TMEM176B_uc003whw.3_Silent_p.V147V	NM_001101313	NP_001094783	Q3YBM2	T176B_HUMAN	transmembrane protein 176B isoform a	147	Helical; (Potential).				cell differentiation|organ morphogenesis	integral to membrane|nuclear membrane				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGAAGCTATTCACGCAGAGGA	0.522													4	47	---	---	---	---	PASS
GALNT11	63917	broad.mit.edu	37	7	151791525	151791525	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:151791525C>G	uc010lqg.1	+	2	443	c.213C>G	c.(211-213)TTC>TTG	p.F71L	GALNT11_uc011kvm.1_Intron|GALNT11_uc003wku.2_Missense_Mutation_p.F71L|GALNT11_uc003wkv.1_Missense_Mutation_p.F71L|GALNT11_uc011kvn.1_RNA	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	71	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AGCCACAGTTCAAAGCAAACA	0.458													11	81	---	---	---	---	PASS
UBE3C	9690	broad.mit.edu	37	7	156974312	156974312	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr7:156974312G>A	uc010lqs.2	+	7	1029	c.717G>A	c.(715-717)GAG>GAA	p.E239E	UBE3C_uc003wnf.2_Silent_p.E196E|UBE3C_uc003wng.2_Silent_p.E239E	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	239					protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TTTTGCTAGAGAATGTTCTAA	0.353													14	104	---	---	---	---	PASS
DLGAP2	9228	broad.mit.edu	37	8	1645454	1645454	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:1645454C>A	uc003wpl.2	+	11	2795	c.2698C>A	c.(2698-2700)CCG>ACG	p.P900T	DLGAP2_uc003wpm.2_Missense_Mutation_p.P886T	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	979					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GATGGAGTCCCCGGAAAGAAA	0.582													28	83	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3087750	3087750	+	Nonsense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:3087750G>C	uc011kwk.1	-	27	4550	c.4160C>G	c.(4159-4161)TCA>TGA	p.S1387*	CSMD1_uc011kwj.1_Nonsense_Mutation_p.S779*|CSMD1_uc003wqe.2_Nonsense_Mutation_p.S543*	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1387	Extracellular (Potential).|CUB 8.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GGCTGCAATTGAGGCTGCAAA	0.507													6	27	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3565986	3565986	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:3565986C>T	uc011kwk.1	-	7	1349	c.959G>A	c.(958-960)AGA>AAA	p.R320K		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	320	Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTTGACTCCTCTTGACTTCAA	0.438													6	28	---	---	---	---	PASS
TNKS	8658	broad.mit.edu	37	8	9590841	9590841	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:9590841G>C	uc003wss.2	+	15	2205	c.2200G>C	c.(2200-2202)GAG>CAG	p.E734Q	TNKS_uc011kww.1_Missense_Mutation_p.E497Q|TNKS_uc010lrt.1_5'Flank	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related	734	ANK 11.				mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)		TGAGGTGGCTGAGCTTTTAGT	0.408													15	109	---	---	---	---	PASS
PPP3CC	5533	broad.mit.edu	37	8	22386063	22386063	+	Nonsense_Mutation	SNP	G	T	T	rs139802616		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:22386063G>T	uc003xbs.2	+	10	1441	c.1114G>T	c.(1114-1116)GAA>TAA	p.E372*	PPP3CC_uc011kzi.1_Nonsense_Mutation_p.E372*|PPP3CC_uc003xbt.2_Nonsense_Mutation_p.E372*|PPP3CC_uc011kzj.1_Nonsense_Mutation_p.E87*	NM_005605	NP_005596	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma	372					activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		CTCTGATGACGAACTGATTTC	0.333													13	80	---	---	---	---	PASS
SCARA3	51435	broad.mit.edu	37	8	27516290	27516290	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:27516290C>T	uc003xga.1	+	5	744	c.603C>T	c.(601-603)GGC>GGT	p.G201G	SCARA3_uc003xgb.1_Silent_p.G201G	NM_016240	NP_057324	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3 isoform 1	201	Extracellular (Potential).				response to oxidative stress|UV protection	collagen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	scavenger receptor activity			skin(2)|ovary(1)|breast(1)	4		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		CCACAGCTGGCCTGGACCTCT	0.607													11	41	---	---	---	---	PASS
DDHD2	23259	broad.mit.edu	37	8	38107250	38107250	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:38107250C>A	uc003xlb.2	+	11	1650	c.1273C>A	c.(1273-1275)CAG>AAG	p.Q425K	DDHD2_uc003xlc.2_Missense_Mutation_p.Q425K|DDHD2_uc011lbl.1_Missense_Mutation_p.Q237K|DDHD2_uc003xld.2_Missense_Mutation_p.Q44K	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1	425	SAM.				lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			CCGAGATCTTCAGGAAATAGG	0.368													7	68	---	---	---	---	PASS
WHSC1L1	54904	broad.mit.edu	37	8	38153399	38153399	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:38153399C>T	uc003xli.2	-	16	3348	c.2830G>A	c.(2830-2832)GAA>AAA	p.E944K	WHSC1L1_uc011lbm.1_Missense_Mutation_p.E944K|WHSC1L1_uc010lwe.2_Missense_Mutation_p.E895K	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long	944	PHD-type 3.				cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CAGCAGCCTTCTGGCATTTCT	0.418			T	NUP98	AML								75	105	---	---	---	---	PASS
MYST3	7994	broad.mit.edu	37	8	41790175	41790175	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:41790175T>A	uc010lxb.2	-	18	6107	c.5563A>T	c.(5563-5565)ATT>TTT	p.I1855F	MYST3_uc010lxc.2_Missense_Mutation_p.I1855F|MYST3_uc003xon.3_Missense_Mutation_p.I1855F	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	1855					histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)			CGGATGGAAATGTGCCCCTTC	0.587													8	34	---	---	---	---	PASS
KIAA0146	23514	broad.mit.edu	37	8	48647946	48647946	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:48647946G>A	uc003xqd.2	+	20	2691	c.2682G>A	c.(2680-2682)CCG>CCA	p.P894P	KIAA0146_uc011ldc.1_Silent_p.P824P|KIAA0146_uc011ldd.1_Missense_Mutation_p.D835N|KIAA0146_uc003xqe.2_Silent_p.P369P|KIAA0146_uc003xqf.2_RNA|KIAA0146_uc010lxt.2_3'UTR|KIAA0146_uc011ldf.1_Silent_p.P399P|KIAA0146_uc011ldg.1_Silent_p.P384P|KIAA0146_uc003xqg.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514	894											0		Lung NSC(58;0.175)				CCGCCCACCCGACCAGCTGCA	0.527													18	158	---	---	---	---	PASS
VCPIP1	80124	broad.mit.edu	37	8	67547363	67547363	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:67547363C>G	uc003xwn.2	-	3	3301	c.3042G>C	c.(3040-3042)AAG>AAC	p.K1014N		NM_025054	NP_079330	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex	1014					protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity			lung(2)|ovary(2)|central_nervous_system(1)|breast(1)|skin(1)|kidney(1)	8		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			GCTCAGATTTCTTTTTCACTA	0.448													24	212	---	---	---	---	PASS
C8orf34	116328	broad.mit.edu	37	8	69445345	69445345	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:69445345G>C	uc010lyz.2	+	7	857	c.808G>C	c.(808-810)GAA>CAA	p.E270Q	C8orf34_uc010lyy.1_Missense_Mutation_p.E270Q|C8orf34_uc003xyb.2_Missense_Mutation_p.E245Q	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	270					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TGTAACAGAAGAAGATATTGA	0.358													30	108	---	---	---	---	PASS
CALB1	793	broad.mit.edu	37	8	91078134	91078134	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:91078134C>T	uc003yel.1	-	6	624	c.442G>A	c.(442-444)GAC>AAC	p.D148N	CALB1_uc011lge.1_Missense_Mutation_p.D91N	NM_004929	NP_004920	P05937	CALB1_HUMAN	calbindin 1	148	EF-hand 4.					nucleus	calcium ion binding|vitamin D binding			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.00953)			ACCATTAGGTCTGTATACTCG	0.353													25	78	---	---	---	---	PASS
RUNX1T1	862	broad.mit.edu	37	8	92982910	92982910	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:92982910G>C	uc003yfd.2	-	10	1599	c.1515C>G	c.(1513-1515)ATC>ATG	p.I505M	RUNX1T1_uc003yfc.1_Missense_Mutation_p.I478M|RUNX1T1_uc003yfe.1_Missense_Mutation_p.I468M|RUNX1T1_uc010mao.2_Missense_Mutation_p.I478M|RUNX1T1_uc011lgi.1_Missense_Mutation_p.I516M|RUNX1T1_uc010man.1_Missense_Mutation_p.I130M|RUNX1T1_uc003yfb.1_Missense_Mutation_p.I468M	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	505					generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CCTGCTGATTGATAACTGCCA	0.522													14	61	---	---	---	---	PASS
PDP1	54704	broad.mit.edu	37	8	94935387	94935387	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:94935387G>C	uc003yge.2	+	2	1369	c.1100G>C	c.(1099-1101)AGA>ACA	p.R367T	PDP1_uc003ygf.2_Missense_Mutation_p.R392T|PDP1_uc010max.2_Missense_Mutation_p.R392T|PDP1_uc011lgm.1_Missense_Mutation_p.R367T|PDP1_uc011lgn.1_Missense_Mutation_p.R426T	NM_018444	NP_060914	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic	367					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						CTTCAAAAGAGAGTGATAGAA	0.443													16	146	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100155294	100155294	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:100155294C>G	uc003yiv.2	+	13	1855	c.1744C>G	c.(1744-1746)CTT>GTT	p.L582V	VPS13B_uc003yiw.2_Missense_Mutation_p.L582V|VPS13B_uc003yit.2_Missense_Mutation_p.L582V|VPS13B_uc003yiu.1_Missense_Mutation_p.L582V|VPS13B_uc003yix.1_Missense_Mutation_p.L53V	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	582					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TATAGGTCCTCTTGATTTTCG	0.398													20	160	---	---	---	---	PASS
ABRA	137735	broad.mit.edu	37	8	107782077	107782077	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:107782077G>A	uc003ymm.3	-	1	396	c.342C>T	c.(340-342)GTC>GTT	p.V114V		NM_139166	NP_631905	Q8N0Z2	ABRA_HUMAN	actin-binding Rho activating protein	114					positive regulation of Rho protein signal transduction|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent|transmembrane transport	actin cytoskeleton|plasma membrane|sarcomere	actin binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			AAGTCTTGCTGACCACCGTTT	0.547													18	266	---	---	---	---	PASS
TTC35	9694	broad.mit.edu	37	8	109462667	109462667	+	Silent	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:109462667A>T	uc003ymw.1	+	3	200	c.165A>T	c.(163-165)ATA>ATT	p.I55I		NM_014673	NP_055488	Q15006	TTC35_HUMAN	tetratricopeptide repeat domain 35	55						endoplasmic reticulum|nucleus	binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.34e-10)			TTTGGATCATATATGAACAGG	0.303													97	135	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113651004	113651004	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:113651004G>T	uc003ynu.2	-	21	3606	c.3447C>A	c.(3445-3447)CTC>CTA	p.L1149L	CSMD3_uc003yns.2_Silent_p.L421L|CSMD3_uc003ynt.2_Silent_p.L1109L|CSMD3_uc011lhx.1_Silent_p.L1045L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1149	Extracellular (Potential).|CUB 6.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						AATTTCCATAGAGACCAGCAT	0.378										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			21	113	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116426593	116426593	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:116426593G>A	uc003ynz.2	-	6	3963	c.3504C>T	c.(3502-3504)ATC>ATT	p.I1168I	TRPS1_uc011lhy.1_Silent_p.I1172I|TRPS1_uc003yny.2_Silent_p.I1181I|TRPS1_uc010mcy.2_Silent_p.I1168I	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	1168	Transcriptional repressor domain (By similarity).|Mediates interaction with RNF4 (By similarity).				negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TGGAATGCTTGATCGCCAAAT	0.443									Langer-Giedion_syndrome				11	113	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116616834	116616834	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:116616834G>A	uc003ynz.2	-	3	1782	c.1323C>T	c.(1321-1323)TTC>TTT	p.F441F	TRPS1_uc011lhy.1_Silent_p.F445F|TRPS1_uc003yny.2_Silent_p.F454F|TRPS1_uc010mcy.2_Silent_p.F441F	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	441					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			ACTCACAGCTGAAACTACAAA	0.463									Langer-Giedion_syndrome				17	99	---	---	---	---	PASS
TAF2	6873	broad.mit.edu	37	8	120772851	120772851	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:120772851C>T	uc003you.2	-	20	2956	c.2686G>A	c.(2686-2688)GAT>AAT	p.D896N		NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2	896					G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTAGTATAATCAACAACTGCT	0.353													16	111	---	---	---	---	PASS
WDR67	93594	broad.mit.edu	37	8	124132346	124132346	+	Nonsense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:124132346T>A	uc003ypp.1	+	11	1578	c.1488T>A	c.(1486-1488)TAT>TAA	p.Y496*	WDR67_uc011lig.1_Nonsense_Mutation_p.Y496*|WDR67_uc011lih.1_Nonsense_Mutation_p.Y386*|WDR67_uc003ypq.1_RNA|WDR67_uc003yps.1_Nonsense_Mutation_p.Y209*	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1	496	Rab-GAP TBC.					centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			ACACACCATATCTTCCACTCT	0.299													7	70	---	---	---	---	PASS
WDR67	93594	broad.mit.edu	37	8	124132347	124132347	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:124132347C>T	uc003ypp.1	+	11	1579	c.1489C>T	c.(1489-1491)CTT>TTT	p.L497F	WDR67_uc011lig.1_Missense_Mutation_p.L497F|WDR67_uc011lih.1_Missense_Mutation_p.L387F|WDR67_uc003ypq.1_RNA|WDR67_uc003yps.1_Missense_Mutation_p.L210F	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1	497	Rab-GAP TBC.					centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			CACACCATATCTTCCACTCTT	0.294													7	69	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	132051841	132051841	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:132051841C>A	uc003ytd.3	-	1	995	c.739G>T	c.(739-741)GTG>TTG	p.V247L	ADCY8_uc010mds.2_Missense_Mutation_p.V247L	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	247	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CAGGTGACCACGCCGCTGTAC	0.637										HNSCC(32;0.087)			3	63	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139160775	139160775	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:139160775G>C	uc003yuy.2	-	14	3607	c.3436C>G	c.(3436-3438)CAT>GAT	p.H1146D	FAM135B_uc003yux.2_Missense_Mutation_p.H1047D|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.H708D|FAM135B_uc003yvb.2_Missense_Mutation_p.P673R	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	1146										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TCCAGGCCATGGACACAGACA	0.353										HNSCC(54;0.14)			20	95	---	---	---	---	PASS
SLURP1	57152	broad.mit.edu	37	8	143822632	143822632	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:143822632C>T	uc003ywy.2	-	3	267	c.241G>A	c.(241-243)GAC>AAC	p.D81N		NM_020427	NP_065160	P55000	SLUR1_HUMAN	ARS component B precursor	81					cell activation|cell adhesion	extracellular space	cytokine activity				0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CTGTCGGGGTCGGTGGCCACA	0.662													7	35	---	---	---	---	PASS
TOP1MT	116447	broad.mit.edu	37	8	144407560	144407560	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:144407560C>T	uc003yxz.2	-	5	646	c.627G>A	c.(625-627)CTG>CTA	p.L209L	TOP1MT_uc011lkd.1_Silent_p.L111L|TOP1MT_uc011lke.1_Silent_p.L111L|TOP1MT_uc010mfb.2_Silent_p.L111L|TOP1MT_uc011lkf.1_Silent_p.L4L|TOP1MT_uc010mfd.1_Silent_p.L4L	NM_052963	NP_443195	Q969P6	TOP1M_HUMAN	mitochondrial topoisomerase I precursor	209					DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	TCCTTCTCTTCAGCATCCCCA	0.592													9	78	---	---	---	---	PASS
EEF1D	1936	broad.mit.edu	37	8	144663474	144663474	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:144663474C>A	uc011lki.1	-	4	483	c.214G>T	c.(214-216)GGC>TGC	p.G72C	NAPRT1_uc003yym.3_5'Flank|NAPRT1_uc003yyn.3_5'Flank|NAPRT1_uc011lkh.1_5'Flank|NAPRT1_uc003yyo.3_5'Flank|EEF1D_uc003yyp.1_Missense_Mutation_p.G414C|EEF1D_uc003yyq.1_Missense_Mutation_p.G488C|EEF1D_uc011lkj.1_Missense_Mutation_p.G437C|EEF1D_uc003yyr.2_Missense_Mutation_p.G438C|EEF1D_uc003yyt.2_Missense_Mutation_p.G438C|EEF1D_uc011lkk.1_Missense_Mutation_p.G72C|EEF1D_uc003yys.2_Missense_Mutation_p.G72C|EEF1D_uc003yyv.2_Missense_Mutation_p.G48C|EEF1D_uc003yyu.2_Missense_Mutation_p.G72C|EEF1D_uc011lkl.1_Missense_Mutation_p.G72C	NM_001130057	NP_001123529	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta	72					positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CCGCTGGTGCCGCTGGAGGCC	0.692													5	47	---	---	---	---	PASS
HSF1	3297	broad.mit.edu	37	8	145537690	145537690	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:145537690G>A	uc003zbt.3	+	12	1527	c.1357G>A	c.(1357-1359)GAG>AAG	p.E453K	HSF1_uc003zbu.3_RNA	NM_005526	NP_005517	Q00613	HSF1_HUMAN	heat shock transcription factor 1	453	Transactivation domain.					cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			CAGGCCTCCCGAGGCAGAGAA	0.687													8	71	---	---	---	---	PASS
NFKBIL2	4796	broad.mit.edu	37	8	145665533	145665533	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:145665533C>G	uc011llg.1	-	11	1366	c.1351G>C	c.(1351-1353)GAG>CAG	p.E451Q		NM_013432	NP_038460	Q96HA7	TONSL_HUMAN	NF-kappa-B inhibitor-like protein 2	451	Glu-rich.				cytoplasmic sequestering of transcription factor|double-strand break repair via homologous recombination|replication fork processing	cytoplasm|nuclear replication fork	histone binding|transcription corepressor activity				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GTTTCGGTCTCAGGGGCCTCC	0.517													35	93	---	---	---	---	PASS
RPL8	6132	broad.mit.edu	37	8	146016768	146016768	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:146016768C>T	uc003zeb.2	-	4	504	c.393G>A	c.(391-393)GGG>GGA	p.G131G	RPL8_uc003zdz.2_RNA|RPL8_uc003zea.2_Silent_p.G95G|RPL8_uc003zec.2_Silent_p.G131G|RPL8_uc010mgc.2_3'UTR	NM_033301	NP_150644	P62917	RL8_HUMAN	ribosomal protein L8	131					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	rRNA binding|structural constituent of ribosome				0	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.191)		TGGCATAGTTCCCTGATGCCC	0.592													6	100	---	---	---	---	PASS
ZNF7	7553	broad.mit.edu	37	8	146067569	146067569	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr8:146067569G>A	uc003zeg.3	+	5	1214	c.1077G>A	c.(1075-1077)GAG>GAA	p.E359E	ZNF7_uc010mge.2_Silent_p.E370E|ZNF7_uc011lln.1_Silent_p.E263E|ZNF7_uc003zeh.2_Intron|ZNF7_uc003zek.3_Silent_p.E263E|COMMD5_uc003zel.1_Intron	NM_003416	NP_003407	P17097	ZNF7_HUMAN	zinc finger protein 7	359					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		ACACTGGGGAGAGGCCCTACC	0.552													5	96	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8375957	8375957	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:8375957C>G	uc003zkk.2	-	38	5351	c.4640G>C	c.(4639-4641)GGT>GCT	p.G1547A	PTPRD_uc003zkp.2_Missense_Mutation_p.G1141A|PTPRD_uc003zkq.2_Missense_Mutation_p.G1140A|PTPRD_uc003zkr.2_Missense_Mutation_p.G1131A|PTPRD_uc003zks.2_Missense_Mutation_p.G1140A|PTPRD_uc003zkl.2_Missense_Mutation_p.G1538A|PTPRD_uc003zkm.2_Missense_Mutation_p.G1534A|PTPRD_uc003zkn.2_Missense_Mutation_p.G1136A|PTPRD_uc003zko.2_Missense_Mutation_p.G1137A	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1547	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		AACCATCGGACCAGCATCGGG	0.468										TSP Lung(15;0.13)			4	62	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8484269	8484269	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:8484269C>A	uc003zkk.2	-	29	3974	c.3263G>T	c.(3262-3264)CGT>CTT	p.R1088L	PTPRD_uc003zkp.2_Missense_Mutation_p.R677L|PTPRD_uc003zkq.2_Missense_Mutation_p.R677L|PTPRD_uc003zkr.2_Missense_Mutation_p.R672L|PTPRD_uc003zks.2_Missense_Mutation_p.R667L|PTPRD_uc003zkl.2_Missense_Mutation_p.R1079L|PTPRD_uc003zkm.2_Missense_Mutation_p.R1075L|PTPRD_uc003zkn.2_Missense_Mutation_p.R677L|PTPRD_uc003zko.2_Missense_Mutation_p.R674L	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1088	Fibronectin type-III 8.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ACTGTTTCCACGATTTGTCAG	0.478										TSP Lung(15;0.13)			27	77	---	---	---	---	PASS
MTAP	4507	broad.mit.edu	37	9	21837927	21837927	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:21837927C>T	uc003zph.2	+	5	481	c.368C>T	c.(367-369)TCC>TTC	p.S123F	MTAP_uc003zpi.1_Intron|MTAP_uc010mit.2_RNA|MTAP_uc011lnk.1_Missense_Mutation_p.S140F|MTAP_uc011lnl.1_Missense_Mutation_p.S56F	NM_002451	NP_002442	Q13126	MTAP_HUMAN	5'-methylthioadenosine phosphorylase	123					nucleoside metabolic process	cytoplasm	phosphorylase activity|S-methyl-5-thioadenosine phosphorylase activity			central_nervous_system(1)	1		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)	Adenine(DB00173)	AGACCTCAGTCCTTCTATGAT	0.443													13	254	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32543158	32543158	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:32543158C>A	uc003zrb.2	-	3	1532	c.1365G>T	c.(1363-1365)ACG>ACT	p.T455T	TOPORS_uc003zrc.2_Silent_p.T388T	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	455	Required for sumoylation and localization to discrete nuclear foci.|Interaction with SUMO1.				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		GTATCTGAGACGTGGCTCCTC	0.403													21	138	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32630838	32630838	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:32630838C>A	uc003zrg.1	-	1	4830	c.4740G>T	c.(4738-4740)AAG>AAT	p.K1580N	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1580	Bromo 2.				male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GACTCTGATACTTGTGCTTGG	0.383													33	160	---	---	---	---	PASS
C9orf100	84904	broad.mit.edu	37	9	35662700	35662700	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:35662700G>T	uc003zxm.1	-	7	824	c.712C>A	c.(712-714)CCT>ACT	p.P238T	C9orf100_uc003zxl.2_RNA	NM_032818	NP_116207	Q8N4T4	CI100_HUMAN	hypothetical protein LOC84904	238	PH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CCATGGGGAGGCACCACTAAC	0.607													7	2	---	---	---	---	PASS
FBXO10	26267	broad.mit.edu	37	9	37541208	37541208	+	Silent	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:37541208T>A	uc004aab.2	-	2	607	c.558A>T	c.(556-558)CCA>CCT	p.P186P	FBXO10_uc004aac.2_Silent_p.P202P|FBXO10_uc004aad.2_Intron	NM_012166	NP_036298	Q9UK96	FBX10_HUMAN	F-box protein 10	186						ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(5)	5				GBM - Glioblastoma multiforme(29;0.0107)		AGAACCAGGCTGGCGTGAAGA	0.537													29	91	---	---	---	---	PASS
MCART1	92014	broad.mit.edu	37	9	37887804	37887804	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:37887804C>G	uc004aau.2	-	3	1488	c.744G>C	c.(742-744)CAG>CAC	p.Q248H	MCART1_uc004aar.1_Intron|MCART1_uc004aaq.1_Intron|uc004aat.1_5'Flank|MCART1_uc004aav.2_Missense_Mutation_p.Q248H	NM_033412	NP_219480	Q9H1U9	MCAR1_HUMAN	mitochondrial carrier triple repeat 1	248	Solcar 3.				transport	integral to membrane|mitochondrial inner membrane				ovary(2)|breast(1)	3				GBM - Glioblastoma multiforme(29;0.00559)|Lung(182;0.0422)		TGGGGAAAGACTGAAATTCCC	0.418													11	68	---	---	---	---	PASS
APBA1	320	broad.mit.edu	37	9	72091005	72091005	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:72091005G>C	uc004ahh.2	-	3	1531	c.1255C>G	c.(1255-1257)CTT>GTT	p.L419V		NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,	419	LIN-2/CASK binding.|Pro-rich.				axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						CTGGGGTGAAGAGATGTGCTT	0.498													8	55	---	---	---	---	PASS
TLE4	7091	broad.mit.edu	37	9	82323125	82323125	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:82323125G>A	uc004ald.2	+	13	1953	c.1104G>A	c.(1102-1104)TTG>TTA	p.L368L	TLE4_uc004alc.2_Silent_p.L343L|TLE4_uc010mpr.2_Silent_p.L222L|TLE4_uc004ale.2_5'UTR|TLE4_uc011lsq.1_Silent_p.L311L|TLE4_uc010mps.2_Silent_p.L267L|TLE4_uc004alf.2_Silent_p.L282L	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4	Error:Variant_position_missing_in_O60756_after_alignment										lung(2)|ovary(1)|breast(1)|skin(1)	5						CTCCCGGATTGAGGCCTGTAC	0.418													15	141	---	---	---	---	PASS
C9orf3	84909	broad.mit.edu	37	9	97842985	97842985	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:97842985C>T	uc004ava.2	+	14	2377	c.2242C>T	c.(2242-2244)CGG>TGG	p.R748W	C9orf3_uc004auy.2_Missense_Mutation_p.R649W|C9orf3_uc004auz.1_Missense_Mutation_p.R649W|C9orf3_uc004avc.2_Missense_Mutation_p.R203W|C9orf3_uc011luj.1_Missense_Mutation_p.R110W|C9orf3_uc011luk.1_Missense_Mutation_p.R89W|C9orf3_uc004avd.2_Missense_Mutation_p.R110W	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O	748					leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		GGTTCGCCATCGGTGGTGTGA	0.542													15	149	---	---	---	---	PASS
ANKS6	203286	broad.mit.edu	37	9	101530382	101530382	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:101530382C>G	uc004ayu.2	-	11	2144	c.2123G>C	c.(2122-2124)GGC>GCC	p.G708A	ANKS6_uc004ayt.2_Missense_Mutation_p.G407A|ANKS6_uc004ayv.1_Missense_Mutation_p.G170A|ANKS6_uc004ayw.1_Missense_Mutation_p.G290A|ANKS6_uc004ayx.1_RNA|ANKS6_uc004ayy.1_RNA	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain	708	Ser-rich.									ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)				AGGAGCGCTGCCACCTGCAGG	0.607													14	26	---	---	---	---	PASS
TEX10	54881	broad.mit.edu	37	9	103090163	103090163	+	Silent	SNP	G	C	C	rs145080863		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:103090163G>C	uc004bas.2	-	8	1922	c.1707C>G	c.(1705-1707)CTC>CTG	p.L569L	TEX10_uc011lvf.1_Silent_p.L408L|TEX10_uc011lvg.1_Silent_p.L572L	NM_017746	NP_060216	Q9NXF1	TEX10_HUMAN	testis expressed 10 isoform 1	569						integral to membrane|MLL1 complex|nuclear membrane|nucleolus	binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		GCTGTGTAGAGAGCTCAGGAT	0.428													9	54	---	---	---	---	PASS
SMC2	10592	broad.mit.edu	37	9	106877046	106877046	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:106877046C>T	uc004bbv.2	+	13	1895	c.1607C>T	c.(1606-1608)TCT>TTT	p.S536F	SMC2_uc004bbu.1_Missense_Mutation_p.S536F|SMC2_uc004bbw.2_Missense_Mutation_p.S536F|SMC2_uc011lvl.1_Missense_Mutation_p.S536F|SMC2_uc004bbx.2_Missense_Mutation_p.S536F	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	536	Flexible hinge.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						AAAGACACTTCTGCAACCACA	0.338													7	93	---	---	---	---	PASS
SMC2	10592	broad.mit.edu	37	9	106889003	106889003	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:106889003G>C	uc004bbv.2	+	19	2821	c.2533G>C	c.(2533-2535)GAA>CAA	p.E845Q	SMC2_uc004bbw.2_Missense_Mutation_p.E845Q|SMC2_uc011lvl.1_Missense_Mutation_p.E845Q|SMC2_uc004bbx.2_Missense_Mutation_p.E845Q|SMC2_uc004bby.2_5'Flank	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	845	Potential.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						AGCTGTAAATGAAGCTATCAA	0.348													13	67	---	---	---	---	PASS
KIAA0368	23392	broad.mit.edu	37	9	114131428	114131428	+	Missense_Mutation	SNP	C	T	T	rs145249965	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:114131428C>T	uc004bfe.1	-	47	5534	c.5534G>A	c.(5533-5535)CGG>CAG	p.R1845Q		NM_001080398	NP_001073867			KIAA0368 protein												0						TTTGGTTGTCCGGACCCCACT	0.418													8	79	---	---	---	---	PASS
SUSD1	64420	broad.mit.edu	37	9	114873987	114873987	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:114873987G>C	uc004bfu.2	-	8	1159	c.1118C>G	c.(1117-1119)TCC>TGC	p.S373C	SUSD1_uc010mui.2_Missense_Mutation_p.S373C|SUSD1_uc010muj.2_Missense_Mutation_p.S373C	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor	373	Extracellular (Potential).					integral to membrane	calcium ion binding				0						AGGTGCTGTGGAGATGTTCAC	0.547													12	136	---	---	---	---	PASS
DBC1	1620	broad.mit.edu	37	9	122075482	122075482	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:122075482G>T	uc004bkc.2	-	2	608	c.152C>A	c.(151-153)TCC>TAC	p.S51Y	DBC1_uc004bkd.2_Missense_Mutation_p.S51Y	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	51					cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8						GTAGCTCCTGGAGTGGTGGAA	0.483													17	113	---	---	---	---	PASS
MRRF	92399	broad.mit.edu	37	9	125054075	125054075	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:125054075G>C	uc004bmb.2	+	5	622	c.507G>C	c.(505-507)CTG>CTC	p.L169L	MRRF_uc004bmc.2_Silent_p.L169L|MRRF_uc010mvz.1_RNA|MRRF_uc010mwa.2_Silent_p.L169L|MRRF_uc011lyr.1_Silent_p.L117L|MRRF_uc004bmd.2_Silent_p.L169L|MRRF_uc004bme.2_RNA	NM_138777	NP_620132	Q96E11	RRFM_HUMAN	mitochondrial ribosome recycling factor isoform	169					ribosome disassembly|translation	mitochondrion	sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						GAATGAATCTGAACCCAGAAG	0.408													18	168	---	---	---	---	PASS
PBX3	5090	broad.mit.edu	37	9	128509835	128509835	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:128509835G>A	uc004bqb.2	+	1	219	c.103G>A	c.(103-105)GAA>AAA	p.E35K	PBX3_uc004bqc.2_5'UTR|PBX3_uc004bqd.2_5'UTR|PBX3_uc011lzw.1_5'Flank	NM_006195	NP_006186	P40426	PBX3_HUMAN	pre-B-cell leukemia homeobox 3 isoform 1	35					anterior compartment pattern formation|posterior compartment specification		sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1						GCACGGCCACGAAGGGGCGGA	0.662													9	32	---	---	---	---	PASS
NUP188	23511	broad.mit.edu	37	9	131768572	131768572	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:131768572G>A	uc004bws.1	+	43	5020	c.4998G>A	c.(4996-4998)GCG>GCA	p.A1666A		NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1666					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7						TCTCTCAGGCGATGCGGTACC	0.572											OREG0019528	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	243	---	---	---	---	PASS
COL5A1	1289	broad.mit.edu	37	9	137642704	137642704	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:137642704G>A	uc004cfe.2	+	13	2020	c.1638G>A	c.(1636-1638)GCG>GCA	p.A546A		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	546	Interrupted collagenous region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGTCCCAGGCGCAAGCCATTC	0.632													8	21	---	---	---	---	PASS
QSOX2	169714	broad.mit.edu	37	9	139115921	139115921	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:139115921C>A	uc010nbi.2	-	4	554	c.516G>T	c.(514-516)ATG>ATT	p.M172I		NM_181701	NP_859052	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2 precursor	172	Thioredoxin.				cell redox homeostasis	extracellular region|integral to membrane|nuclear membrane|plasma membrane	thiol oxidase activity			ovary(1)	1		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		GGAAGTCAATCATCGTCTGTC	0.617													20	101	---	---	---	---	PASS
LCN8	138307	broad.mit.edu	37	9	139651029	139651029	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:139651029C>G	uc004cjb.1	-	3	520	c.171G>C	c.(169-171)GAG>GAC	p.E57D	LCN8_uc004cja.2_5'Flank|LCN8_uc004cjc.1_Missense_Mutation_p.E57D	NM_178469	NP_848564	Q6JVE9	LCN8_HUMAN	lipocalin 8	80					transport	extracellular region	binding			pancreas(1)	1	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		TCTTCTCTATCTCACAGCTTC	0.547													18	121	---	---	---	---	PASS
TPRN	286262	broad.mit.edu	37	9	140093946	140093946	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:140093946G>T	uc004clt.2	-	1	1035	c.1035C>A	c.(1033-1035)CTC>CTA	p.L345L	TPRN_uc004clu.2_Silent_p.L345L	NM_173691	NP_775962	Q4KMQ1	TPRN_HUMAN	hypothetical protein LOC286262 isoform 2	406					sensory perception of sound	stereocilium					0						CCCGGTCAGCGAGGGCGGTGG	0.697													4	16	---	---	---	---	PASS
CACNA1B	774	broad.mit.edu	37	9	140967951	140967951	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:140967951C>G	uc004cog.2	+	32	4831	c.4686C>G	c.(4684-4686)ATC>ATG	p.I1562M	CACNA1B_uc004coi.2_Missense_Mutation_p.I774M|CACNA1B_uc004cok.1_5'Flank|CACNA1B_uc010ncp.1_5'Flank	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	1562	Extracellular (Potential).|IV.				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	ACAATTTCATCAACCTCAGCT	0.567													10	141	---	---	---	---	PASS
CACNA1B	774	broad.mit.edu	37	9	141010056	141010056	+	Missense_Mutation	SNP	A	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr9:141010056A>C	uc004cog.2	+	41	5847	c.5702A>C	c.(5701-5703)CAG>CCG	p.Q1901P	CACNA1B_uc004coi.2_Missense_Mutation_p.Q1113P	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	1901	Cytoplasmic (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	GAGCAGACACAGCCGGCTGTG	0.587													49	109	---	---	---	---	PASS
ANKRD16	54522	broad.mit.edu	37	10	5929903	5929903	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:5929903C>T	uc010qat.1	-	2	985	c.442G>A	c.(442-444)GGC>AGC	p.G148S	ANKRD16_uc009xie.2_Missense_Mutation_p.G148S|ANKRD16_uc009xif.2_Missense_Mutation_p.G148S|ANKRD16_uc001iiq.2_Missense_Mutation_p.G148S|FBXO18_uc001iir.2_5'Flank|FBXO18_uc001iis.2_5'Flank|FBXO18_uc009xig.2_5'Flank	NM_019046	NP_061919	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16 isoform a	148	ANK 4.										0						AGAGGGTCGCCTTCTCGACTG	0.537													11	69	---	---	---	---	PASS
RBM17	84991	broad.mit.edu	37	10	6155486	6155486	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:6155486C>G	uc001ijb.2	+	9	1098	c.872C>G	c.(871-873)TCA>TGA	p.S291*	RBM17_uc010qav.1_Nonsense_Mutation_p.S291*|RBM17_uc001ijc.2_5'Flank	NM_032905	NP_116294	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	291					mRNA processing|RNA splicing	spliceosomal complex	nucleotide binding|protein binding|RNA binding				0						TCCAAGAAGTCAGATTCAAAT	0.393													18	137	---	---	---	---	PASS
ITIH2	3698	broad.mit.edu	37	10	7762923	7762923	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:7762923G>A	uc001ijs.2	+	7	897	c.735G>A	c.(733-735)CAG>CAA	p.Q245Q		NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide	245					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3						AAGGACAACAGAAGGTACCCT	0.502													11	67	---	---	---	---	PASS
ANKRD26	22852	broad.mit.edu	37	10	27368049	27368049	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:27368049G>T	uc001ith.2	-	7	954	c.782C>A	c.(781-783)TCA>TAA	p.S261*	ANKRD26_uc001itg.2_5'UTR|ANKRD26_uc009xku.1_Nonsense_Mutation_p.S261*	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	261						centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						TTCGTCATCTGAGGTAGGCCA	0.318													11	100	---	---	---	---	PASS
KIAA1462	57608	broad.mit.edu	37	10	30318354	30318354	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:30318354C>T	uc001iux.2	-	2	782	c.723G>A	c.(721-723)CTG>CTA	p.L241L	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Silent_p.L103L|KIAA1462_uc009xle.1_Silent_p.L241L	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	241										ovary(4)	4						CCGTGCAACTCAGGCTCTCGG	0.453													31	119	---	---	---	---	PASS
SLC18A3	6572	broad.mit.edu	37	10	50820179	50820179	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:50820179G>T	uc001jhw.2	+	1	1833	c.1393G>T	c.(1393-1395)GTC>TTC	p.V465F	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank|CHAT_uc001jia.2_5'Flank|CHAT_uc001jhz.2_5'Flank|CHAT_uc010qgs.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	465	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(2)	2						CTATGCTCCCGTCTTGCTGCT	0.642													32	38	---	---	---	---	PASS
TFAM	7019	broad.mit.edu	37	10	60154126	60154126	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:60154126G>A	uc001jkf.2	+	6	678	c.546G>A	c.(544-546)CTG>CTA	p.L182L	TFAM_uc001jkg.2_RNA|TFAM_uc001jkh.2_Silent_p.L150L	NM_003201	NP_003192	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial precursor	182	HMG box 2.				DNA-dependent DNA replication|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase I promoter|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	mitochondrial light strand promoter sense binding|protein binding|sequence-specific DNA binding transcription factor activity				0						AGGAAAAGCTGAAGACTGTAA	0.348													11	136	---	---	---	---	PASS
ARID5B	84159	broad.mit.edu	37	10	63851828	63851828	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:63851828C>G	uc001jlt.1	+	10	2632	c.2606C>G	c.(2605-2607)TCT>TGT	p.S869C		NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	869					liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)					GAAAACAGTTCTTTTCCTTCC	0.483													21	133	---	---	---	---	PASS
HK1	3098	broad.mit.edu	37	10	71158397	71158397	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:71158397G>T	uc001jpl.3	+	17	2523	c.2422G>T	c.(2422-2424)GGT>TGT	p.G808C	HK1_uc001jpg.3_Missense_Mutation_p.G796C|HK1_uc001jph.3_Missense_Mutation_p.G812C|HK1_uc001jpi.3_Missense_Mutation_p.G812C|HK1_uc001jpj.3_Missense_Mutation_p.G843C|HK1_uc001jpk.3_Missense_Mutation_p.G807C	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI	808	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1						CCAGCAGCTAGGTCTGAATAG	0.617													16	27	---	---	---	---	PASS
ADAMTS14	140766	broad.mit.edu	37	10	72503414	72503414	+	Missense_Mutation	SNP	G	A	A	rs149001845		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:72503414G>A	uc001jrh.2	+	13	2035	c.2035G>A	c.(2035-2037)GTC>ATC	p.V679I	ADAMTS14_uc001jrg.2_Missense_Mutation_p.V682I|ADAMTS14_uc001jri.1_Missense_Mutation_p.V202I	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	679	Cys-rich.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	p.V682I(1)		ovary(5)|upper_aerodigestive_tract(1)	6						CCCATACAGCGTCTGTGCGCG	0.657													4	31	---	---	---	---	PASS
NUDT13	25961	broad.mit.edu	37	10	74879866	74879866	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:74879866G>A	uc001jtj.2	+	3	299	c.174G>A	c.(172-174)CTG>CTA	p.L58L	NUDT13_uc010qkc.1_5'UTR|NUDT13_uc010qkd.1_5'UTR|NUDT13_uc009xqw.2_RNA|NUDT13_uc001jtk.2_Silent_p.L58L|NUDT13_uc010qke.1_5'UTR|NUDT13_uc001jtl.2_Silent_p.L58L	NM_015901	NP_056985	Q86X67	NUD13_HUMAN	nudix-type motif 13	58							hydrolase activity|metal ion binding				0	Prostate(51;0.0119)					TGGCTCCTCTGCTTCAGACTT	0.498													19	70	---	---	---	---	PASS
TCTN3	26123	broad.mit.edu	37	10	97444366	97444366	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:97444366C>G	uc001klb.3	-	9	1229	c.985G>C	c.(985-987)GAG>CAG	p.E329Q	TCTN3_uc001kla.3_Missense_Mutation_p.E178Q|TCTN3_uc010qoi.1_Intron|TCTN3_uc001kld.2_Missense_Mutation_p.E347Q|TCTN3_uc009xux.1_Missense_Mutation_p.E151Q|TCTN3_uc009xuy.1_RNA	NM_015631	NP_056446	Q6NUS6	TECT3_HUMAN	tectonic 3 isoform a precursor	329	Extracellular (Potential).				apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		CCATTGGTCTCTATCTCATAG	0.408													8	69	---	---	---	---	PASS
CCNJ	54619	broad.mit.edu	37	10	97817990	97817990	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:97817990G>C	uc001klm.2	+	6	1470	c.1111G>C	c.(1111-1113)GAA>CAA	p.E371Q	uc001klg.1_Intron|uc001klj.1_Intron|uc009xvb.1_Intron|CCNJ_uc010qoq.1_Missense_Mutation_p.E382Q|CCNJ_uc001kln.2_Missense_Mutation_p.E370Q	NM_019084	NP_061957	Q5T5M9	CCNJ_HUMAN	cyclin J isoform 2	371						nucleus				ovary(1)	1				Epithelial(162;6.1e-08)|all cancers(201;2.32e-06)		TCCATGTTTTGAAAGGTGATT	0.398													8	100	---	---	---	---	PASS
PIK3AP1	118788	broad.mit.edu	37	10	98411116	98411116	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:98411116T>A	uc001kmq.2	-	6	1005	c.877A>T	c.(877-879)AAC>TAC	p.N293Y	PIK3AP1_uc001kmp.2_Missense_Mutation_p.N115Y	NM_152309	NP_689522	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	293	DBB.					cytoplasm|plasma membrane				upper_aerodigestive_tract(3)|ovary(1)|skin(1)	5		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		GTCTCTGTGTTGTAGGGCACA	0.448													7	84	---	---	---	---	PASS
PAX2	5076	broad.mit.edu	37	10	102566224	102566224	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:102566224G>C	uc001krk.3	+	7	1273	c.723G>C	c.(721-723)CAG>CAC	p.Q241H	PAX2_uc001krl.3_Missense_Mutation_p.Q218H|PAX2_uc001krm.3_Missense_Mutation_p.Q241H|PAX2_uc001kro.3_Missense_Mutation_p.Q218H|PAX2_uc001krn.3_Missense_Mutation_p.Q218H|PAX2_uc010qps.1_Missense_Mutation_p.Q217H|PAX2_uc001krp.1_Missense_Mutation_p.Q214H	NM_003990	NP_003981	Q02962	PAX2_HUMAN	paired box protein 2 isoform e	241					anti-apoptosis|axonogenesis|brain morphogenesis|branching involved in ureteric bud morphogenesis|cell fate determination|cellular response to glucose stimulus|cellular response to hydrogen peroxide|cellular response to retinoic acid|cochlea development|glial cell differentiation|inner ear morphogenesis|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesodermal cell fate specification|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric mesenchymal cell differentiation|metanephric nephron tubule formation|negative regulation of caspase activity|negative regulation of cytolysis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|negative regulation of reactive oxygen species metabolic process|negative regulation of transcription, DNA-dependent|nephric duct formation|neural tube closure|optic chiasma development|optic cup morphogenesis involved in camera-type eye development|optic nerve structural organization|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of metanephric glomerulus development|positive regulation of optic nerve formation|positive regulation of transcription from RNA polymerase II promoter|pronephric field specification|protein kinase B signaling cascade|reactive oxygen species metabolic process|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of metanephros size|retinal pigment epithelium development|stem cell differentiation|transcription from RNA polymerase II promoter|ureter maturation|vestibulocochlear nerve formation|visual perception	centriolar satellite|nucleus|protein complex|protein-DNA complex	core promoter proximal region sequence-specific DNA binding|superoxide-generating NADPH oxidase activity				0		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		GAGATTCCCAGAGTGGTGTGG	0.582													90	153	---	---	---	---	PASS
SUFU	51684	broad.mit.edu	37	10	104353392	104353392	+	Splice_Site	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:104353392G>C	uc001kvy.1	+	5	744	c.598_splice	c.e5-1	p.I200_splice	SUFU_uc001kvw.1_Splice_Site_p.I200_splice|SUFU_uc001kvx.2_Splice_Site_p.I200_splice	NM_016169	NP_057253	Q9UMX1	SUFU_HUMAN	suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		CTGGGCCTCAGATCGTTGGTG	0.587			D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				16	72	---	---	---	---	PASS
PNLIPRP2	5408	broad.mit.edu	37	10	118383557	118383557	+	Missense_Mutation	SNP	G	T	T	rs62623669	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:118383557G>T	uc001lcq.2	+	5	177	c.154G>T	c.(154-156)GAC>TAC	p.D52Y	PNLIPRP2_uc009xyu.1_RNA|PNLIPRP2_uc009xyv.1_RNA	NM_005396	NP_005387	P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2	51					galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			large_intestine(1)	1				all cancers(201;0.015)		GTCCCCCGAGGACATTGACAC	0.488													65	74	---	---	---	---	PASS
FANK1	92565	broad.mit.edu	37	10	127693514	127693514	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:127693514G>T	uc001ljh.3	+	7	705	c.601G>T	c.(601-603)GCT>TCT	p.A201S	FANK1_uc009yan.2_Missense_Mutation_p.A227S|FANK1_uc001lji.2_Missense_Mutation_p.A195S	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains	201	ANK 3.					cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				AAGACATGGCGCTTCTTGGCA	0.517													80	94	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129903801	129903801	+	Silent	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr10:129903801T>A	uc001lke.2	-	13	6498	c.6303A>T	c.(6301-6303)ATA>ATT	p.I2101I	MKI67_uc001lkf.2_Silent_p.I1741I|MKI67_uc009yav.1_Silent_p.I1676I|MKI67_uc009yaw.1_Silent_p.I1251I	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	2101	16 X 122 AA approximate repeats.|10.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				ATTTGCAGGCTATTTTGGTAG	0.488													241	259	---	---	---	---	PASS
NUP98	4928	broad.mit.edu	37	11	3735181	3735181	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:3735181G>A	uc001lyh.2	-	19	2735	c.2444C>T	c.(2443-2445)ACA>ATA	p.T815I	NUP98_uc001lyi.2_Missense_Mutation_p.T815I|NUP98_uc001lyj.1_Missense_Mutation_p.T815I|NUP98_uc001lyk.1_Missense_Mutation_p.T832I	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	832	Peptidase S59.				carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		ACAACGAGATGTTTTATCTGT	0.363			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								15	90	---	---	---	---	PASS
OR52B2	255725	broad.mit.edu	37	11	6190633	6190633	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:6190633C>A	uc010qzy.1	-	1	924	c.924G>T	c.(922-924)CGG>CGT	p.R308R		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	308	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCAAAGAACCGGTGGGCTA	0.478													26	68	---	---	---	---	PASS
PTH	5741	broad.mit.edu	37	11	13514120	13514120	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:13514120C>T	uc001mlb.2	-	3	295	c.180G>A	c.(178-180)CAG>CAA	p.Q60Q		NM_000315	NP_000306	P01270	PTHY_HUMAN	parathyroid hormone preproprotein	60	Important for receptor binding.				bone resorption|cAMP metabolic process|cell-cell signaling|cellular calcium ion homeostasis|cellular macromolecule biosynthetic process|induction of apoptosis by hormones|positive regulation of cAMP biosynthetic process|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|skeletal system development		hormone activity|peptide hormone receptor binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(625;0.00116)|Epithelial(150;0.0357)|LUSC - Lung squamous cell carcinoma(625;0.0836)		TGTGCACATCCTGCAGCTTCT	0.488													14	78	---	---	---	---	PASS
PDE3B	5140	broad.mit.edu	37	11	14880628	14880628	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:14880628C>T	uc001mln.2	+	13	2913	c.2560C>T	c.(2560-2562)CAT>TAT	p.H854Y	PDE3B_uc010rcr.1_Missense_Mutation_p.H803Y	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B	854	Catalytic (By similarity).				cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0						GGAAAATCATCATGCTGCGTC	0.343													20	109	---	---	---	---	PASS
HPS5	11234	broad.mit.edu	37	11	18301471	18301471	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:18301471C>A	uc001mod.1	-	23	3626	c.3348G>T	c.(3346-3348)ATG>ATT	p.M1116I	HPS5_uc001moe.1_Missense_Mutation_p.M1002I|HPS5_uc001mof.1_Missense_Mutation_p.M1002I	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a	1116						cytosol				ovary(1)|pancreas(1)|skin(1)	3						ATTTTTCAAGCATGCTTTGTA	0.393									Hermansky-Pudlak_syndrome				23	33	---	---	---	---	PASS
TMEM86A	144110	broad.mit.edu	37	11	18723292	18723292	+	Silent	SNP	T	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:18723292T>G	uc001moz.1	+	3	542	c.459T>G	c.(457-459)CTT>CTG	p.L153L		NM_153347	NP_699178	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	153	Helical; (Potential).					integral to membrane				ovary(1)	1						ATGTGGCCCTTATCGGCTTCA	0.637													13	41	---	---	---	---	PASS
PRRG4	79056	broad.mit.edu	37	11	32874918	32874918	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:32874918C>G	uc001mtx.2	+	6	779	c.526C>G	c.(526-528)CCA>GCA	p.P176A		NM_024081	NP_076986	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4	176	Cytoplasmic (Potential).					extracellular region|Golgi apparatus|integral to membrane	calcium ion binding				0	Breast(20;0.206)					TGCCTTGTCTCCATTGCCGCC	0.517													15	93	---	---	---	---	PASS
OR5F1	338674	broad.mit.edu	37	11	55761778	55761778	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:55761778C>T	uc010riv.1	-	1	324	c.324G>A	c.(322-324)GCG>GCA	p.A108A		NM_003697	NP_003688	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)					ATTCGGTTGTCGCCAGGGAGA	0.483													20	170	---	---	---	---	PASS
OR5AS1	219447	broad.mit.edu	37	11	55798745	55798745	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:55798745T>A	uc010riw.1	+	1	851	c.851T>A	c.(850-852)ATG>AAG	p.M284K		NM_001001921	NP_001001921	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS,	284	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|liver(1)|skin(1)	5	Esophageal squamous(21;0.00693)					GTATTTCCCATGTTTAATCCA	0.343													24	86	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57077747	57077747	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:57077747G>C	uc001njr.2	-	5	2750	c.2438C>G	c.(2437-2439)TCT>TGT	p.S813C	TNKS1BP1_uc001njs.2_Missense_Mutation_p.S813C|TNKS1BP1_uc009ymd.1_Missense_Mutation_p.S264C	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	813	Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				CCCTGGGGCAGACACTTTACT	0.637													45	289	---	---	---	---	PASS
SLC43A3	29015	broad.mit.edu	37	11	57182517	57182517	+	Missense_Mutation	SNP	G	A	A	rs151251549		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:57182517G>A	uc001nkg.2	-	10	1242	c.832C>T	c.(832-834)CGC>TGC	p.R278C	PRG2_uc001nke.2_Missense_Mutation_p.R177C|SLC43A3_uc001nkh.2_Missense_Mutation_p.R278C|SLC43A3_uc010rjr.1_Missense_Mutation_p.R291C|SLC43A3_uc009yme.2_Missense_Mutation_p.R278C|SLC43A3_uc001nki.2_Missense_Mutation_p.R278C|SLC43A3_uc009ymf.1_Missense_Mutation_p.R278C	NM_014096	NP_054815	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	278					transmembrane transport	integral to membrane				central_nervous_system(1)	1						CAGGCAAAGCGCCGAGAGAAA	0.582													18	196	---	---	---	---	PASS
OR5B3	441608	broad.mit.edu	37	11	58170611	58170611	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:58170611G>C	uc010rkf.1	-	1	272	c.272C>G	c.(271-273)TCT>TGT	p.S91C		NM_001005469	NP_001005469	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B,	91	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGCATTGTAAGAGATGACCTT	0.433													16	183	---	---	---	---	PASS
GLYATL1	92292	broad.mit.edu	37	11	58723411	58723411	+	Missense_Mutation	SNP	C	A	A	rs140092025		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:58723411C>A	uc001nnf.2	+	8	1196	c.820C>A	c.(820-822)CGC>AGC	p.R274S	uc001nng.1_Intron|GLYATL1_uc001nnh.1_Missense_Mutation_p.R305S|GLYATL1_uc001nni.1_Missense_Mutation_p.R274S|GLYATL1_uc001nnj.1_Missense_Mutation_p.R274S			Q969I3	GLYL1_HUMAN	SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;	274						mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)	TGAAGACTCCCGCAGATTTGT	0.448													84	97	---	---	---	---	PASS
OR4D9	390199	broad.mit.edu	37	11	59282956	59282956	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:59282956G>C	uc010rkv.1	+	1	571	c.571G>C	c.(571-573)GAC>CAC	p.D191H		NM_001004711	NP_001004711	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D,	191	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TGCCTGCACTGACACCTTCAC	0.453													23	268	---	---	---	---	PASS
CCDC86	79080	broad.mit.edu	37	11	60617696	60617696	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:60617696G>C	uc001nqa.2	+	4	1150	c.981G>C	c.(979-981)AAG>AAC	p.K327N	CCDC86_uc001nqb.2_Missense_Mutation_p.K71N	NM_024098	NP_077003	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	327					interspecies interaction between organisms	nucleus					0						ACCCCGCCAAGCTCAAGCGGG	0.637													25	107	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62298072	62298072	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:62298072C>T	uc001ntl.2	-	5	4117	c.3817G>A	c.(3817-3819)GAA>AAA	p.E1273K	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1273					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				ACATCCACTTCTCGGCCCTCT	0.547													117	361	---	---	---	---	PASS
SLC22A10	387775	broad.mit.edu	37	11	63064845	63064845	+	Missense_Mutation	SNP	G	T	T	rs113851643		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:63064845G>T	uc009yor.2	+	3	785	c.577G>T	c.(577-579)GCT>TCT	p.A193S	SLC22A10_uc010rmo.1_RNA|SLC22A10_uc001nwu.3_RNA|SLC22A10_uc010rmp.1_Intron	NM_001039752	NP_001034841	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	193	Cytoplasmic (Potential).					integral to membrane	transmembrane transporter activity			ovary(2)	2						CGCTGCCTTCGCTCCCACCTT	0.428													51	202	---	---	---	---	PASS
FERMT3	83706	broad.mit.edu	37	11	63987220	63987220	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:63987220C>A	uc001nyl.2	+	9	1187	c.1038C>A	c.(1036-1038)CTC>CTA	p.L346L	FERMT3_uc001nym.2_Silent_p.L346L	NM_178443	NP_848537	Q86UX7	URP2_HUMAN	fermitin family homolog 3 long form	346	FERM.				integrin activation|leukocyte cell-cell adhesion|platelet aggregation|regulation of cell-cell adhesion mediated by integrin	cell junction|cell projection|podosome	integrin binding			ovary(1)	1						AGGACAGCCTCACCACCATCC	0.622													24	241	---	---	---	---	PASS
NUDT22	84304	broad.mit.edu	37	11	63997459	63997459	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:63997459C>T	uc001nyp.3	+	6	1089	c.909C>T	c.(907-909)CTC>CTT	p.L303L	NUDT22_uc009ype.2_Silent_p.L303L|NUDT22_uc001nyq.3_Silent_p.L270L|NUDT22_uc010rng.1_RNA|uc001nyr.1_3'UTR|DNAJC4_uc001nys.2_5'Flank|DNAJC4_uc001nyt.2_5'Flank|DNAJC4_uc001nyu.2_5'Flank	NM_032344	NP_115720	Q9BRQ3	NUD22_HUMAN	nudix (nucleoside diphosphate linked moiety	303							hydrolase activity				0						TCCCGCCGCTCTGAAAATAAT	0.547													9	91	---	---	---	---	PASS
SF1	7536	broad.mit.edu	37	11	64544043	64544043	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:64544043C>T	uc001obb.1	-	2	464	c.87G>A	c.(85-87)CAG>CAA	p.Q29Q	SF1_uc010rnn.1_Silent_p.Q3Q|SF1_uc001oaz.1_Silent_p.Q154Q|SF1_uc001oba.1_Silent_p.Q29Q|SF1_uc001obc.1_Silent_p.Q29Q|SF1_uc001obd.1_Silent_p.Q29Q|SF1_uc001obe.1_5'UTR|SF1_uc010rno.1_5'UTR|SF1_uc001obf.2_Silent_p.Q29Q	NM_004630	NP_004621	Q15637	SF01_HUMAN	splicing factor 1 isoform 1	29					nuclear mRNA 3'-splice site recognition|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ribosome|spliceosomal complex	protein binding|RNA binding|transcription corepressor activity|zinc ion binding			ovary(1)|breast(1)|skin(1)	3						TCACTGTCTTCTGTTCCATTG	0.428													12	164	---	---	---	---	PASS
MAP4K2	5871	broad.mit.edu	37	11	64557882	64557882	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:64557882G>A	uc001obh.2	-	28	2237	c.2145C>T	c.(2143-2145)ATC>ATT	p.I715I	MAP4K2_uc001obg.2_RNA|MAP4K2_uc001obi.2_Silent_p.I707I	NM_004579	NP_004570	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase	715	CNH.				activation of JUN kinase activity|immune response|positive regulation of JNK cascade|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2						AGCTGACTAGGATTGTGTCCC	0.632													17	143	---	---	---	---	PASS
ATG2A	23130	broad.mit.edu	37	11	64664301	64664301	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:64664301C>A	uc001obx.2	-	38	5306	c.5191G>T	c.(5191-5193)GAG>TAG	p.E1731*	ATG2A_uc001obw.2_Nonsense_Mutation_p.E496*	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1731							protein binding			ovary(1)|central_nervous_system(1)	2						TGCAGCCACTCGTTGAGGGCA	0.632											OREG0004026	type=REGULATORY REGION|Gene=BC027481|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	29	---	---	---	---	PASS
SNX15	29907	broad.mit.edu	37	11	64803125	64803125	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:64803125C>G	uc001oci.3	+	9	1307	c.654C>G	c.(652-654)TTC>TTG	p.F218L	SNX15_uc009ypy.2_Missense_Mutation_p.F218L|SNX15_uc001ocj.2_Missense_Mutation_p.F218L|SNX15_uc001ock.2_Missense_Mutation_p.F218L	NM_013306	NP_037438	Q9NRS6	SNX15_HUMAN	sorting nexin 15 isoform A	218					cell communication|intracellular protein transport	cytoplasmic vesicle membrane|cytosol	phosphatidylinositol binding|protein transporter activity			ovary(1)	1						TCGACCCCTTCTCCAAGGAAG	0.637													22	226	---	---	---	---	PASS
ZFPL1	7542	broad.mit.edu	37	11	64854843	64854843	+	Silent	SNP	A	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:64854843A>C	uc001ocq.1	+	7	849	c.684A>C	c.(682-684)GGA>GGC	p.G228G		NM_006782	NP_006773	O95159	ZFPL1_HUMAN	zinc finger protein-like 1	228	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|vesicle-mediated transport	Golgi apparatus|integral to membrane|nucleus	DNA binding|zinc ion binding			ovary(1)	1						GCCTCCATGGAGACTGTGACG	0.602													86	115	---	---	---	---	PASS
MAP3K11	4296	broad.mit.edu	37	11	65375870	65375870	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:65375870C>T	uc001oew.2	-	2	1282	c.789G>A	c.(787-789)CTG>CTA	p.L263L	MAP3K11_uc001oev.2_5'Flank|MAP3K11_uc010rol.1_Silent_p.L6L|MAP3K11_uc001oex.1_5'UTR	NM_002419	NP_002410	Q16584	M3K11_HUMAN	mitogen-activated protein kinase kinase kinase	263	Protein kinase.			ILLLQPIESDDMEHKTLKITDFGLAR -> SEFLGAWLGVA WLWYTPAPNLPLSLA (in Ref. 3; BAD92892).	activation of JUN kinase activity|cell proliferation|G1 phase of mitotic cell cycle|microtubule-based process|positive regulation of JNK cascade|protein autophosphorylation	centrosome|microtubule	ATP binding|JUN kinase kinase kinase activity|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity	p.L263L(1)		breast(3)|lung(1)|central_nervous_system(1)|skin(1)	6						CGGTGATCTTCAGGGTCTTGT	0.572													11	83	---	---	---	---	PASS
CTSW	1521	broad.mit.edu	37	11	65650870	65650870	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:65650870C>G	uc001ogc.1	+	9	1037	c.995C>G	c.(994-996)TCC>TGC	p.S332C	CTSW_uc001ogb.1_Missense_Mutation_p.S332C	NM_001335	NP_001326	P56202	CATW_HUMAN	cathepsin W preproprotein	332					immune response|proteolysis		cysteine-type endopeptidase activity			central_nervous_system(1)	1				READ - Rectum adenocarcinoma(159;0.168)		CTGAAGAACTCCTGGGGGGCC	0.602													12	231	---	---	---	---	PASS
BRMS1	25855	broad.mit.edu	37	11	66108320	66108320	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:66108320C>G	uc001ohp.1	-	6	607	c.460G>C	c.(460-462)GAC>CAC	p.D154H	BRMS1_uc001oho.1_Missense_Mutation_p.D154H|BRMS1_uc009yre.2_Missense_Mutation_p.M1I	NM_015399	NP_056214	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1 isoform 1	154					apoptosis|negative regulation of anti-apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of anoikis|positive regulation of protein deacetylation|transcription, DNA-dependent	cytoplasm|nucleus	NF-kappaB binding				0						TGCAGCGTGTCATAGAGCAGC	0.647													24	35	---	---	---	---	PASS
PC	5091	broad.mit.edu	37	11	66618620	66618620	+	Nonsense_Mutation	SNP	G	C	C	rs113994146		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:66618620G>C	uc001ojn.1	-	15	2163	c.2114C>G	c.(2113-2115)TCA>TGA	p.S705*	PC_uc001ojo.1_Nonsense_Mutation_p.S705*|PC_uc001ojp.1_Nonsense_Mutation_p.S705*|PC_uc001ojm.1_5'Flank	NM_022172	NP_071504	P11498	PYC_HUMAN	pyruvate carboxylase precursor	705	Carboxyltransferase.				gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	GCCCGTGTATGAGATGGCAGC	0.617													7	95	---	---	---	---	PASS
TBC1D10C	374403	broad.mit.edu	37	11	67171760	67171760	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:67171760C>T	uc001ola.2	+	2	116	c.87C>T	c.(85-87)AGC>AGT	p.S29S	PPP1CA_uc009yro.1_5'Flank|PPP1CA_uc001okt.1_5'Flank|PPP1CA_uc001oku.1_5'Flank|PPP1CA_uc001okv.1_5'Flank|PPP1CA_uc001okw.1_5'Flank|PPP1CA_uc001okx.1_Intron|PPP1CA_uc001oky.2_5'Flank|TBC1D10C_uc001okz.2_Silent_p.S29S|TBC1D10C_uc001olb.2_RNA	NM_198517	NP_940919	Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	29						intracellular	Rab GTPase activator activity				0			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CAGAGCTCAGCGGGCCTGGCC	0.687													6	55	---	---	---	---	PASS
CPT1A	1374	broad.mit.edu	37	11	68571486	68571486	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:68571486G>C	uc001oog.3	-	5	707	c.537C>G	c.(535-537)GTC>GTG	p.V179V	CPT1A_uc001oof.3_Silent_p.V179V|CPT1A_uc009ysj.2_Silent_p.V179V	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform	179	Cytoplasmic (Potential).				carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)	CAGTGTCTTTGACAGCCGGGA	0.493													9	80	---	---	---	---	PASS
RNF121	55298	broad.mit.edu	37	11	71706589	71706589	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:71706589C>T	uc001ora.2	+	8	1195	c.855C>T	c.(853-855)TTC>TTT	p.F285F	RNF121_uc001ord.2_Silent_p.F204F|RNF121_uc001orb.2_Silent_p.F253F|RNF121_uc009yst.2_3'UTR	NM_018320	NP_060790	Q9H920	RN121_HUMAN	ring finger protein 121	285						integral to membrane	zinc ion binding				0						AGAGGATGTTCAGCAATCCGT	0.542													3	24	---	---	---	---	PASS
ARHGEF17	9828	broad.mit.edu	37	11	73075604	73075604	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:73075604A>G	uc001otu.2	+	18	5530	c.5509A>G	c.(5509-5511)AAC>GAC	p.N1837D		NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1837					actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0						TGGCTGCCAGAACCGAGTCCT	0.612													47	71	---	---	---	---	PASS
UCP3	7352	broad.mit.edu	37	11	73717284	73717284	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:73717284C>T	uc001our.2	-	3	622	c.267G>A	c.(265-267)ATG>ATA	p.M89I	UCP3_uc001ous.2_Missense_Mutation_p.M89I	NM_003356	NP_003347	P55916	UCP3_HUMAN	uncoupling protein 3 isoform UCP3L	89	Solcar 1.|Helical; Name=2; (Potential).				mitochondrial transport|respiratory electron transport chain|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	binding			pancreas(1)	1	Breast(11;2.08e-05)					AGGCGAAGCTCATCTGGCGCT	0.637													5	37	---	---	---	---	PASS
C2CD3	26005	broad.mit.edu	37	11	73811650	73811650	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:73811650C>G	uc001ouu.2	-	15	2879	c.2652G>C	c.(2650-2652)TGG>TGC	p.W884C		NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	884						centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					GCACCTTATTCCAAGTTTCAA	0.448													62	81	---	---	---	---	PASS
CHRDL2	25884	broad.mit.edu	37	11	74414013	74414013	+	Splice_Site	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:74414013C>T	uc001ovi.2	-	9	1200	c.947_splice	c.e9-1	p.E316_splice	CHRDL2_uc001ovg.2_Splice_Site_p.E200_splice|CHRDL2_uc001ovh.2_Splice_Site_p.E316_splice|CHRDL2_uc001ovj.1_Intron|CHRDL2_uc001ovk.1_Intron			Q6WN34	CRDL2_HUMAN	RecName: Full=Chordin-like protein 2; AltName: Full=Chordin-related protein 2; AltName: Full=Breast tumor novel factor 1;          Short=BNF-1; Flags: Precursor;						cartilage development|cell differentiation|ossification	extracellular region|mitochondrion					0	Hepatocellular(1;0.098)					GCTTTGTCCTCTGGAGAGACA	0.502											OREG0021223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	173	---	---	---	---	PASS
PRSS23	11098	broad.mit.edu	37	11	86519517	86519517	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:86519517C>T	uc001pcb.2	+	2	1048	c.832C>T	c.(832-834)CAC>TAC	p.H278Y	PRSS23_uc001pcc.1_Intron|PRSS23_uc010rts.1_Missense_Mutation_p.H246Y	NM_007173	NP_009104	O95084	PRS23_HUMAN	protease, serine, 23 precursor	278					proteolysis	extracellular region|nucleus	serine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GGGCAGAATTCACTTCTCTGG	0.483													24	148	---	---	---	---	PASS
NAALAD2	10003	broad.mit.edu	37	11	89892410	89892410	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:89892410C>A	uc001pdf.3	+	8	1003	c.894C>A	c.(892-894)TAC>TAA	p.Y298*	NAALAD2_uc009yvx.2_Intron|NAALAD2_uc009yvy.2_Intron|NAALAD2_uc001pdd.2_3'UTR|NAALAD2_uc001pde.2_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	298	Extracellular (Potential).|NAALADase.				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				TTGTCAGCTACTTGGGAGGAA	0.348													41	60	---	---	---	---	PASS
CNTN5	53942	broad.mit.edu	37	11	100064360	100064360	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:100064360G>C	uc001pga.2	+	15	2188	c.1849G>C	c.(1849-1851)GAG>CAG	p.E617Q	CNTN5_uc009ywv.1_Missense_Mutation_p.E617Q|CNTN5_uc001pfz.2_Missense_Mutation_p.E617Q|CNTN5_uc001pgb.2_Missense_Mutation_p.E543Q|CNTN5_uc010ruk.1_5'UTR	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	617	Ig-like C2-type 6.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TATTGATTTCGAGGAAGAGGG	0.373													11	55	---	---	---	---	PASS
CADM1	23705	broad.mit.edu	37	11	115049489	115049489	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:115049489C>T	uc001ppi.3	-	9	1214	c.1085G>A	c.(1084-1086)CGA>CAA	p.R362Q	CADM1_uc001ppf.3_Missense_Mutation_p.R334Q|CADM1_uc001ppk.3_Missense_Mutation_p.R334Q|CADM1_uc001ppj.3_Missense_Mutation_p.R363Q|CADM1_uc001pph.3_Missense_Mutation_p.R125Q	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	362	Extracellular (Potential).				adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		TTCACCTGCTCGGGAATCTGT	0.552													13	86	---	---	---	---	PASS
C2CD2L	9854	broad.mit.edu	37	11	118986832	118986832	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:118986832C>G	uc001pvo.2	+	14	2346	c.1987C>G	c.(1987-1989)CAC>GAC	p.H663D	C2CD2L_uc001pvn.2_Missense_Mutation_p.H664D	NM_014807	NP_055622	O14523	C2C2L_HUMAN	transmembrane protein 24	663						integral to membrane					0						GAGCCAATCACACGATGACCT	0.587													5	58	---	---	---	---	PASS
C2CD2L	9854	broad.mit.edu	37	11	118986933	118986933	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:118986933C>G	uc001pvo.2	+	14	2447	c.2088C>G	c.(2086-2088)CCC>CCG	p.P696P	C2CD2L_uc001pvn.2_Silent_p.P697P	NM_014807	NP_055622	O14523	C2C2L_HUMAN	transmembrane protein 24	696						integral to membrane					0						AATCCAAACCCAAGGCCAATG	0.587													7	46	---	---	---	---	PASS
PVRL1	5818	broad.mit.edu	37	11	119535989	119535989	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:119535989G>A	uc001pwv.2	-	6	1194	c.1022C>T	c.(1021-1023)TCT>TTT	p.S341F	PVRL1_uc001pwu.1_Intron	NM_002855	NP_002846	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 isoform 1	341	Extracellular (Potential).				adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		TTCGGGAGGAGACGGGGTGTA	0.662													20	42	---	---	---	---	PASS
PRDM10	56980	broad.mit.edu	37	11	129800974	129800974	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr11:129800974C>T	uc001qfm.2	-	11	1699	c.1467G>A	c.(1465-1467)GAG>GAA	p.E489E	PRDM10_uc001qfj.2_Silent_p.E403E|PRDM10_uc001qfk.2_Silent_p.E403E|PRDM10_uc001qfl.2_Silent_p.E403E|PRDM10_uc010sbx.1_Silent_p.E403E|PRDM10_uc001qfn.2_Silent_p.E489E|PRDM10_uc009zct.1_Silent_p.E521E	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	489					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		GCACCACGCTCTCTTCATGCT	0.617													46	60	---	---	---	---	PASS
CCDC77	84318	broad.mit.edu	37	12	521043	521043	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:521043G>C	uc001qig.2	+	4	349	c.169G>C	c.(169-171)GAG>CAG	p.E57Q	CCDC77_uc009zdk.2_Missense_Mutation_p.E25Q|CCDC77_uc010sdp.1_Missense_Mutation_p.E25Q|CCDC77_uc010sdq.1_Missense_Mutation_p.E25Q	NM_032358	NP_115734	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77 isoform a	57	Potential.					centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			TCCTTCTAAGGAGCTCCTGGA	0.498													31	77	---	---	---	---	PASS
AKAP3	10566	broad.mit.edu	37	12	4737262	4737262	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:4737262C>A	uc001qnb.3	-	4	1035	c.806G>T	c.(805-807)CGA>CTA	p.R269L		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	269					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6						TTCCTGCCCTCGAAACCTCTT	0.443													28	67	---	---	---	---	PASS
NOP2	4839	broad.mit.edu	37	12	6666601	6666601	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:6666601G>A	uc001qph.1	-	16	2165	c.1985C>T	c.(1984-1986)TCT>TTT	p.S662F	IFFO1_uc001qpe.1_5'Flank|IFFO1_uc010sfe.1_5'Flank|IFFO1_uc001qpf.1_5'Flank|IFFO1_uc001qpc.1_5'Flank|IFFO1_uc001qpd.1_5'Flank|NOP2_uc009zeq.1_3'UTR|NOP2_uc001qpi.1_Missense_Mutation_p.S662F|NOP2_uc001qpj.1_Missense_Mutation_p.S91F	NM_001033714	NP_001028886	P46087	NOP2_HUMAN	nucleolar protein 1, 120kDa	666					positive regulation of cell proliferation|rRNA processing	nucleolus	protein binding|RNA binding|S-adenosylmethionine-dependent methyltransferase activity			ovary(2)	2						CTTTGTGACAGAAGGTACAGT	0.527													14	108	---	---	---	---	PASS
ING4	51147	broad.mit.edu	37	12	6761577	6761577	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:6761577C>G	uc001qpw.3	-	6	549	c.508G>C	c.(508-510)GAG>CAG	p.E170Q	ING4_uc001qpv.3_Missense_Mutation_p.E169Q|ING4_uc001qpy.3_Missense_Mutation_p.E166Q|ING4_uc001qpx.3_Missense_Mutation_p.E167Q|ING4_uc009zes.2_Intron|ING4_uc009zet.2_Missense_Mutation_p.E146Q|ING4_uc009zeu.2_Intron|ING4_uc009zev.2_RNA	NM_001127582	NP_001121054	Q9UNL4	ING4_HUMAN	inhibitor of growth family, member 4 isoform 9	170					apoptosis|cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|negative regulation of cell proliferation|negative regulation of growth|negative regulation of transcription, DNA-dependent|positive regulation of apoptosis	histone acetyltransferase complex	protein binding|transcription coactivator activity|zinc ion binding			central_nervous_system(3)|ovary(1)	4						ATCCCATACTCAGGACTTCTG	0.522													18	145	---	---	---	---	PASS
SLC2A14	144195	broad.mit.edu	37	12	7981421	7981421	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:7981421C>A	uc001qtk.2	-	11	1417	c.624G>T	c.(622-624)TGG>TGT	p.W208C	SLC2A14_uc001qtl.2_Missense_Mutation_p.W185C|SLC2A14_uc001qtm.2_Missense_Mutation_p.W185C|SLC2A14_uc010sgg.1_Missense_Mutation_p.W99C|SLC2A14_uc001qtn.2_Missense_Mutation_p.W208C|SLC2A14_uc001qto.2_Intron|SLC2A14_uc010sgh.1_Missense_Mutation_p.W223C	NM_153449	NP_703150	Q8TDB8	GTR14_HUMAN	glucose transporter 14	208	Helical; Name=6; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)		ATAGCACCGGCCATAGCTCTT	0.443													49	83	---	---	---	---	PASS
WBP11	51729	broad.mit.edu	37	12	14943483	14943483	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:14943483G>A	uc001rci.2	-	10	1377	c.1216C>T	c.(1216-1218)CCC>TCC	p.P406S		NM_016312	NP_057396	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	406	Pro-rich.				mRNA processing|RNA splicing|rRNA processing	cytoplasm	single-stranded DNA binding|WW domain binding			ovary(1)|lung(1)	2						CCTGGCATGGGAGGTGCTTGT	0.577													53	106	---	---	---	---	PASS
PIK3C2G	5288	broad.mit.edu	37	12	18576938	18576938	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:18576938C>T	uc001rdt.2	+	17	2462	c.2346C>T	c.(2344-2346)TCC>TCT	p.S782S	PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Silent_p.S823S|PIK3C2G_uc010sic.1_Silent_p.S601S	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma	782					cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				TCCACCGCTCCTTGCAGAGCA	0.428													9	19	---	---	---	---	PASS
C12orf11	55726	broad.mit.edu	37	12	27081799	27081799	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:27081799G>A	uc001rhk.3	-	4	877	c.340C>T	c.(340-342)CGG>TGG	p.R114W	C12orf11_uc010sjk.1_Missense_Mutation_p.R13W	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	114					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)					GGATCTGCCCGAGGATTAGGA	0.418													6	49	---	---	---	---	PASS
ABCD2	225	broad.mit.edu	37	12	40001441	40001441	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:40001441C>A	uc001rmb.2	-	3	1622	c.1196G>T	c.(1195-1197)GGA>GTA	p.G399V		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	399	ABC transmembrane type-1.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6						AGCATCAGCTCCAGAGGCCAG	0.328													38	91	---	---	---	---	PASS
SFRS2IP	9169	broad.mit.edu	37	12	46322405	46322405	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:46322405G>A	uc001rox.2	-	11	1366	c.1079C>T	c.(1078-1080)TCT>TTT	p.S360F	SFRS2IP_uc001row.2_Missense_Mutation_p.S45F|SFRS2IP_uc001roy.1_Missense_Mutation_p.S434F	NM_004719	NP_004710	Q99590	SCAFB_HUMAN	splicing factor, arginine/serine-rich 2,	360					spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)		CTCAGCTGAAGAGGGAACACT	0.443													47	133	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49444670	49444670	+	Silent	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:49444670T>A	uc001rta.3	-	10	2796	c.2796A>T	c.(2794-2796)CCA>CCT	p.P932P		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	932	Pro-rich.			Missing (in Ref. 1; AAC51734).	chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						TCCCCTTACCTGGTGGCATCA	0.537			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			33	76	---	---	---	---	PASS
KRT6B	3854	broad.mit.edu	37	12	52841347	52841347	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:52841347C>T	uc001sak.2	-	8	1483	c.1435G>A	c.(1435-1437)GAA>AAA	p.E479K		NM_005555	NP_005546	P04259	K2C6B_HUMAN	keratin 6B	479	Tail.				ectoderm development	keratin filament	structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.083)		CCAACGCCTTCGCCATTCAGC	0.552													41	69	---	---	---	---	PASS
KRT8	3856	broad.mit.edu	37	12	53292299	53292299	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:53292299C>T	uc001sbd.2	-	7	1310	c.1207G>A	c.(1207-1209)GAG>AAG	p.E403K	KRT8_uc009zmj.2_Intron|KRT8_uc009zmk.1_Missense_Mutation_p.E431K|KRT8_uc009zml.1_Missense_Mutation_p.E403K|KRT8_uc009zmm.1_Missense_Mutation_p.E403K	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8	403	Tail.				cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ATCCCAGACTCCAGCCTGTAC	0.617													7	36	---	---	---	---	PASS
PFDN5	5204	broad.mit.edu	37	12	53691675	53691675	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:53691675C>A	uc001scl.2	+	4	366	c.249C>A	c.(247-249)CTC>CTA	p.L83L	PFDN5_uc001scm.2_Silent_p.L38L|PFDN5_uc001scn.2_RNA|PFDN5_uc001sco.2_RNA|C12orf10_uc010sof.1_5'Flank|C12orf10_uc001scp.3_5'Flank|C12orf10_uc009zmx.2_5'Flank|C12orf10_uc001scq.3_5'Flank	NM_002624	NP_002615	Q99471	PFD5_HUMAN	prefoldin subunit 5 isoform alpha	83					'de novo' posttranslational protein folding|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent	nucleus|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)	1						AACACGTGCTCATCGATGTGG	0.507													11	146	---	---	---	---	PASS
SMARCC2	6601	broad.mit.edu	37	12	56559219	56559219	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:56559219C>T	uc001skb.2	-	26	3128	c.3022G>A	c.(3022-3024)GGC>AGC	p.G1008S	SMARCC2_uc001skd.2_Missense_Mutation_p.G1039S|SMARCC2_uc001ska.2_Missense_Mutation_p.G1039S|SMARCC2_uc001skc.2_Missense_Mutation_p.G1038S|SMARCC2_uc010sqf.1_Missense_Mutation_p.G928S	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	1008	Pro-rich.				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			TCAGAAGGGCCCAAACTTCCT	0.667													4	48	---	---	---	---	PASS
PAN2	9924	broad.mit.edu	37	12	56721407	56721407	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:56721407C>T	uc001skx.2	-	6	1033	c.660G>A	c.(658-660)CTG>CTA	p.L220L	PAN2_uc001skz.2_Silent_p.L220L|PAN2_uc001sky.2_Silent_p.L220L	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	220					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						GGAGGTCTCTCAGGGAAACCT	0.453													18	91	---	---	---	---	PASS
STAT2	6773	broad.mit.edu	37	12	56737278	56737278	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:56737278C>T	uc001slc.2	-	24	2529	c.2451G>A	c.(2449-2451)CCG>CCA	p.P817P	STAT2_uc001slb.2_Silent_p.P359P|STAT2_uc001sld.2_Silent_p.P813P	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription	817					interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3						GGTCACCATTCGGCATGATTT	0.512													16	79	---	---	---	---	PASS
PRIM1	5557	broad.mit.edu	37	12	57127988	57127988	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:57127988C>G	uc001smd.2	-	12	1250	c.1186G>C	c.(1186-1188)GAA>CAA	p.E396Q		NM_000946	NP_000937	P49642	PRI1_HUMAN	DNA primase polypeptide 1	396					DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	DNA primase activity|metal ion binding				0						AGAAAATGTTCAAAAACTTTC	0.323													9	73	---	---	---	---	PASS
XPOT	11260	broad.mit.edu	37	12	64816962	64816962	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:64816962G>T	uc001ssb.2	+	11	1546	c.1120G>T	c.(1120-1122)GCA>TCA	p.A374S		NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	374	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		TTATTCTTAGGCAATCATGTT	0.274													9	71	---	---	---	---	PASS
XPOT	11260	broad.mit.edu	37	12	64828360	64828360	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:64828360G>C	uc001ssb.2	+	20	2952	c.2526G>C	c.(2524-2526)CAG>CAC	p.Q842H		NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	842	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		CAATTGCACAGAAAACATGTT	0.358													20	115	---	---	---	---	PASS
MYF5	4617	broad.mit.edu	37	12	81111177	81111177	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:81111177C>A	uc001szg.2	+	1	470	c.335C>A	c.(334-336)ACC>AAC	p.T112N		NM_005593	NP_005584	P13349	MYF5_HUMAN	myogenic factor 5	112	Helix-loop-helix motif.				muscle cell fate commitment|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1						TGTACCACGACCAACCCCAAC	0.592													25	122	---	---	---	---	PASS
C12orf63	374467	broad.mit.edu	37	12	97151357	97151357	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:97151357A>T	uc001tet.1	+	25	3384	c.3306A>T	c.(3304-3306)TTA>TTT	p.L1102F		NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN	hypothetical protein LOC374467	1102										skin(6)|ovary(1)	7						GATCACCATTAACACTTAAGG	0.313													3	26	---	---	---	---	PASS
TMPO	7112	broad.mit.edu	37	12	98921682	98921682	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:98921682G>A	uc001tfj.2	+	2	535	c.298G>A	c.(298-300)GAT>AAT	p.D100N	TMPO_uc001tfi.1_Missense_Mutation_p.D100N|TMPO_uc001tfk.2_Missense_Mutation_p.D100N|TMPO_uc001tfl.2_RNA|TMPO_uc001tfh.1_Missense_Mutation_p.D100N	NM_001032283	NP_001027454	P42167	LAP2B_HUMAN	thymopoietin isoform beta	100	Linker.|Nucleoplasmic (Potential).					integral to membrane|nuclear inner membrane	DNA binding|lamin binding			ovary(2)	2						AAAAAAAACTGATAAACCCAG	0.343													17	109	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104134531	104134531	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:104134531C>A	uc001tjw.2	+	55	6064	c.5878C>A	c.(5878-5880)CAG>AAG	p.Q1960K	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1960	Extracellular (Potential).|Laminin EGF-like 2.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						GCGAGACTGTCAGGGTGAGGG	0.562													17	137	---	---	---	---	PASS
NT5DC3	51559	broad.mit.edu	37	12	104208723	104208723	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:104208723C>T	uc010swe.1	-	2	426	c.385G>A	c.(385-387)GAA>AAA	p.E129K		NM_001031701	NP_001026871	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	129							hydrolase activity|metal ion binding			ovary(2)|skin(1)	3						ACCCGGTGTTCATTGATGAGA	0.463													18	155	---	---	---	---	PASS
TRPV4	59341	broad.mit.edu	37	12	110252339	110252339	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:110252339G>C	uc001tpj.1	-	1	358	c.263C>G	c.(262-264)TCC>TGC	p.S88C	TRPV4_uc001tpg.1_Missense_Mutation_p.S54C|TRPV4_uc001tph.1_Missense_Mutation_p.S88C|TRPV4_uc001tpi.1_Missense_Mutation_p.S88C|TRPV4_uc001tpk.1_Missense_Mutation_p.S88C|TRPV4_uc001tpl.1_Missense_Mutation_p.S88C	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,	88	Cytoplasmic (Potential).				actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						ATATAGGGTGGACTCCAGCAG	0.602													11	60	---	---	---	---	PASS
IFT81	28981	broad.mit.edu	37	12	110655899	110655899	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:110655899G>A	uc001tqi.2	+	19	2029	c.1899G>A	c.(1897-1899)ATG>ATA	p.M633I	IFT81_uc001tqh.2_Missense_Mutation_p.M633I|IFT81_uc001tqj.2_RNA	NM_001143779	NP_001137251	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81-like isoform 1	633					cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1						GTCCAAATATGAAACAAGCAA	0.323													12	104	---	---	---	---	PASS
GPN3	51184	broad.mit.edu	37	12	110893649	110893649	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:110893649C>G	uc001tqr.2	-	5	593	c.537G>C	c.(535-537)CTG>CTC	p.L179L	GPN3_uc001tqs.2_Silent_p.L189L	NM_016301	NP_057385	Q9UHW5	GPN3_HUMAN	GPN-loop GTPase 3 isoform 1	179						protein complex	GTP binding				0						CTTTTTTACTCAGCAGATCCA	0.388													8	68	---	---	---	---	PASS
HPD	3242	broad.mit.edu	37	12	122281695	122281695	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:122281695G>A	uc001ubj.2	-	12	915	c.875C>T	c.(874-876)CCC>CTC	p.P292L	HPD_uc001ubk.2_Missense_Mutation_p.P253L	NM_002150	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	292					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	GTACGTGGAGGGAACAGATAA	0.547													7	56	---	---	---	---	PASS
CCDC62	84660	broad.mit.edu	37	12	123265748	123265748	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:123265748C>G	uc001udc.2	+	3	412	c.267C>G	c.(265-267)CTC>CTG	p.L89L	CCDC62_uc010tah.1_RNA|CCDC62_uc001udf.2_Silent_p.L89L|CCDC62_uc001ude.2_5'UTR	NM_201435	NP_958843	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62 isoform b	89	Potential.					cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		TCAGGTCACTCACGAAGAAGG	0.388													10	82	---	---	---	---	PASS
SBNO1	55206	broad.mit.edu	37	12	123812522	123812522	+	Nonsense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:123812522G>C	uc010tap.1	-	10	1349	c.1349C>G	c.(1348-1350)TCA>TGA	p.S450*	SBNO1_uc010tao.1_Nonsense_Mutation_p.S449*|SBNO1_uc010taq.1_Intron|SBNO1_uc001uet.2_Nonsense_Mutation_p.S450*|SBNO1_uc001ueu.2_Nonsense_Mutation_p.S449*|SBNO1_uc001uev.2_Nonsense_Mutation_p.S448*|SBNO1_uc009zxy.1_Nonsense_Mutation_p.S415*	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	450							ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GGTTGGCTTTGAAGAACCAAC	0.348													15	126	---	---	---	---	PASS
ATP6V0A2	23545	broad.mit.edu	37	12	124228439	124228439	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:124228439C>T	uc001ufr.2	+	10	1394	c.1146C>T	c.(1144-1146)ATC>ATT	p.I382I		NM_012463	NP_036595	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	382	Cytoplasmic (Potential).				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		TTCAGAACATCGTGGATGCTT	0.453													24	197	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124289380	124289380	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:124289380G>C	uc001uft.3	+	17	2451	c.2426G>C	c.(2425-2427)GGC>GCC	p.G809A	DNAH10_uc010tav.1_Missense_Mutation_p.G351A|DNAH10_uc010taw.1_Missense_Mutation_p.G294A	NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	809	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TTCTCTCCAGGCGTGAAGGAA	0.478													40	227	---	---	---	---	PASS
CCDC92	80212	broad.mit.edu	37	12	124422051	124422051	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:124422051G>T	uc001ufw.1	-	5	697	c.550C>A	c.(550-552)CCC>ACC	p.P184T	CCDC92_uc001ufv.1_Missense_Mutation_p.P167T|CCDC92_uc001ufx.1_Missense_Mutation_p.P184T|CCDC92_uc001ufy.1_Missense_Mutation_p.P167T	NM_025140	NP_079416	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	184											0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)		GCCAGCACGGGGCTCCCTGAC	0.662													3	81	---	---	---	---	PASS
SFRS8	6433	broad.mit.edu	37	12	132250835	132250835	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:132250835G>C	uc001uja.1	+	13	2264	c.2124G>C	c.(2122-2124)GAG>GAC	p.E708D	SFRS8_uc010tbn.1_Missense_Mutation_p.E708D|SFRS8_uc001ujb.1_Missense_Mutation_p.E501D	NM_004592	NP_004583	Q12872	SFSWA_HUMAN	splicing factor, arginine/serine-rich 8	708					mRNA splice site selection|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|RNA binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.44e-07)|Epithelial(86;2.94e-06)|all cancers(50;4.82e-05)		AAATTGAGGAGAGTCCTTTCA	0.483													22	172	---	---	---	---	PASS
EP400	57634	broad.mit.edu	37	12	132522540	132522540	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:132522540G>A	uc001ujn.2	+	31	6141	c.6106G>A	c.(6106-6108)GAT>AAT	p.D2036N	EP400_uc001ujl.2_Missense_Mutation_p.D2035N|EP400_uc001ujm.2_Missense_Mutation_p.D1955N	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	2072					histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TCCCATGGATGATGCTGGCTT	0.483													59	174	---	---	---	---	PASS
ANKLE2	23141	broad.mit.edu	37	12	133327418	133327418	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:133327418C>G	uc001ukx.2	-	3	725	c.658G>C	c.(658-660)GAA>CAA	p.E220Q	ANKLE2_uc001uky.3_Missense_Mutation_p.E158Q	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	220						cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		TTTTTATTTTCATAAACATAG	0.413													8	76	---	---	---	---	PASS
GOLGA3	2802	broad.mit.edu	37	12	133357410	133357410	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr12:133357410C>A	uc001ukz.1	-	18	4115	c.3556G>T	c.(3556-3558)GAG>TAG	p.E1186*	GOLGA3_uc001ula.1_Nonsense_Mutation_p.E1186*	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1186	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		TTCACCTTCTCCTTCTCCTTC	0.562													13	172	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23909195	23909195	+	Silent	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:23909195T>C	uc001uon.2	-	10	9409	c.8820A>G	c.(8818-8820)ACA>ACG	p.T2940T	SACS_uc001uoo.2_Silent_p.T2793T|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	2940					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ACACTGATAATGTTGGATCAG	0.358													5	171	---	---	---	---	PASS
MTMR6	9107	broad.mit.edu	37	13	25823374	25823374	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:25823374C>T	uc001uqf.3	-	14	2181	c.1862G>A	c.(1861-1863)TGT>TAT	p.C621Y	MTMR6_uc001uqe.1_Intron	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	621						cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		ATGAGTCTAACAAGTCATTCT	0.383													35	69	---	---	---	---	PASS
PRHOXNB	646625	broad.mit.edu	37	13	28562754	28562754	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:28562754G>A	uc010aan.1	-	1	21	c.21C>T	c.(19-21)AAC>AAT	p.N7N		NM_001105577	NP_001099047	A6NGE7	URAD_HUMAN	parahox cluster neighbor	7					allantoin biosynthetic process|purine base metabolic process	peroxisome	carboxy-lyase activity				0	all_cancers(110;0.12)|all_hematologic(3;0.0119)|Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)		GGTCCATGGAGTTGACCTTCT	0.537													19	66	---	---	---	---	PASS
FLT1	2321	broad.mit.edu	37	13	29041227	29041227	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:29041227C>T	uc001usb.3	-	3	486	c.201G>A	c.(199-201)GTG>GTA	p.V67V	FLT1_uc010aar.1_Silent_p.V67V|FLT1_uc001usc.3_Silent_p.V67V|FLT1_uc010tdp.1_Silent_p.V67V|FLT1_uc001usd.2_Silent_p.V67V	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	67	Ig-like C2-type 1.|Extracellular (Potential).				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	TTTCCTTACTCACCATTTCAG	0.448													17	131	---	---	---	---	PASS
NBEA	26960	broad.mit.edu	37	13	35733368	35733368	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:35733368C>T	uc001uvb.2	+	23	3266	c.3060C>T	c.(3058-3060)GTC>GTT	p.V1020V	NBEA_uc010abi.2_5'Flank	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	1020						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ATTACCCTGTCAGCACAGATA	0.423													7	57	---	---	---	---	PASS
MRPS31	10240	broad.mit.edu	37	13	41333178	41333178	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:41333178C>T	uc001uxm.3	-	3	580	c.505G>A	c.(505-507)GAT>AAT	p.D169N		NM_005830	NP_005821	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31 precursor	169						mitochondrion|ribosome	protein domain specific binding				0		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		GTTTGCTTATCAAAAGGGAGA	0.428													11	94	---	---	---	---	PASS
RB1	5925	broad.mit.edu	37	13	48916850	48916850	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:48916850G>T	uc001vcb.2	+	3	546	c.380G>T	c.(379-381)AGT>ATT	p.S127I	RB1_uc010acs.1_Intron	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	127					androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(4)|p.S127I(1)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	ATAGAAATCAGGTAAAGTTTC	0.343		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			25	52	---	---	---	---	PASS
FARP1	10160	broad.mit.edu	37	13	99092218	99092218	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:99092218G>A	uc001vnj.2	+	22	2773	c.2437G>A	c.(2437-2439)GAG>AAG	p.E813K	FARP1_uc001vnh.2_Missense_Mutation_p.E844K	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	813	PH 1.				regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CCCACAGATTGAGGAGAGCGA	0.627													44	297	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109661274	109661274	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:109661274G>T	uc001vqt.1	+	22	2532	c.2406G>T	c.(2404-2406)ATG>ATT	p.M802I	MYO16_uc010agk.1_Missense_Mutation_p.M824I|MYO16_uc001vqu.1_Missense_Mutation_p.M602I|MYO16_uc010tjh.1_Missense_Mutation_p.M314I	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	802	Myosin head-like 1.				cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			ATGAGAAGATGCACCACTATA	0.338													30	44	---	---	---	---	PASS
TUBGCP3	10426	broad.mit.edu	37	13	113158973	113158973	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr13:113158973G>A	uc001vse.1	-	18	2329	c.2142C>T	c.(2140-2142)TTC>TTT	p.F714F	TUBGCP3_uc010tjq.1_Silent_p.F704F|TUBGCP3_uc001vsf.2_Silent_p.F714F	NM_006322	NP_006313	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	714					G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					TCTGATGAATGAAATGGACCA	0.413													8	27	---	---	---	---	PASS
PPP2R3C	55012	broad.mit.edu	37	14	35554831	35554831	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:35554831C>T	uc001wss.2	-	13	1681	c.1327G>A	c.(1327-1329)GAC>AAC	p.D443N	PPP2R3C_uc001wst.2_Missense_Mutation_p.D327N|PPP2R3C_uc010tpr.1_Missense_Mutation_p.D327N|PPP2R3C_uc001wsu.2_RNA	NM_017917	NP_060387	Q969Q6	P2R3C_HUMAN	serine/threonine-protein phosphatase 2A	443						centrosome|nucleus	calcium ion binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		TTTTCACTGTCATTTGCAACA	0.383													9	119	---	---	---	---	PASS
PPP2R3C	55012	broad.mit.edu	37	14	35554858	35554858	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:35554858C>T	uc001wss.2	-	13	1654	c.1300G>A	c.(1300-1302)GAG>AAG	p.E434K	PPP2R3C_uc001wst.2_Missense_Mutation_p.E318K|PPP2R3C_uc010tpr.1_Missense_Mutation_p.E318K|PPP2R3C_uc001wsu.2_RNA	NM_017917	NP_060387	Q969Q6	P2R3C_HUMAN	serine/threonine-protein phosphatase 2A	434						centrosome|nucleus	calcium ion binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		TCTCTGTTCTCGTAAGTCCAG	0.378													12	128	---	---	---	---	PASS
FAM179B	23116	broad.mit.edu	37	14	45512921	45512921	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:45512921G>C	uc001wvv.2	+	12	4054	c.3845G>C	c.(3844-3846)AGA>ACA	p.R1282T	FAM179B_uc001wvw.2_Missense_Mutation_p.R1282T|FAM179B_uc010anc.2_RNA	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	1282							binding			skin(2)|upper_aerodigestive_tract(1)	3						AATTTTATTAGATGCTTAGCT	0.343													33	88	---	---	---	---	PASS
C14orf106	55320	broad.mit.edu	37	14	45706889	45706889	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:45706889G>A	uc001wwf.2	-	5	1638	c.1179C>T	c.(1177-1179)ATC>ATT	p.I393I	C14orf106_uc010anh.2_RNA	NM_018353	NP_060823	Q6P0N0	M18BP_HUMAN	chromosome 14 open reading frame 106	393					cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0						TATTATTATTGATGCTTTTAA	0.274													11	135	---	---	---	---	PASS
CDKL1	8814	broad.mit.edu	37	14	50844896	50844896	+	Silent	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:50844896T>C	uc010anu.1	-	9	1353	c.1353A>G	c.(1351-1353)GCA>GCG	p.A451A	CDKL1_uc001wxz.2_Intron	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1	Error:Variant_position_missing_in_Q00532_after_alignment						cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)|stomach(1)	2	all_epithelial(31;0.000746)|Breast(41;0.0102)					ttcctttacctgcagacctta	0.000													21	58	---	---	---	---	PASS
GCH1	2643	broad.mit.edu	37	14	55369083	55369083	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:55369083G>A	uc001xbh.1	-	1	460	c.299C>T	c.(298-300)TCG>TTG	p.S100L	GCH1_uc001xbi.1_Missense_Mutation_p.S100L|GCH1_uc001xbj.1_Missense_Mutation_p.S100L|GCH1_uc001xbk.1_Missense_Mutation_p.S100L|GCH1_uc010aol.1_Missense_Mutation_p.S100L|GCH1_uc001xbl.1_Missense_Mutation_p.S100L	NM_001024024	NP_001019195	P30793	GCH1_HUMAN	GTP cyclohydrolase 1 isoform 1	100					dopamine biosynthetic process|GTP catabolic process|neuromuscular process controlling posture|nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|protein homooligomerization|response to interferon-gamma|response to lipopolysaccharide|response to pain|response to tumor necrosis factor|tetrahydrobiopterin biosynthetic process|tetrahydrofolate biosynthetic process	cytoplasmic vesicle|cytosol|nuclear membrane|protein complex	GTP binding|GTP cyclohydrolase I activity|protein homodimerization activity|zinc ion binding			skin(1)	1						CTGCATGGCCGAGGCCGCCCT	0.687													5	71	---	---	---	---	PASS
KTN1	3895	broad.mit.edu	37	14	56117286	56117286	+	Splice_Site	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:56117286G>T	uc001xcb.2	+	25	2799	c.2497_splice	c.e25-1	p.D833_splice	KTN1_uc001xce.2_Splice_Site_p.D833_splice|KTN1_uc001xcc.2_Splice_Site_p.D833_splice|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Splice_Site_p.D833_splice|KTN1_uc001xcf.1_Intron|KTN1_uc010aoq.2_Splice_Site_p.D128_splice	NM_182926	NP_891556	Q86UP2	KTN1_HUMAN	kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7						TCATTGTCAAGGATTTGAAAC	0.348			T	RET	papillary thryoid								17	92	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64461905	64461905	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:64461905C>T	uc001xgm.2	+	23	3155	c.2925C>T	c.(2923-2925)CTC>CTT	p.L975L	SYNE2_uc001xgl.2_Silent_p.L975L	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	975	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CCAAGGGTCTCATCAAAGAAC	0.313													13	95	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64537597	64537597	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:64537597G>C	uc001xgm.2	+	52	10896	c.10666G>C	c.(10666-10668)GAA>CAA	p.E3556Q	SYNE2_uc001xgl.2_Missense_Mutation_p.E3556Q|SYNE2_uc010apw.1_Missense_Mutation_p.E262Q	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3556	Potential.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGCATTTCAAGAAATTACTTC	0.373													10	110	---	---	---	---	PASS
ESR2	2100	broad.mit.edu	37	14	64724059	64724059	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:64724059C>G	uc001xha.1	-	6	1444	c.976G>C	c.(976-978)GAC>CAC	p.D326H	ESR2_uc001xgu.2_Missense_Mutation_p.D326H|ESR2_uc001xgv.2_Missense_Mutation_p.D326H|ESR2_uc001xgw.2_Intron|ESR2_uc001xgx.2_Missense_Mutation_p.D326H|ESR2_uc001xgy.1_Missense_Mutation_p.D326H|ESR2_uc001xgz.1_Missense_Mutation_p.D326H|ESR2_uc010aqb.1_RNA|ESR2_uc010aqc.1_Intron|ESR2_uc010aqd.1_RNA	NM_001437	NP_001428	Q92731	ESR2_HUMAN	estrogen receptor beta isoform 1	326	Steroid-binding.				cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CGCACTTGGTCGAACAGGCTG	0.572													16	188	---	---	---	---	PASS
AKAP5	9495	broad.mit.edu	37	14	64936211	64936211	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:64936211G>C	uc001xhd.3	+	2	1477	c.1099G>C	c.(1099-1101)GAA>CAA	p.E367Q	ZBTB25_uc001xhc.2_Intron	NM_004857	NP_004848	P24588	AKAP5_HUMAN	A-kinase anchor protein 5	367					energy reserve metabolic process|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting|regulation of insulin secretion|signal transduction|synaptic transmission	cytosol	adenylate cyclase binding|calmodulin binding				0				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		AATTTCAGCTGAAAATGAGCA	0.323													20	293	---	---	---	---	PASS
SPTB	6710	broad.mit.edu	37	14	65246467	65246467	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:65246467G>A	uc001xht.2	-	20	4503	c.4449C>T	c.(4447-4449)ATC>ATT	p.I1483I	SPTB_uc001xhr.2_Silent_p.I1483I|SPTB_uc001xhs.2_Silent_p.I1483I|SPTB_uc001xhu.2_Silent_p.I1483I|SPTB_uc010aqi.2_Silent_p.I144I	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b	1483	Spectrin 12.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		AGTCCCGGCTGATCTGCAGCT	0.592													34	219	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68249978	68249978	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:68249978G>C	uc001xka.2	-	21	4030	c.3891C>G	c.(3889-3891)CTC>CTG	p.L1297L	ZFYVE26_uc010tsz.1_RNA|ZFYVE26_uc001xkc.3_Silent_p.L1297L	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1297					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TGAGGGCTGGGAGTGATGAGT	0.577													28	320	---	---	---	---	PASS
ZFP36L1	677	broad.mit.edu	37	14	69256726	69256726	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:69256726C>G	uc001xkh.1	-	2	671	c.541G>C	c.(541-543)GAG>CAG	p.E181Q	ZFP36L1_uc001xki.1_Missense_Mutation_p.E181Q	NM_004926	NP_004917	Q07352	TISB_HUMAN	butyrate response factor 1	181					regulation of mRNA stability	cytosol|nucleus	DNA binding|mRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GCACGGCGCTCTTCAGCGTTG	0.612											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	68	---	---	---	---	PASS
ACOT4	122970	broad.mit.edu	37	14	74061929	74061929	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:74061929G>A	uc001xoo.2	+	3	1091	c.837G>A	c.(835-837)CTG>CTA	p.L279L		NM_152331	NP_689544	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	279					acyl-CoA metabolic process|dicarboxylic acid metabolic process|long-chain fatty acid metabolic process|saturated monocarboxylic acid metabolic process|short-chain fatty acid metabolic process|succinyl-CoA metabolic process|unsaturated monocarboxylic acid metabolic process|very long-chain fatty acid metabolic process	peroxisome	carboxylesterase activity|palmitoyl-CoA hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00331)		GCTATGACCTGAGGAGAATCA	0.473													16	152	---	---	---	---	PASS
YLPM1	56252	broad.mit.edu	37	14	75230773	75230773	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:75230773C>A	uc001xqj.3	+	1	705	c.581C>A	c.(580-582)TCC>TAC	p.S194Y		NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	37	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CCTTCGCAGTCCCCACCTTCC	0.597													7	105	---	---	---	---	PASS
MLH3	27030	broad.mit.edu	37	14	75513083	75513083	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:75513083C>T	uc001xrd.1	-	2	3492	c.3276G>A	c.(3274-3276)GAG>GAA	p.E1092E	MLH3_uc001xre.1_Silent_p.E1092E|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	1092					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)		ACTTACCATTCTCAAGTACAA	0.423								MMR					10	145	---	---	---	---	PASS
MLH3	27030	broad.mit.edu	37	14	75513680	75513680	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:75513680C>A	uc001xrd.1	-	2	2895	c.2679G>T	c.(2677-2679)ATG>ATT	p.M893I	MLH3_uc001xre.1_Missense_Mutation_p.M893I|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	893					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TAAAACGACTCATCATCCCCA	0.373								MMR					30	382	---	---	---	---	PASS
MLH3	27030	broad.mit.edu	37	14	75513683	75513683	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:75513683C>T	uc001xrd.1	-	2	2892	c.2676G>A	c.(2674-2676)ATG>ATA	p.M892I	MLH3_uc001xre.1_Missense_Mutation_p.M892I|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	892					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)		AACGACTCATCATCCCCATTG	0.363								MMR					31	376	---	---	---	---	PASS
MLH3	27030	broad.mit.edu	37	14	75514218	75514218	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:75514218G>A	uc001xrd.1	-	2	2357	c.2141C>T	c.(2140-2142)TCC>TTC	p.S714F	MLH3_uc001xre.1_Missense_Mutation_p.S714F|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	714					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GAAAGAGGGGGATGTATCAGA	0.378								MMR					22	196	---	---	---	---	PASS
FOS	2353	broad.mit.edu	37	14	75747297	75747297	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:75747297G>A	uc001xrn.2	+	3	633	c.428G>A	c.(427-429)CGA>CAA	p.R143Q	FOS_uc010tva.1_Intron|FOS_uc010asi.2_Missense_Mutation_p.R29Q|FOS_uc001xro.2_5'UTR	NM_005252	NP_005243	P01100	FOS_HUMAN	v-fos FBJ murine osteosarcoma viral oncogene	143	Basic motif.			SPEEEEKRRIRR -> ISRRRREKENPK (in Ref. 6; no nucleotide entry).	cellular response to reactive oxygen species|DNA methylation|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|transforming growth factor beta receptor signaling pathway		protein dimerization activity|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(2)|ovary(1)	3		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)		BRCA - Breast invasive adenocarcinoma(234;0.0117)		AGGAGAATCCGAAGGGAAAGG	0.468													11	58	---	---	---	---	PASS
C14orf174	161394	broad.mit.edu	37	14	77857401	77857401	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:77857401C>G	uc001xtq.1	+	3	1839	c.1839C>G	c.(1837-1839)TTC>TTG	p.F613L		NM_001010860	NP_001010860	Q9P1V8	SAM15_HUMAN	hypothetical protein LOC161394	613											0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0278)		AGCCATTATTCAAACGCTCCA	0.383													9	134	---	---	---	---	PASS
SEL1L	6400	broad.mit.edu	37	14	81972508	81972508	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:81972508C>A	uc010tvv.1	-	4	535	c.418G>T	c.(418-420)GAA>TAA	p.E140*	SEL1L_uc001xvo.3_Nonsense_Mutation_p.E140*	NM_005065	NP_005056	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like precursor	140	Lumenal (Potential).|Interaction with ERLEC1, OS9 and SYVN1.|Fibronectin type-II.				Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)		GATGTACATTCATCATACTCC	0.438													18	144	---	---	---	---	PASS
C14orf102	55051	broad.mit.edu	37	14	90798204	90798204	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:90798204A>T	uc001xyi.1	-	1	76	c.45T>A	c.(43-45)GAT>GAA	p.D15E	C14orf102_uc001xyj.1_5'UTR	NM_017970	NP_060440	Q9H7Z3	CN102_HUMAN	hypothetical protein LOC55051 isoform 1	15							protein binding			ovary(2)|lung(1)	3		all_cancers(154;0.118)		COAD - Colon adenocarcinoma(157;0.218)		AGCTCCCGCCATCGGGAGCCT	0.607													26	187	---	---	---	---	PASS
CATSPERB	79820	broad.mit.edu	37	14	92191510	92191510	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:92191510C>A	uc001xzs.1	-	3	222	c.82G>T	c.(82-84)GAT>TAT	p.D28Y		NM_024764	NP_079040	Q9H7T0	CTSRB_HUMAN	cation channel, sperm-associated, beta	28					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|skin(2)|ovary(1)	5		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TTCTCTGTATCATCTAAATAA	0.289													3	56	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94125580	94125580	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:94125580G>C	uc001ybv.1	+	38	6233	c.6150G>C	c.(6148-6150)TTG>TTC	p.L2050F	KIAA1409_uc001ybs.1_Missense_Mutation_p.L2028F	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	2205						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		TTTGCCTCTTGAAGATCCCTT	0.303													7	57	---	---	---	---	PASS
EML1	2009	broad.mit.edu	37	14	100405640	100405640	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:100405640C>G	uc001ygs.2	+	21	2367	c.2298C>G	c.(2296-2298)TTC>TTG	p.F766L	EML1_uc010tww.1_Missense_Mutation_p.F754L|EML1_uc001ygr.2_Missense_Mutation_p.F785L	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	766	WD 10.					cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				TGCACCTCTTCTCATACCCCT	0.537													28	110	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105409022	105409022	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:105409022C>A	uc010axc.1	-	7	12886	c.12766G>T	c.(12766-12768)GTC>TTC	p.V4256F	AHNAK2_uc001ypx.2_Missense_Mutation_p.V4156F	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4256						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACCTCCACGACGGGGGTCATC	0.642													105	231	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105409053	105409053	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:105409053C>G	uc010axc.1	-	7	12855	c.12735G>C	c.(12733-12735)CTG>CTC	p.L4245L	AHNAK2_uc001ypx.2_Silent_p.L4145L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4245						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGGCCTTTCAGGTCCAGCT	0.637													34	325	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105414670	105414670	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:105414670G>C	uc010axc.1	-	7	7238	c.7118C>G	c.(7117-7119)GCT>GGT	p.A2373G	AHNAK2_uc001ypx.2_Missense_Mutation_p.A2273G	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2373						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CTCCAGGTCAGCGGAAGGGGG	0.652													10	371	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105417072	105417072	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:105417072G>C	uc010axc.1	-	7	4836	c.4716C>G	c.(4714-4716)CTC>CTG	p.L1572L	AHNAK2_uc001ypx.2_Silent_p.L1472L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1572						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGTGCCCTTTGAGGCCGGCTC	0.607													41	360	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105420059	105420059	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:105420059C>T	uc010axc.1	-	7	1849	c.1729G>A	c.(1729-1731)GAA>AAA	p.E577K	AHNAK2_uc001ypx.2_Missense_Mutation_p.E477K	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	577						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ATCTGTCCTTCTGTGTCTTCC	0.502													38	422	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105421375	105421375	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:105421375G>C	uc010axc.1	-	6	690	c.570C>G	c.(568-570)ATC>ATG	p.I190M	AHNAK2_uc001ypx.2_Missense_Mutation_p.I90M	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	190	PDZ.					nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCTGCCGTCTGATTTTGAACT	0.507													30	58	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106091400	106091400	+	RNA	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:106091400T>C	uc010tyt.1	-	3647		c.62108A>G			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0						CTTGGCATTATGCACCTCCAC	0.612													47	355	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106691922	106691922	+	RNA	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr14:106691922C>T	uc010tyt.1	-	754		c.20441G>A								Parts of antibodies, mostly variable regions.												0						TCAGGGACCCCCCAGGCTTGA	0.587													5	217	---	---	---	---	PASS
ATP10A	57194	broad.mit.edu	37	15	26026276	26026276	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:26026276G>A	uc010ayu.2	-	2	650	c.544C>T	c.(544-546)CTG>TTG	p.L182L		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	182	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GAGAGCAGCAGAATGTCCGCA	0.557													4	92	---	---	---	---	PASS
GJD2	57369	broad.mit.edu	37	15	35044789	35044789	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:35044789C>T	uc001zis.1	-	2	856	c.856G>A	c.(856-858)GGG>AGG	p.G286R	uc001zit.1_5'Flank	NM_020660	NP_065711	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	286	Cytoplasmic (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		GCCTGAGCCCCTCGCACAGCC	0.512													5	103	---	---	---	---	PASS
CASC5	57082	broad.mit.edu	37	15	40949569	40949569	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:40949569C>T	uc010bbs.1	+	25	6850	c.6689C>T	c.(6688-6690)TCA>TTA	p.S2230L	CASC5_uc010bbt.1_Missense_Mutation_p.S2204L	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1	2230	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GAAGAATTCTCACTGGTAGTG	0.333													8	164	---	---	---	---	PASS
ZSCAN29	146050	broad.mit.edu	37	15	43654029	43654029	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:43654029G>A	uc001zrk.1	-	5	1948	c.1801C>T	c.(1801-1803)CTT>TTT	p.L601F	ZSCAN29_uc001zrj.1_Missense_Mutation_p.L481F|ZSCAN29_uc010bdf.1_Silent_p.I529I|ZSCAN29_uc001zrl.1_RNA|ZSCAN29_uc010bdg.1_Missense_Mutation_p.L211F	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690	601					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		CCCTGATGAAGATACCGGGGA	0.433													8	225	---	---	---	---	PASS
CTDSPL2	51496	broad.mit.edu	37	15	44751303	44751303	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:44751303G>C	uc001ztr.2	+	2	507	c.91G>C	c.(91-93)GAT>CAT	p.D31H	CTDSPL2_uc001zts.2_Missense_Mutation_p.D31H|CTDSPL2_uc001ztt.2_Missense_Mutation_p.D31H|CTDSPL2_uc010bdv.2_Missense_Mutation_p.D31H	NM_016396	NP_057480	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	31							phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		TTCAGAGGTTGATGATAGCCT	0.408													5	127	---	---	---	---	PASS
SLTM	79811	broad.mit.edu	37	15	59191709	59191709	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:59191709C>T	uc002afp.2	-	7	1105	c.1017G>A	c.(1015-1017)AAG>AAA	p.K339K	SLTM_uc002afo.2_Silent_p.K321K|SLTM_uc002afq.2_Intron|SLTM_uc010bgd.2_Intron|SLTM_uc002afr.1_Silent_p.K238K	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	339					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						AGGGCCCTTTCTTCAAAGTAT	0.438													16	114	---	---	---	---	PASS
CT62	196993	broad.mit.edu	37	15	71404515	71404515	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:71404515G>A	uc002ata.2	-	3	620	c.107C>T	c.(106-108)TCC>TTC	p.S36F		NM_001102658	NP_001096128	P0C5K7	CT62_HUMAN	cancer/testis antigen 62	36											0						TGCAGGCTGGGAACCACAGGA	0.552													4	42	---	---	---	---	PASS
HEXA	3073	broad.mit.edu	37	15	72641494	72641494	+	Missense_Mutation	SNP	G	C	C	rs121907960		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:72641494G>C	uc002aun.3	-	8	1119	c.912C>G	c.(910-912)TTC>TTG	p.F304L	uc002aug.2_Intron|CELF6_uc002auk.3_Intron|HEXA_uc010ukn.1_Missense_Mutation_p.F315L|HEXA_uc002auo.3_Missense_Mutation_p.F167L|HEXA_uc010bix.2_Missense_Mutation_p.F304L|HEXA_uc010biy.2_Missense_Mutation_p.F167L|HEXA_uc010uko.1_Missense_Mutation_p.F130L|HEXA_uc010biz.1_RNA	NM_000520	NP_000511	P06865	HEXA_HUMAN	hexosaminidase A preproprotein	304			Missing (in GM2G1; infantile; Moroccan Jewish).		cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4						CTTCTAAGAAGAATGTGCTCA	0.463													13	69	---	---	---	---	PASS
CCDC33	80125	broad.mit.edu	37	15	74573116	74573116	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:74573116C>A	uc002axo.2	+	9	1391	c.997C>A	c.(997-999)CTT>ATT	p.L333I	CCDC33_uc002axp.2_Missense_Mutation_p.L155I	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1	536							protein binding			ovary(3)|skin(2)	5						CTTGGACGGGCTTCACGTGGA	0.507													32	58	---	---	---	---	PASS
PTPN9	5780	broad.mit.edu	37	15	75762311	75762311	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:75762311G>C	uc002bal.2	-	12	1897	c.1389C>G	c.(1387-1389)TTC>TTG	p.F463L		NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type	463	Tyrosine-protein phosphatase.					cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2						TCAAGAACTGGAAGTGGGTCA	0.498													11	68	---	---	---	---	PASS
PTPN9	5780	broad.mit.edu	37	15	75763113	75763113	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:75763113G>C	uc002bal.2	-	11	1775	c.1267C>G	c.(1267-1269)CGG>GGG	p.R423G		NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type	423	Tyrosine-protein phosphatase.					cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2						AATCGGATCCGAGAGTCTTTT	0.463													17	109	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79059041	79059041	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:79059041T>C	uc002bej.3	-	19	3423	c.3212A>G	c.(3211-3213)AAT>AGT	p.N1071S	ADAMTS7_uc010und.1_3'UTR	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1071					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						CTCGTGGAAATTGATGAAATT	0.617													4	58	---	---	---	---	PASS
AP3B2	8120	broad.mit.edu	37	15	83349908	83349908	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:83349908G>A	uc010uoh.1	-	6	721	c.544C>T	c.(544-546)CAG>TAG	p.Q182*	AP3B2_uc010uoi.1_Nonsense_Mutation_p.Q182*|AP3B2_uc010uoj.1_Nonsense_Mutation_p.Q150*|AP3B2_uc010uog.1_5'Flank	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	182					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)			TCTATCAGCTGATCCTTCTGG	0.577													3	19	---	---	---	---	PASS
ALPK3	57538	broad.mit.edu	37	15	85383714	85383714	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:85383714G>T	uc002ble.2	+	5	1977	c.1810G>T	c.(1810-1812)GCC>TCC	p.A604S		NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	604					heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGCCCAGAAGGCCCCTGGCCC	0.637													10	38	---	---	---	---	PASS
CIB1	10519	broad.mit.edu	37	15	90774374	90774374	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:90774374C>T	uc002bpb.3	-	5	580	c.418G>A	c.(418-420)GAG>AAG	p.E140K		NM_006384	NP_006375	Q99828	CIB1_HUMAN	calcium and integrin binding 1	140					apoptosis|cell adhesion|double-strand break repair	apical plasma membrane|endoplasmic reticulum|filopodium|nucleoplasm	calcium ion binding|protein binding				0	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CGTGTGTCCTCGCCCTCTCCC	0.582													29	116	---	---	---	---	PASS
IQGAP1	8826	broad.mit.edu	37	15	91020916	91020916	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:91020916C>G	uc002bpl.1	+	26	3225	c.3124C>G	c.(3124-3126)CAA>GAA	p.Q1042E		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1042	Ras-GAP.|C1.				energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AGATCAGATTCAAGAGATTGT	0.403													13	148	---	---	---	---	PASS
FURIN	5045	broad.mit.edu	37	15	91423120	91423120	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:91423120C>G	uc002bpu.1	+	12	1498	c.1282C>G	c.(1282-1284)CTT>GTT	p.L428V		NM_002569	NP_002560	P09958	FURIN_HUMAN	furin preproprotein	428					cell proliferation|negative regulation of low-density lipoprotein particle receptor catabolic process|negative regulation of transforming growth factor-beta1 production|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|Notch signaling pathway|peptide biosynthetic process|peptidyl-glutamic acid carboxylation|post-translational protein modification|secretion by cell|signal peptide processing|transforming growth factor beta receptor signaling pathway|viral assembly, maturation, egress, and release	cell surface|Golgi lumen|Golgi membrane|integral to membrane|membrane raft|plasma membrane|trans-Golgi network|trans-Golgi network transport vesicle	metal ion binding|nerve growth factor binding|peptide binding|protease binding|serine-type endopeptidase activity|serine-type endopeptidase inhibitor activity			central_nervous_system(4)|lung(2)|breast(1)	7	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TGGCTACGGGCTTTTGGACGC	0.617													36	82	---	---	---	---	PASS
CHSY1	22856	broad.mit.edu	37	15	101718886	101718886	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr15:101718886C>G	uc002bwt.1	-	4	1599	c.1116G>C	c.(1114-1116)GAG>GAC	p.E372D	CHSY1_uc010usd.1_Missense_Mutation_p.E100D	NM_014918	NP_055733	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	372	Lumenal (Potential).				chondroitin sulfate biosynthetic process	Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity				0	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ATTCCAGAATCTCCTCTCGCT	0.532													38	96	---	---	---	---	PASS
OR1F1	4992	broad.mit.edu	37	16	3254937	3254937	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:3254937A>G	uc010uwu.1	+	1	691	c.691A>G	c.(691-693)ACA>GCA	p.T231A		NM_012360	NP_036492	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F,	231	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GGTCCCATCCACAAAGGGAAG	0.498													49	137	---	---	---	---	PASS
BTBD12	84464	broad.mit.edu	37	16	3633150	3633150	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:3633150C>G	uc002cvp.2	-	14	5728	c.5101G>C	c.(5101-5103)GAA>CAA	p.E1701Q		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	1701	Interaction with PLK1 and TERF2-TERF2IP.|Interaction with SLX1.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0						GCCACGGATTCTTGAGAGGCT	0.577								Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				15	141	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3778105	3778105	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:3778105T>A	uc002cvv.2	-	31	7147	c.6943A>T	c.(6943-6945)AGC>TGC	p.S2315C	CREBBP_uc002cvw.2_Missense_Mutation_p.S2277C	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	2315					cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TGCTGGGGGCTCATGGGGTTC	0.627			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				20	113	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3779748	3779748	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:3779748G>A	uc002cvv.2	-	31	5504	c.5300C>T	c.(5299-5301)TCA>TTA	p.S1767L	CREBBP_uc002cvw.2_Missense_Mutation_p.S1729L	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1767	TAZ-type 2.|Interaction with TRERF1.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CAGCCGGCGTGACTCCTGGGG	0.642			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				5	39	---	---	---	---	PASS
GLYR1	84656	broad.mit.edu	37	16	4863804	4863804	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:4863804G>A	uc002cxx.3	-	12	1090	c.1053C>T	c.(1051-1053)ATC>ATT	p.I351I	GLYR1_uc002cxy.2_RNA|GLYR1_uc002cxz.1_Silent_p.I265I|GLYR1_uc002cya.2_Silent_p.I345I|GLYR1_uc010uxv.1_Silent_p.I270I	NM_032569	NP_115958	Q49A26	GLYR1_HUMAN	cytokine-like nuclear factor n-pac	351					pentose-phosphate shunt	nucleus	coenzyme binding|DNA binding|methylated histone residue binding|phosphogluconate dehydrogenase (decarboxylating) activity				0						TCCCAGGGCGGATCCCTTGCA	0.627													5	32	---	---	---	---	PASS
SEC14L5	9717	broad.mit.edu	37	16	5055943	5055943	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:5055943G>T	uc002cye.2	+	12	1511	c.1331G>T	c.(1330-1332)AGG>ATG	p.R444M		NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5	444	CRAL-TRIO.					integral to membrane|intracellular	transporter activity				0						GAGAACACCAGGCGGAAGTTC	0.423													8	18	---	---	---	---	PASS
TEKT5	146279	broad.mit.edu	37	16	10775923	10775923	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:10775923C>A	uc002czz.1	-	4	862	c.790G>T	c.(790-792)GAG>TAG	p.E264*		NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5	264					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2						AAGCACTTCTCATCGATACAC	0.537													36	231	---	---	---	---	PASS
SMG1	23049	broad.mit.edu	37	16	18827768	18827768	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:18827768C>G	uc002dfm.2	-	58	10521	c.10158G>C	c.(10156-10158)CAG>CAC	p.Q3386H	SMG1_uc010bwb.2_Missense_Mutation_p.Q3246H|SMG1_uc010bwa.2_Missense_Mutation_p.Q2117H	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	3386					DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						GAATTGCCCTCTGAGTAGACA	0.423													5	80	---	---	---	---	PASS
TMC5	79838	broad.mit.edu	37	16	19501728	19501728	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:19501728C>T	uc002dgc.3	+	18	3334	c.2585C>T	c.(2584-2586)TCA>TTA	p.S862L	TMC5_uc010vaq.1_Missense_Mutation_p.S810L|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Missense_Mutation_p.S862L|TMC5_uc002dgd.1_Missense_Mutation_p.S616L|TMC5_uc002dge.3_Missense_Mutation_p.S616L|TMC5_uc002dgf.3_Missense_Mutation_p.S545L|TMC5_uc002dgg.3_Missense_Mutation_p.S503L	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	862	Cytoplasmic (Potential).					integral to membrane				skin(1)	1						TTGAAGCCTTCAGCTGACTGT	0.507													30	197	---	---	---	---	PASS
C16orf88	400506	broad.mit.edu	37	16	19718331	19718331	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:19718331C>T	uc002dgq.2	-	5	1293	c.1278G>A	c.(1276-1278)TGG>TGA	p.W426*		NM_001012991	NP_001013009	Q1ED39	CP088_HUMAN	hypothetical protein LOC400506	426	Interaction with ZFP106 (By similarity).					nucleolus					0						GGCTGTACTTCCAGCTCATGG	0.592													28	168	---	---	---	---	PASS
SULT1A1	6817	broad.mit.edu	37	16	28631386	28631386	+	Translation_Start_Site	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:28631386T>C	uc002dqn.2	-	2	484	c.-67A>G	c.(-69--65)ATATG>ATGTG		uc010vct.1_Intron|SULT1A1_uc002dqm.2_Missense_Mutation_p.M46V|SULT1A1_uc002dqo.2_Translation_Start_Site|SULT1A1_uc002dqp.2_Translation_Start_Site	NM_177534	NP_803878	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A,						3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0						TGTCTTACCATATAGGTGTTC	0.254													12	48	---	---	---	---	PASS
ZNF668	79759	broad.mit.edu	37	16	31075372	31075372	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:31075372C>G	uc010caf.2	-	2	766	c.409G>C	c.(409-411)GAA>CAA	p.E137Q	ZNF668_uc002eao.2_Missense_Mutation_p.E137Q|ZNF668_uc010cag.1_Missense_Mutation_p.E137Q	NM_024706	NP_078982	Q96K58	ZN668_HUMAN	zinc finger protein 668	137					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(4)	4						AAGGGCAGTTCGCCAGCGTGC	0.701													9	23	---	---	---	---	PASS
ITGAM	3684	broad.mit.edu	37	16	31273035	31273035	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:31273035C>G	uc002ebq.2	+	2	149	c.51C>G	c.(49-51)TTC>TTG	p.F17L	ITGAM_uc002ebr.2_Missense_Mutation_p.F17L	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor	17	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						GTCATGGGTTCAACTTGGACA	0.473													12	30	---	---	---	---	PASS
HSD11B2	3291	broad.mit.edu	37	16	67470609	67470609	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:67470609C>G	uc002etd.2	+	5	1037	c.921C>G	c.(919-921)TTC>TTG	p.F307L		NM_000196	NP_000187	P80365	DHI2_HUMAN	hydroxysteroid (11-beta) dehydrogenase 2	307					glucocorticoid biosynthetic process	endoplasmic reticulum|microsome					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0401)|Epithelial(162;0.0891)	NADH(DB00157)	ATGGGCAGTTCCTGCACTCGC	0.617													30	130	---	---	---	---	PASS
RANBP10	57610	broad.mit.edu	37	16	67763247	67763247	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:67763247C>A	uc002eud.2	-	10	1404	c.1288G>T	c.(1288-1290)GAG>TAG	p.E430*	RANBP10_uc010ceo.2_Nonsense_Mutation_p.E201*|RANBP10_uc010vju.1_Nonsense_Mutation_p.E374*|RANBP10_uc010vjv.1_Nonsense_Mutation_p.E313*|RANBP10_uc010vjw.1_Nonsense_Mutation_p.E91*	NM_020850	NP_065901	Q6VN20	RBP10_HUMAN	RAN binding protein 10	430	Ser-rich.									ovary(1)	1		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		GAGTTGGACTCGGAGTAATTG	0.408													3	78	---	---	---	---	PASS
EDC4	23644	broad.mit.edu	37	16	67914814	67914814	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:67914814G>A	uc002eur.2	+	18	2618	c.2452G>A	c.(2452-2454)GAG>AAG	p.E818K	EDC4_uc010cer.2_Missense_Mutation_p.E437K|EDC4_uc002eus.2_Missense_Mutation_p.E548K|EDC4_uc002eut.1_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	818					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CTTGACCCAGGAGGCCTCGAC	0.642													5	144	---	---	---	---	PASS
EDC4	23644	broad.mit.edu	37	16	67916221	67916221	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:67916221C>G	uc002eur.2	+	24	3433	c.3267C>G	c.(3265-3267)CTC>CTG	p.L1089L	EDC4_uc010cer.2_Silent_p.L708L|EDC4_uc002eus.2_Silent_p.L819L|EDC4_uc002eut.1_5'Flank|NRN1L_uc002euu.2_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	1089					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CCAAGCTGCTCAAGTCCAAGG	0.582													13	28	---	---	---	---	PASS
DPEP2	64174	broad.mit.edu	37	16	68026025	68026025	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:68026025G>A	uc010cey.2	-	3	626	c.462C>T	c.(460-462)GAC>GAT	p.D154D	DPEP2_uc002evd.3_Silent_p.D154D|DPEP2_uc002eve.2_Silent_p.D154D|DPEP2_uc002evf.2_RNA|DPEP2_uc002evg.2_Missense_Mutation_p.T112I	NM_022355	NP_071750	Q9H4A9	DPEP2_HUMAN	dipeptidase 2 precursor	154					hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|proteolysis	anchored to membrane|plasma membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		GGCGTATGAGGTCAATCTGCT	0.572													12	131	---	---	---	---	PASS
NQO1	1728	broad.mit.edu	37	16	69748870	69748870	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:69748870G>A	uc002exp.2	-	4	605	c.414C>T	c.(412-414)TTC>TTT	p.F138F	NQO1_uc010cfm.2_Silent_p.F117F|NQO1_uc002exq.2_Silent_p.F138F|NQO1_uc002exr.2_Intron|NQO1_uc010vll.1_Intron	NM_000903	NP_000894	P15559	NQO1_HUMAN	NAD(P)H menadione oxidoreductase 1,	138					nitric oxide biosynthetic process|regulation of cellular amino acid metabolic process|response to toxin|synaptic transmission, cholinergic|xenobiotic metabolic process	cytosol	coenzyme binding|cytochrome-b5 reductase activity|electron carrier activity|NAD(P)H dehydrogenase (quinone) activity				0					Dicumarol(DB00266)|Menadione(DB00170)	CACCTACCCGGAAGGGTCCTT	0.438													39	258	---	---	---	---	PASS
SF3B3	23450	broad.mit.edu	37	16	70578410	70578410	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:70578410C>T	uc002ezf.2	+	10	1514	c.1303C>T	c.(1303-1305)CTG>TTG	p.L435L		NM_012426	NP_036558	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3	435					protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)				CCGATCATCTCTGAGAGTCCT	0.443													20	134	---	---	---	---	PASS
WDR59	79726	broad.mit.edu	37	16	74990499	74990499	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:74990499G>C	uc002fdh.1	-	3	216	c.114C>G	c.(112-114)TTC>TTG	p.F38L	WDR59_uc002fdi.2_Missense_Mutation_p.F38L|WDR59_uc002fdj.2_Missense_Mutation_p.F38L	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	38										ovary(1)|breast(1)	2						CGATGTATAAGAATCTGCGGC	0.398													15	79	---	---	---	---	PASS
TRAPPC2L	51693	broad.mit.edu	37	16	88923573	88923573	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr16:88923573C>T	uc002fmc.2	+	1	68	c.15C>T	c.(13-15)ATC>ATT	p.I5I	GALNS_uc002fly.3_5'Flank|GALNS_uc010cid.2_5'Flank|GALNS_uc002flz.3_5'Flank|GALNS_uc002fma.2_5'Flank|TRAPPC2L_uc010cie.2_Intron|TRAPPC2L_uc002fmd.3_Silent_p.I5I|TRAPPC2L_uc002fme.3_Silent_p.I5I|TRAPPC2L_uc002fmf.2_5'Flank	NM_016209	NP_057293	Q9UL33	TPC2L_HUMAN	trafficking protein particle complex 2-like	5					ER to Golgi vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm					0				BRCA - Breast invasive adenocarcinoma(80;0.0477)		CGGTGTGCATCGCGGTGATTG	0.682													3	11	---	---	---	---	PASS
GEMIN4	50628	broad.mit.edu	37	17	648684	648684	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:648684G>A	uc002frs.1	-	2	2718	c.2599C>T	c.(2599-2601)CAG>TAG	p.Q867*		NM_015721	NP_056536	P57678	GEMI4_HUMAN	gemin 4	867					rRNA processing|spliceosomal snRNP assembly	Cajal body|cytosol|nucleolus|small nuclear ribonucleoprotein complex|spliceosomal complex	protein binding			ovary(2)|kidney(1)|skin(1)	4		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TGCCACTCCTGAGGGCTGCAC	0.562													4	38	---	---	---	---	PASS
SHPK	23729	broad.mit.edu	37	17	3539509	3539509	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:3539509G>A	uc002fvz.1	-	1	108	c.5C>T	c.(4-6)GCT>GTT	p.A2V	CTNS_uc002fwa.2_5'Flank|CTNS_uc002fwb.2_5'Flank|CTNS_uc010ckj.2_5'Flank|CTNS_uc010vrv.1_5'Flank|CTNS_uc010vrw.1_5'Flank	NM_013276	NP_037408	Q9UHJ6	SHPK_HUMAN	carbohydrate kinase-like	2					carbohydrate metabolic process	cytoplasm	ATP binding|sedoheptulokinase activity			ovary(1)	1				COAD - Colon adenocarcinoma(5;0.0828)		CGGCCGCGCAGCCATTATCTC	0.706													5	35	---	---	---	---	PASS
SLC16A11	162515	broad.mit.edu	37	17	6945349	6945349	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:6945349C>T	uc002gei.1	-	3	1490	c.1152G>A	c.(1150-1152)ATG>ATA	p.M384I		NM_153357	NP_699188	Q8NCK7	MOT11_HUMAN	solute carrier family 16, member 11	384	Helical; (Potential).					integral to membrane|plasma membrane	symporter activity			ovary(1)	1						CCCCGAGGCTCATCAGCATCA	0.637													17	24	---	---	---	---	PASS
DLG4	1742	broad.mit.edu	37	17	7095304	7095304	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:7095304G>A	uc002get.3	-	20	3214	c.2013C>T	c.(2011-2013)CTC>CTT	p.L671L	DLG4_uc010vtm.1_Intron|DLG4_uc010vtn.1_Silent_p.L568L|DLG4_uc010cly.2_Silent_p.L625L|DLG4_uc010vto.1_Silent_p.L668L	NM_001365	NP_001356	P78352	DLG4_HUMAN	post-synaptic density protein 95 isoform 1	628	Guanylate kinase-like.				axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2						CCGAGACATCGAGGATGCAGT	0.692													4	27	---	---	---	---	PASS
TNFSF13	8741	broad.mit.edu	37	17	7462439	7462439	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:7462439C>G	uc002ghk.2	+	1	831	c.83C>G	c.(82-84)TCA>TGA	p.S28*	SENP3_uc002ghm.2_5'Flank|TNFSF12-TNFSF13_uc002ghi.1_Intron|TNFSF13_uc002ghj.2_Nonsense_Mutation_p.S28*|TNFSF13_uc002ghl.2_Nonsense_Mutation_p.S28*|TNFSF13_uc010cmk.2_Nonsense_Mutation_p.S28*|TNFSF13_uc010vua.1_Nonsense_Mutation_p.S28*	NM_003808	NP_003799	O75888	TNF13_HUMAN	tumor necrosis factor ligand superfamily, member	28					mRNA metabolic process|positive regulation of cell proliferation|positive regulation of isotype switching to IgA isotypes|signal transduction	extracellular space|nucleoplasm	cytokine activity|tumor necrosis factor receptor binding			skin(1)	1		Prostate(122;0.157)				CCGGCACTCTCAGTTGCCCTC	0.632													8	74	---	---	---	---	PASS
TNFSF13	8741	broad.mit.edu	37	17	7462449	7462449	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:7462449C>T	uc002ghk.2	+	1	841	c.93C>T	c.(91-93)CTC>CTT	p.L31L	SENP3_uc002ghm.2_5'Flank|TNFSF12-TNFSF13_uc002ghi.1_Intron|TNFSF13_uc002ghj.2_Silent_p.L31L|TNFSF13_uc002ghl.2_Silent_p.L31L|TNFSF13_uc010cmk.2_Silent_p.L31L|TNFSF13_uc010vua.1_Silent_p.L31L	NM_003808	NP_003799	O75888	TNF13_HUMAN	tumor necrosis factor ligand superfamily, member	31					mRNA metabolic process|positive regulation of cell proliferation|positive regulation of isotype switching to IgA isotypes|signal transduction	extracellular space|nucleoplasm	cytokine activity|tumor necrosis factor receptor binding			skin(1)	1		Prostate(122;0.157)				CAGTTGCCCTCTGGTTGAGTT	0.637													6	70	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7579378	7579378	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:7579378G>T	uc002gim.2	-	4	503	c.309C>A	c.(307-309)TAC>TAA	p.Y103*	TP53_uc002gig.1_Nonsense_Mutation_p.Y103*|TP53_uc002gih.2_Nonsense_Mutation_p.Y103*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Nonsense_Mutation_p.Y103*|TP53_uc010cni.1_Nonsense_Mutation_p.Y103*|TP53_uc002gij.2_Nonsense_Mutation_p.Y103*|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Nonsense_Mutation_p.Y64*|TP53_uc010cnk.1_Nonsense_Mutation_p.Y118*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	103	Interaction with HIPK1 (By similarity).||Interaction with WWOX.				activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.0?(7)|p.G59fs*23(3)|p.Y103*(2)|p.V73fs*9(1)|p.Y103Y(1)|p.Y103_Q104>**(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103_L111>L(1)|p.Y103fs*15(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		AGCTGCCCTGGTAGGTTTTCT	0.637		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			56	53	---	---	---	---	PASS
WDR16	146845	broad.mit.edu	37	17	9490041	9490041	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:9490041G>A	uc002gly.2	+	3	366	c.297G>A	c.(295-297)AAG>AAA	p.K99K	WDR16_uc002glz.2_Silent_p.K31K|WDR16_uc010coc.2_Silent_p.K109K	NM_145054	NP_659491	Q8N1V2	WDR16_HUMAN	WD40-repeat protein upregulated in HCC isoform	99	WD 1.					cytoplasm|intracellular membrane-bounded organelle	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4						GGGATTATAAGAACAGAGAGC	0.473													37	54	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10450818	10450818	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:10450818C>G	uc010coi.2	-	4	450	c.322G>C	c.(322-324)GAA>CAA	p.E108Q	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.E108Q|MYH2_uc010coj.2_Missense_Mutation_p.E108Q	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	108	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						GCATAACGTTCTTTGAGGTTG	0.488													54	146	---	---	---	---	PASS
ELAC2	60528	broad.mit.edu	37	17	12905820	12905820	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:12905820G>C	uc002gnz.3	-	13	1251	c.1156C>G	c.(1156-1158)CAA>GAA	p.Q386E	ELAC2_uc002gnu.3_5'Flank|ELAC2_uc002gnv.3_Missense_Mutation_p.F15L|ELAC2_uc002gnw.3_Missense_Mutation_p.Q44E|ELAC2_uc002gnx.3_Missense_Mutation_p.Q146E|ELAC2_uc010vvo.1_Missense_Mutation_p.Q184E|ELAC2_uc010vvp.1_Missense_Mutation_p.Q367E|ELAC2_uc010vvq.1_Missense_Mutation_p.Q386E|ELAC2_uc010vvr.1_Missense_Mutation_p.Q346E	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	386					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						AGCTGGGTTTGAATCTTGTGG	0.562									Hereditary_Prostate_Cancer		OREG0024189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	17	---	---	---	---	PASS
COX10	1352	broad.mit.edu	37	17	13980228	13980228	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:13980228G>C	uc002gof.3	+	3	558	c.354G>C	c.(352-354)TTG>TTC	p.L118F	COX10_uc010vvs.1_Intron|COX10_uc010vvt.1_5'UTR	NM_001303	NP_001294	Q12887	COX10_HUMAN	heme A:farnesyltransferase precursor	118					heme a biosynthetic process|heme O biosynthetic process|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		AAAAGGAATTGATAGAACTAG	0.413													34	43	---	---	---	---	PASS
FLCN	201163	broad.mit.edu	37	17	17122399	17122399	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:17122399G>A	uc002gra.3	-	9	1500	c.996C>T	c.(994-996)CTC>CTT	p.L332L	PLD6_uc010cpn.2_Intron	NM_144997	NP_659434	Q8NFG4	FLCN_HUMAN	folliculin isoform 1	332					regulation of protein phosphorylation	cytoplasm|nucleus|plasma membrane	protein binding			thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	3						CACAGCCTGAGAGAGAGGAGG	0.642									Birt-Hogg-Dub__syndrome|Familial_Non-VHL_Clear_Cell_Renal_Cancer				14	121	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18045066	18045066	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:18045066C>A	uc010vxh.1	+	22	5969	c.5631C>A	c.(5629-5631)TAC>TAA	p.Y1877*		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	1877	Myosin head-like.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					CAAACATGTACCGTGTTGGGG	0.557											OREG0024223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	71	94	---	---	---	---	PASS
SMCR8	140775	broad.mit.edu	37	17	18221365	18221365	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:18221365C>T	uc002gsy.3	+	1	2772	c.2262C>T	c.(2260-2262)GTC>GTT	p.V754V		NM_144775	NP_658988	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region,	754										central_nervous_system(1)	1						CTATCTTTGTCCCCAGCTATG	0.532													26	81	---	---	---	---	PASS
CYTSB	92521	broad.mit.edu	37	17	20108650	20108650	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:20108650C>G	uc002gwq.2	+	4	1433	c.1288C>G	c.(1288-1290)CGA>GGA	p.R430G	CYTSB_uc010cqx.2_Missense_Mutation_p.R430G|CYTSB_uc002gwr.2_Missense_Mutation_p.R430G|CYTSB_uc002gws.2_Missense_Mutation_p.R430G|CYTSB_uc002gwv.2_Missense_Mutation_p.R349G|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Missense_Mutation_p.R206G|CYTSB_uc002gwt.2_Missense_Mutation_p.R349G|CYTSB_uc002gwu.2_Missense_Mutation_p.R349G	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b	430						nucleus					0						TCATCAGCATCGAGAGAGGGC	0.413													19	90	---	---	---	---	PASS
TOP2A	7153	broad.mit.edu	37	17	38555128	38555128	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:38555128G>C	uc002huq.2	-	26	3476	c.3350C>G	c.(3349-3351)TCC>TGC	p.S1117C		NM_001067	NP_001058	P11388	TOP2A_HUMAN	DNA topoisomerase II, alpha isozyme	1117					apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	ATCTGTTACGGAGTCACTCTT	0.353													13	96	---	---	---	---	PASS
KRT37	8688	broad.mit.edu	37	17	39578372	39578372	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:39578372C>T	uc002hwp.1	-	5	1016	c.969G>A	c.(967-969)CTG>CTA	p.L323L	uc002hwo.1_Intron	NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	323	Coil 2.|Rod.					intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)				CCGTGCATCTCAGCTCCAGGA	0.602													25	130	---	---	---	---	PASS
KRT37	8688	broad.mit.edu	37	17	39578435	39578435	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:39578435G>A	uc002hwp.1	-	5	953	c.906C>T	c.(904-906)ATC>ATT	p.I302I	uc002hwo.1_Intron	NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	302	Coil 2.|Rod.					intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)				CCTGCAGGCTGATGCCTTCAG	0.612													28	127	---	---	---	---	PASS
KRT37	8688	broad.mit.edu	37	17	39578672	39578672	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:39578672C>T	uc002hwp.1	-	4	794	c.747G>A	c.(745-747)CTG>CTA	p.L249L	uc002hwo.1_Intron	NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	249	Rod.|Coil 1B.					intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)				GCTGACTCCTCAGAATCTTTA	0.567													28	207	---	---	---	---	PASS
SC65	10609	broad.mit.edu	37	17	39968008	39968008	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:39968008C>G	uc002hxt.2	-	1	444	c.160G>C	c.(160-162)GAG>CAG	p.E54Q	FKBP10_uc002hxv.2_5'Flank|SC65_uc002hxu.2_Missense_Mutation_p.E145Q	NM_006455	NP_006446	Q92791	SC65_HUMAN	synaptonemal complex protein SC65	54					synaptonemal complex assembly	nucleolus|synaptonemal complex	binding				0		Breast(137;0.000162)		BRCA - Breast invasive adenocarcinoma(366;0.149)		CGCGCGCTCTCGCGCCAGCTC	0.741													2	6	---	---	---	---	PASS
LRRC37A	9884	broad.mit.edu	37	17	44408844	44408844	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:44408844G>A	uc002ikg.2	+	9	4204	c.4201G>A	c.(4201-4203)GAT>AAT	p.D1401N	ARL17A_uc002iki.3_Intron|ARL17A_uc002ikh.3_Intron|ARL17B_uc002ikf.2_Intron|LRRC37A_uc002ikj.2_Missense_Mutation_p.D362N|LRRC37A_uc010daw.1_Missense_Mutation_p.D331N	NM_014834	NP_055649	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A precursor	1401	Extracellular (Potential).					integral to membrane					0		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		TGAAGAAAATGATTTTATGGA	0.373													9	52	---	---	---	---	PASS
CACNA1G	8913	broad.mit.edu	37	17	48687294	48687294	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:48687294C>G	uc002irk.1	+	26	5129	c.4757C>G	c.(4756-4758)TCA>TGA	p.S1586*	CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Nonsense_Mutation_p.S1563*|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Nonsense_Mutation_p.S1586*|CACNA1G_uc002irq.1_Nonsense_Mutation_p.S1563*|CACNA1G_uc002irr.1_Nonsense_Mutation_p.S1586*|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Nonsense_Mutation_p.S1563*|CACNA1G_uc002iru.1_Intron|CACNA1G_uc002irx.1_Nonsense_Mutation_p.S1499*|CACNA1G_uc002iry.1_Intron|CACNA1G_uc002irz.1_Nonsense_Mutation_p.S1499*|CACNA1G_uc002isa.1_Nonsense_Mutation_p.S1465*|CACNA1G_uc002isb.1_Nonsense_Mutation_p.S1506*|CACNA1G_uc002isc.1_Intron|CACNA1G_uc002isd.1_Intron|CACNA1G_uc002ise.1_Intron|CACNA1G_uc002isf.1_Intron|CACNA1G_uc002isg.1_Intron|CACNA1G_uc002ish.1_Intron|CACNA1G_uc002isi.1_Nonsense_Mutation_p.S1442*	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	1586	Cytoplasmic (Potential).				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGCGCTGCGTCAGGTACTGCG	0.567													18	27	---	---	---	---	PASS
COX11	1353	broad.mit.edu	37	17	53040696	53040696	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:53040696C>G	uc010wng.1	-	3	676	c.619G>C	c.(619-621)GAA>CAA	p.E207Q	COX11_uc010wne.1_RNA|COX11_uc010wnf.1_RNA|COX11_uc002iue.2_RNA|COX11_uc010wnh.1_Missense_Mutation_p.E207Q	NM_004375	NP_004366	Q9Y6N1	COX11_HUMAN	COX11 homolog, cytochrome c oxidase assembly	207	Mitochondrial intermembrane (Potential).|Mitochondrial matrix (Potential).				respiratory chain complex IV assembly|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	copper ion binding|cytochrome-c oxidase activity|electron carrier activity			ovary(1)	1						TGTCCAGCTTCAAATGGAACA	0.353													12	88	---	---	---	---	PASS
OR4D1	26689	broad.mit.edu	37	17	56232861	56232861	+	Nonsense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:56232861C>G	uc010wno.1	+	1	347	c.347C>G	c.(346-348)TCA>TGA	p.S116*	MSX2P1_uc002ivn.2_5'Flank	NM_012374	NP_036506	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D,	116	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TTTTTTCTCTCAGTCATGGCC	0.542													41	72	---	---	---	---	PASS
RNF43	54894	broad.mit.edu	37	17	56438267	56438267	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:56438267C>T	uc002iwf.2	-	6	2682	c.726G>A	c.(724-726)CAG>CAA	p.Q242Q	RNF43_uc010wnv.1_Silent_p.Q201Q|RNF43_uc002iwh.3_Silent_p.Q242Q|RNF43_uc002iwg.3_Silent_p.Q242Q|RNF43_uc010dcw.2_Silent_p.Q115Q	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	242	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGGTGGCCAGCTGGCTGATGG	0.657													26	30	---	---	---	---	PASS
RPS6KB1	6198	broad.mit.edu	37	17	58024015	58024015	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:58024015G>C	uc002ixy.2	+	15	1547	c.1444G>C	c.(1444-1446)GAG>CAG	p.E482Q	RPS6KB1_uc010ddj.1_Intron|RPS6KB1_uc010wom.1_Missense_Mutation_p.E429Q|RPS6KB1_uc010won.1_Missense_Mutation_p.E459Q|RPS6KB1_uc010woo.1_Missense_Mutation_p.E417Q|RPS6KB1_uc002ixz.2_RNA	NM_003161	NP_003152	P23443	KS6B1_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide	482	Autoinhibitory domain.				apoptosis|G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|negative regulation of apoptosis|phosphatidylinositol-mediated signaling|positive regulation of mitotic cell cycle|positive regulation of translational initiation|TOR signaling cascade	cell junction|cytoplasm|cytosol|mitochondrial outer membrane|nucleus|nucleus|synapse|synaptosome	ATP binding|protein binding|protein kinase activity			large_intestine(1)	1	all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.57e-12)|all cancers(12;6.41e-11)			AAGTGGCATAGAGCAGATGGA	0.493													10	76	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60837358	60837358	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:60837358C>T	uc010ddr.2	-	4	458	c.220G>A	c.(220-222)GAG>AAG	p.E74K	MARCH10_uc002jag.3_Missense_Mutation_p.E74K|MARCH10_uc010dds.2_Missense_Mutation_p.E74K|MARCH10_uc002jah.2_Missense_Mutation_p.E74K	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	74							ligase activity|zinc ion binding				0						GCATCCTCCTCACTAGAACTC	0.418													12	128	---	---	---	---	PASS
ACE	1636	broad.mit.edu	37	17	61557861	61557861	+	Silent	SNP	C	T	T	rs148882466	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:61557861C>T	uc002jau.1	+	5	841	c.819C>T	c.(817-819)CTC>CTT	p.L273L	ACE_uc010wpi.1_Silent_p.L273L|ACE_uc010ddu.1_Silent_p.L90L	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme 1 isoform 1	273	Extracellular (Potential).|Peptidase M2 1.				arachidonic acid secretion|hormone catabolic process|kidney development|peptide catabolic process|regulation of smooth muscle cell migration	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	ACATCAACCTCAGGGGACCCA	0.612													14	146	---	---	---	---	PASS
DDX42	11325	broad.mit.edu	37	17	61889493	61889493	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:61889493C>G	uc002jbu.2	+	15	1857	c.1600C>G	c.(1600-1602)CAG>GAG	p.Q534E	DDX42_uc002jbv.2_Missense_Mutation_p.Q534E|DDX42_uc002jbw.1_Missense_Mutation_p.Q270E|DDX42_uc002jbx.2_Missense_Mutation_p.Q270E|DDX42_uc002jby.2_Missense_Mutation_p.Q80E	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein	534	Helicase C-terminal.				protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5						GGATATGGATCAGAGTGAGAG	0.428													24	135	---	---	---	---	PASS
POLG2	11232	broad.mit.edu	37	17	62487068	62487068	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:62487068T>G	uc002jei.2	-	4	897	c.814A>C	c.(814-816)AAC>CAC	p.N272H	POLG2_uc010deg.1_Missense_Mutation_p.N272H	NM_007215	NP_009146	Q9UHN1	DPOG2_HUMAN	DNA polymerase subunit gamma-2, mitochondrial	272					DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			CTGCTGAAGTTAGATGGACTC	0.343													52	71	---	---	---	---	PASS
RHBDF2	79651	broad.mit.edu	37	17	74473802	74473802	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:74473802C>T	uc002jrq.1	-	7	1118	c.825G>A	c.(823-825)CCG>CCA	p.P275P	RHBDF2_uc002jrp.1_Silent_p.P246P|RHBDF2_uc002jrr.1_Silent_p.P127P|RHBDF2_uc010wtf.1_Silent_p.P246P|RHBDF2_uc002jrs.1_Silent_p.P270P	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1	275	Cytoplasmic (Potential).				negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0						CCAGGAAGCTCGGGAAGGCAA	0.627													38	109	---	---	---	---	PASS
ST6GALNAC1	55808	broad.mit.edu	37	17	74623247	74623247	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:74623247C>T	uc002jsh.2	-	4	1248	c.1074G>A	c.(1072-1074)GGG>GGA	p.G358G	ST6GALNAC1_uc002jsi.2_Silent_p.G226G|ST6GALNAC1_uc002jsj.2_RNA	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	sialyltransferase 7A	358	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0						ACCGGAGGCTCCCAGCGGGGA	0.632													7	46	---	---	---	---	PASS
JMJD6	23210	broad.mit.edu	37	17	74717909	74717909	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:74717909C>A	uc002jso.2	-	4	1236	c.912G>T	c.(910-912)GGG>GGT	p.G304G	JMJD6_uc002jsn.1_Silent_p.G304G|JMJD6_uc010dgz.2_Silent_p.G304G	NM_015167	NP_055982	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6 isoform 2	304	JmjC.				mRNA processing|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine|regulation of nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|RNA splicing|sprouting angiogenesis|transcription, DNA-dependent	nucleolus|nucleoplasm	histone demethylase activity (H3-R2 specific)|histone demethylase activity (H4-R3 specific)|identical protein binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-lysine 5-dioxygenase activity|single-stranded RNA binding			skin(2)|ovary(1)	3						ACTTTGGTCTCCCTCTTACCG	0.443													13	104	---	---	---	---	PASS
JMJD6	23210	broad.mit.edu	37	17	74718008	74718008	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:74718008C>G	uc002jso.2	-	4	1137	c.813G>C	c.(811-813)TGG>TGC	p.W271C	JMJD6_uc002jsn.1_Missense_Mutation_p.W271C|JMJD6_uc010dgz.2_Missense_Mutation_p.W271C	NM_015167	NP_055982	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6 isoform 2	271	JmjC.				mRNA processing|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine|regulation of nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|RNA splicing|sprouting angiogenesis|transcription, DNA-dependent	nucleolus|nucleoplasm	histone demethylase activity (H3-R2 specific)|histone demethylase activity (H4-R3 specific)|identical protein binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-lysine 5-dioxygenase activity|single-stranded RNA binding			skin(2)|ovary(1)	3						CAACATGCCACCAGCCTCCTG	0.443													7	49	---	---	---	---	PASS
HGS	9146	broad.mit.edu	37	17	79658588	79658588	+	Missense_Mutation	SNP	G	C	C	rs142599461		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:79658588G>C	uc002kbg.2	+	8	726	c.649G>C	c.(649-651)GAG>CAG	p.E217Q	HGS_uc010wus.1_Missense_Mutation_p.E217Q	NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	217	FYVE-type.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			GCCCTGCTACGAGCAGCTGAA	0.602													22	165	---	---	---	---	PASS
P4HB	5034	broad.mit.edu	37	17	79801953	79801953	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:79801953C>G	uc002kbn.1	-	11	1659	c.1462G>C	c.(1462-1464)GAA>CAA	p.E488Q	P4HB_uc002kbl.1_Missense_Mutation_p.E165Q|P4HB_uc002kbm.1_Missense_Mutation_p.E165Q	NM_000918	NP_000909	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta subunit precursor	488					cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline	cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane	electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			TCTGCTTCTTCCAGGTCCTCG	0.607													63	179	---	---	---	---	PASS
CEP76	79959	broad.mit.edu	37	18	12678316	12678316	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:12678316G>A	uc002kri.2	-	10	1571	c.1415C>T	c.(1414-1416)TCT>TTT	p.S472F	PSMG2_uc002krg.2_Intron|CEP76_uc002krh.3_Missense_Mutation_p.S294F|CEP76_uc010wzz.1_Missense_Mutation_p.S397F	NM_024899	NP_079175	Q8TAP6	CEP76_HUMAN	centrosomal protein 76kDa	472					G2/M transition of mitotic cell cycle|regulation of centriole replication	centriole|cytosol	protein binding				0						TACTGCATCAGAGGGTTGACA	0.433													8	315	---	---	---	---	PASS
C18orf1	753	broad.mit.edu	37	18	13621222	13621222	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:13621222C>T	uc002ksa.2	+	5	956	c.288C>T	c.(286-288)TTC>TTT	p.F96F	C18orf1_uc002ksb.2_Silent_p.F96F|C18orf1_uc002kse.2_Silent_p.F59F|C18orf1_uc002ksf.2_Silent_p.F59F|C18orf1_uc002ksg.1_Silent_p.F19F|C18orf1_uc002ksh.1_Silent_p.F38F|C18orf1_uc002ksi.1_Silent_p.F38F	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1	96	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		CGCGGTCCTTCATCAACCGCC	0.622													16	124	---	---	---	---	PASS
ROCK1	6093	broad.mit.edu	37	18	18588119	18588119	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:18588119G>C	uc002kte.2	-	14	2388	c.1447C>G	c.(1447-1449)CAG>GAG	p.Q483E		NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein	483	Interaction with FHOD1.|Potential.|REM.				actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					TTCTCAATCTGAGACACTGTA	0.333													7	94	---	---	---	---	PASS
SNRPD1	6632	broad.mit.edu	37	18	19202685	19202685	+	Splice_Site	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:19202685G>A	uc002ktj.1	+	2	146	c.15_splice	c.e2-1	p.R5_splice		NM_006938	NP_008869	P62314	SMD1_HUMAN	small nuclear ribonucleoprotein D1 polypeptide						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	catalytic step 2 spliceosome|cytosol|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	protein binding|RNA binding				0						CCTATTTATAGATTTTTGATG	0.343													4	62	---	---	---	---	PASS
HRH4	59340	broad.mit.edu	37	18	22057141	22057141	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:22057141C>T	uc002kvi.2	+	3	888	c.788C>T	c.(787-789)TCA>TTA	p.S263L	HRH4_uc010xbd.1_3'UTR|HRH4_uc010dlx.2_Missense_Mutation_p.S175L	NM_021624	NP_067637	Q9H3N8	HRH4_HUMAN	histamine H4 receptor isoform 1	263	Cytoplasmic (Potential).					integral to membrane|plasma membrane	histamine receptor activity			ovary(2)	2	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Clozapine(DB00363)	ATGTTTTCCTCAAGAACCAAG	0.418													32	244	---	---	---	---	PASS
DSC1	1823	broad.mit.edu	37	18	28710533	28710533	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:28710533G>T	uc002kwn.2	-	16	2891	c.2629C>A	c.(2629-2631)CTA>ATA	p.L877I	DSC1_uc002kwm.2_3'UTR|uc002kwo.1_5'Flank	NM_024421	NP_077739	Q08554	DSC1_HUMAN	desmocollin 1 isoform Dsc1a preproprotein	877	Cytoplasmic (Potential).				homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			AGGTGATCTAGAAACTCCAGT	0.428													19	271	---	---	---	---	PASS
SLC39A6	25800	broad.mit.edu	37	18	33691181	33691181	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:33691181C>T	uc010dmy.2	-	9	2246	c.1956G>A	c.(1954-1956)ATG>ATA	p.M652I	SLC39A6_uc002kzj.2_Missense_Mutation_p.M377I	NM_012319	NP_036451	Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter),	652	Cytoplasmic (Potential).					integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2						GCTTAACGGTCATGCCAGCCT	0.378													5	84	---	---	---	---	PASS
SLC39A6	25800	broad.mit.edu	37	18	33696661	33696661	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:33696661C>T	uc010dmy.2	-	6	1731	c.1441G>A	c.(1441-1443)GAG>AAG	p.E481K	SLC39A6_uc002kzj.2_Missense_Mutation_p.E206K	NM_012319	NP_036451	Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter),	481	Cytoplasmic (Potential).					integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2						ACTTTCTCCTCATTTGTTGAA	0.368													25	79	---	---	---	---	PASS
ATP5A1	498	broad.mit.edu	37	18	43667006	43667006	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:43667006G>C	uc002lbr.1	-	8	1234	c.1144C>G	c.(1144-1146)CCA>GCA	p.P382A	ATP5A1_uc010dnl.1_Missense_Mutation_p.P332A|ATP5A1_uc002lbs.1_Missense_Mutation_p.P332A|ATP5A1_uc002lbt.1_Missense_Mutation_p.P382A	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	382					ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0						ACATTTGTTGGAATGTAAGCA	0.398													7	122	---	---	---	---	PASS
SKA1	220134	broad.mit.edu	37	18	47918511	47918511	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:47918511C>G	uc002let.2	+	7	846	c.662C>G	c.(661-663)ACT>AGT	p.T221S	SKA1_uc002leu.2_Missense_Mutation_p.T221S|SKA1_uc010xdl.1_Missense_Mutation_p.T175S	NM_145060	NP_659497	Q96BD8	SKA1_HUMAN	spindle and KT associated 1	221					cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0						GAGTTCACAACTTTGAAAGCT	0.373													49	179	---	---	---	---	PASS
ZCCHC2	54877	broad.mit.edu	37	18	60242387	60242387	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:60242387G>T	uc002lip.3	+	13	3073	c.3073G>T	c.(3073-3075)GGA>TGA	p.G1025*	ZCCHC2_uc002lio.2_RNA|ZCCHC2_uc002liq.2_Nonsense_Mutation_p.G495*	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	1025					cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding	p.G1025*(1)		lung(1)|prostate(1)	2						TGGGACCAATGGAAACCTTCA	0.502													15	61	---	---	---	---	PASS
SERPINB5	5268	broad.mit.edu	37	18	61160267	61160267	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:61160267G>C	uc002liz.3	+	5	648	c.506G>C	c.(505-507)GGC>GCC	p.G169A	SERPINB5_uc002liy.2_Missense_Mutation_p.G169A	NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	169					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1						TACTTTGTTGGCAAGTGGATG	0.408													106	172	---	---	---	---	PASS
SERPINB12	89777	broad.mit.edu	37	18	61223515	61223515	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:61223515G>T	uc010xen.1	+	1	123	c.123G>T	c.(121-123)ATG>ATT	p.M41I	SERPINB12_uc010xeo.1_Missense_Mutation_p.M41I	NM_080474	NP_536722	Q96P63	SPB12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	41					negative regulation of protein catabolic process|regulation of proteolysis	cytoplasm	enzyme binding|serine-type endopeptidase inhibitor activity				0						CCCTTGGTATGGTACGCTTGG	0.453													83	280	---	---	---	---	PASS
SERPINB4	6318	broad.mit.edu	37	18	61305057	61305057	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:61305057G>C	uc002ljf.2	-	8	1155	c.1069C>G	c.(1069-1071)CCT>GCT	p.P357A	SERPINB4_uc002lje.2_Missense_Mutation_p.P336A|SERPINB4_uc002ljg.2_Missense_Mutation_p.P357A	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	357					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|lung(1)	3						TTAGTTGAAGGAGATGATAAT	0.453													9	139	---	---	---	---	PASS
NETO1	81832	broad.mit.edu	37	18	70417779	70417779	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:70417779C>T	uc002lkw.2	-	9	1343	c.1059G>A	c.(1057-1059)GTG>GTA	p.V353V	NETO1_uc002lkx.1_Silent_p.V352V|NETO1_uc002lky.1_Silent_p.V353V	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	353	Helical; (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)|skin(2)	4		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		TGAGGATGATCACGATGCAGG	0.468													11	120	---	---	---	---	PASS
FBXO15	201456	broad.mit.edu	37	18	71793322	71793322	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:71793322G>C	uc002lle.2	-	6	908	c.572C>G	c.(571-573)TCT>TGT	p.S191C	FBXO15_uc002llf.2_Missense_Mutation_p.S267C	NM_152676	NP_689889	Q8NCQ5	FBX15_HUMAN	F-box protein 15 isoform 1	191										ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		TGCAATTAAAGAATGCCATCG	0.438													48	105	---	---	---	---	PASS
NFATC1	4772	broad.mit.edu	37	18	77246387	77246387	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr18:77246387C>T	uc010xfg.1	+	9	2685	c.2232C>T	c.(2230-2232)CTC>CTT	p.L744L	NFATC1_uc002lnd.2_Silent_p.L744L|NFATC1_uc002lne.2_Silent_p.L272L|NFATC1_uc010xfh.1_Intron|NFATC1_uc010xfj.1_Silent_p.L272L|NFATC1_uc002lnf.2_Silent_p.L731L|NFATC1_uc002lng.2_Silent_p.L731L|NFATC1_uc010xfk.1_Intron	NM_006162	NP_006153	O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytosolic	744	Trans-activation domain B (TAD-B).				intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)		GCTCCTGCCTCGTGGCCGGCT	0.662													26	331	---	---	---	---	PASS
C19orf21	126353	broad.mit.edu	37	19	757477	757477	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:757477G>T	uc002lpo.2	+	2	614	c.531G>T	c.(529-531)CGG>CGT	p.R177R		NM_173481	NP_775752	Q8IVT2	CS021_HUMAN	hypothetical protein LOC126353	177										upper_aerodigestive_tract(1)	1		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000145)|all_lung(49;0.000236)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCACCTCGGTCCACGCCCC	0.672													6	7	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1049354	1049354	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:1049354C>T	uc002lqw.3	+	18	2701	c.2470C>T	c.(2470-2472)CTG>TTG	p.L824L	ABCA7_uc010dsb.1_Silent_p.L686L	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	824	ABC transporter 1.				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGCCAGCCCTGCGGGGGCT	0.672													13	108	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1049377	1049377	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:1049377C>T	uc002lqw.3	+	18	2724	c.2493C>T	c.(2491-2493)TTC>TTT	p.F831F	ABCA7_uc010dsb.1_Silent_p.F693F	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	831	ABC transporter 1.				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCTGGACTTCTACCAGGGCC	0.701													9	102	---	---	---	---	PASS
MIDN	90007	broad.mit.edu	37	19	1251880	1251880	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:1251880G>C	uc002lrp.2	+	4	879	c.364G>C	c.(364-366)GAG>CAG	p.E122Q		NM_177401	NP_796375	Q504T8	MIDN_HUMAN	midnolin	122						nucleolus					0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAAGCTCTCGAGAGTCTCAC	0.632													17	46	---	---	---	---	PASS
DAZAP1	26528	broad.mit.edu	37	19	1418235	1418235	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:1418235G>A	uc002lsn.2	+	3	292	c.103G>A	c.(103-105)GAA>AAA	p.E35K	DAZAP1_uc002lsm.2_Missense_Mutation_p.E35K|DAZAP1_uc002lso.2_Missense_Mutation_p.E35K|DAZAP1_uc002lsl.1_Missense_Mutation_p.E35K	NM_018959	NP_061832	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1 isoform b	35	RRM 1.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleotide binding|RNA binding			breast(1)	1		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAATATGGAGAAGTCGTAGA	0.478													13	108	---	---	---	---	PASS
DAZAP1	26528	broad.mit.edu	37	19	1418262	1418262	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:1418262G>A	uc002lsn.2	+	3	319	c.130G>A	c.(130-132)GAT>AAT	p.D44N	DAZAP1_uc002lsm.2_Missense_Mutation_p.D44N|DAZAP1_uc002lso.2_Missense_Mutation_p.D44N|DAZAP1_uc002lsl.1_Missense_Mutation_p.D44N	NM_018959	NP_061832	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1 isoform b	44	RRM 1.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleotide binding|RNA binding			breast(1)	1		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TATCATGAAAGATAAAACCAC	0.483													17	117	---	---	---	---	PASS
ZNF554	115196	broad.mit.edu	37	19	2834766	2834766	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:2834766G>C	uc002lwm.2	+	5	1731	c.1533G>C	c.(1531-1533)CAG>CAC	p.Q511H	ZNF554_uc002lwl.2_Missense_Mutation_p.Q460H	NM_001102651	NP_001096121	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	511	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACACATCAGAAAACTCACA	0.468													14	114	---	---	---	---	PASS
TLE2	7089	broad.mit.edu	37	19	3005560	3005560	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:3005560C>T	uc002lww.2	-	17	2034	c.1771G>A	c.(1771-1773)GGC>AGC	p.G591S	TLE2_uc010xhb.1_Missense_Mutation_p.G258S|TLE2_uc010dth.2_Missense_Mutation_p.G592S|TLE2_uc010xhc.1_Missense_Mutation_p.G469S|TLE2_uc010dti.2_Missense_Mutation_p.G605S	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1	591	WD 4.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCTGGCGCCGTCCGTGTGG	0.657													4	34	---	---	---	---	PASS
MIR7-3	407045	broad.mit.edu	37	19	4770786	4770786	+	RNA	SNP	T	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:4770786T>G	hsa-mir-7-3|MI0000265	+			c.105T>G			C19orf30_uc002mbd.2_Intron|C19orf30_uc002mbe.2_Intron|C19orf30_uc010xii.1_Intron|uc010xij.1_RNA																	0						GCAGACTCCCTTCGACCTTCG	0.582													29	102	---	---	---	---	PASS
DUS3L	56931	broad.mit.edu	37	19	5785253	5785253	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:5785253G>A	uc002mdc.2	-	13	2011	c.1914C>T	c.(1912-1914)TTC>TTT	p.F638F	PRR22_uc002mdb.1_5'Flank|PRR22_uc010xiv.1_5'Flank|DUS3L_uc002mdd.2_Silent_p.F396F	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like isoform 1	638					tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0						GCAAGAAGGCGAAGCTGGGGG	0.587													5	24	---	---	---	---	PASS
MBD3L1	85509	broad.mit.edu	37	19	8953558	8953558	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:8953558G>C	uc002mko.2	+	1	290	c.204G>C	c.(202-204)CAG>CAC	p.Q68H		NM_145208	NP_660209	Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like	68	Transcription repressor.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						TCTGCTGGCAGAGGAGACTGC	0.507													27	110	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9070300	9070300	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:9070300T>A	uc002mkp.2	-	3	17350	c.17146A>T	c.(17146-17148)ACA>TCA	p.T5716S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5718	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GCAGTGTTTGTATGCATGGAA	0.493													19	92	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9091316	9091316	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:9091316C>T	uc002mkp.2	-	1	703	c.499G>A	c.(499-501)GAG>AAG	p.E167K		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	167	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GTTGAGGTCTCAGTGGGGACT	0.443													39	77	---	---	---	---	PASS
CDC37	11140	broad.mit.edu	37	19	10506652	10506652	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:10506652C>G	uc002mof.1	-	2	446	c.330G>C	c.(328-330)AAG>AAC	p.K110N	CDC37_uc002moe.1_5'Flank|CDC37_uc010dxf.1_5'UTR|CDC37_uc002mog.1_Missense_Mutation_p.K110N|CDC37_uc002moh.2_Missense_Mutation_p.K110N	NM_007065	NP_008996	Q16543	CDC37_HUMAN	cell division cycle 37 protein	110					protein targeting|regulation of cyclin-dependent protein kinase activity|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway		unfolded protein binding				0			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)		AGGGCATGCTCTTCTCCTTCT	0.672													32	232	---	---	---	---	PASS
KEAP1	9817	broad.mit.edu	37	19	10610666	10610666	+	Missense_Mutation	SNP	C	A	A	rs144429440	byFrequency	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:10610666C>A	uc002moq.1	-	2	200	c.44G>T	c.(43-45)CGA>CTA	p.R15L	KEAP1_uc002mor.1_Missense_Mutation_p.R15L	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	15					regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			lung(12)|breast(3)|ovary(1)|pancreas(1)	17			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)			GGGCAGGAATCGGCAGCAGGC	0.662													3	80	---	---	---	---	PASS
ATG4D	84971	broad.mit.edu	37	19	10663612	10663612	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:10663612G>A	uc002mov.2	+	10	1414	c.1294G>A	c.(1294-1296)GAG>AAG	p.E432K	ATG4D_uc010xlh.1_Missense_Mutation_p.E369K|ATG4D_uc010dxh.2_RNA|ATG4D_uc010dxi.2_RNA|ATG4D_uc010dxj.2_Missense_Mutation_p.E99K	NM_032885	NP_116274	Q86TL0	ATG4D_HUMAN	APG4 autophagy 4 homolog D	432					autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CACCCTGGCCGAGGGCCATGC	0.662													12	169	---	---	---	---	PASS
KRI1	65095	broad.mit.edu	37	19	10664823	10664823	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:10664823G>A	uc002moy.1	-	19	1943	c.1934C>T	c.(1933-1935)TCA>TTA	p.S645L	KRI1_uc002mow.1_Missense_Mutation_p.S264L|KRI1_uc002mox.1_Missense_Mutation_p.S641L	NM_023008	NP_075384	Q8N9T8	KRI1_HUMAN	KRI1 homolog	645										ovary(1)	1			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CTTGTGGGGTGATACAGGGGC	0.647													24	203	---	---	---	---	PASS
ZNF441	126068	broad.mit.edu	37	19	11891126	11891126	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:11891126C>T	uc010dyj.2	+	4	681	c.487C>T	c.(487-489)CAG>TAG	p.Q163*	ZNF441_uc002msn.3_Nonsense_Mutation_p.Q119*	NM_152355	NP_689568	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	163					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TGAAAGACCTCAGCATGGAAA	0.423													13	124	---	---	---	---	PASS
ZNF442	79973	broad.mit.edu	37	19	12461659	12461659	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:12461659G>C	uc002mtr.1	-	6	1351	c.740C>G	c.(739-741)CCT>CGT	p.P247R	ZNF442_uc010xmk.1_Missense_Mutation_p.P178R	NM_030824	NP_110451	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	247	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4						ACTGTAAATAGGGAAGGCTTT	0.408													23	286	---	---	---	---	PASS
FARSA	2193	broad.mit.edu	37	19	13035011	13035011	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:13035011G>A	uc002mvs.2	-	12	1390	c.1342C>T	c.(1342-1344)CTT>TTT	p.L448F	FARSA_uc002mvt.2_RNA|FARSA_uc010xmv.1_Missense_Mutation_p.L417F|FARSA_uc010dyy.1_Missense_Mutation_p.L369F	NM_004461	NP_004452	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	448					phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)	TTCTCGGGAAGCCCCATGGGC	0.607													10	170	---	---	---	---	PASS
BRD4	23476	broad.mit.edu	37	19	15350616	15350616	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:15350616G>A	uc002nar.2	-	16	3521	c.3299C>T	c.(3298-3300)TCC>TTC	p.S1100F		NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	1100					interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			CTGGACCACGGAGGCAGCACG	0.706			T	NUT|C15orf55	lethal midline carcinoma of young people								10	76	---	---	---	---	PASS
CYP4F2	8529	broad.mit.edu	37	19	16008360	16008360	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:16008360A>G	uc002nbs.1	-	2	112	c.62T>C	c.(61-63)CTC>CCC	p.L21P	CYP4F2_uc010xot.1_Intron|CYP4F2_uc010xou.1_5'UTR	NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	21					leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2						CAGCAGGAGGAGCAGCCAAGG	0.662													13	27	---	---	---	---	PASS
AP1M1	8907	broad.mit.edu	37	19	16339738	16339738	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:16339738C>T	uc002ndu.2	+	9	1219	c.1046C>T	c.(1045-1047)CCG>CTG	p.P349L	AP1M1_uc002ndv.2_Missense_Mutation_p.P361L|AP1M1_uc010xpd.1_Intron	NM_032493	NP_115882	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	349	MHD.				cellular membrane organization|endosome to melanosome transport|interspecies interaction between organisms|intracellular protein transport|melanosome organization|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(3)|breast(1)	4						AAGTCCTTCCCGGTGAGCACT	0.617													9	53	---	---	---	---	PASS
PLVAP	83483	broad.mit.edu	37	19	17476334	17476334	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:17476334C>A	uc002ngk.1	-	3	990	c.940G>T	c.(940-942)GGC>TGC	p.G314C		NM_031310	NP_112600	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	314	Potential.|Extracellular (Potential).					caveola|integral to membrane|perinuclear region of cytoplasm					0						GCCCGCAGGCCCTGCTGGGCT	0.667													28	58	---	---	---	---	PASS
FAM129C	199786	broad.mit.edu	37	19	17643149	17643149	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:17643149C>T	uc010xpr.1	+	4	495	c.357C>T	c.(355-357)TTC>TTT	p.F119F	FAM129C_uc010xpq.1_Silent_p.F119F|FAM129C_uc010xps.1_Silent_p.F88F|FAM129C_uc010xpt.1_RNA	NM_173544	NP_775815	Q86XR2	NIBL2_HUMAN	B-cell novel protein 1 isoform a	119											0						AGCCGATCTTCTGTGTTCTGC	0.652													18	148	---	---	---	---	PASS
FAM129C	199786	broad.mit.edu	37	19	17653073	17653073	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:17653073C>T	uc010xpr.1	+	11	1530	c.1392C>T	c.(1390-1392)CTC>CTT	p.L464L	FAM129C_uc010xpq.1_Silent_p.L464L|FAM129C_uc002ngy.3_Silent_p.L190L|FAM129C_uc010xpu.1_Silent_p.L190L|FAM129C_uc002ngz.3_RNA|FAM129C_uc010eaw.2_Silent_p.L190L|FAM129C_uc002nhb.2_Silent_p.L63L	NM_173544	NP_775815	Q86XR2	NIBL2_HUMAN	B-cell novel protein 1 isoform a	464											0						TGCAGAGCCTCGTGTTTGGGG	0.552													28	218	---	---	---	---	PASS
JUND	3727	broad.mit.edu	37	19	18391933	18391933	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:18391933G>A	uc002nip.2	-	1	500	c.362C>T	c.(361-363)TCA>TTA	p.S121L	hsa-mir-3188|MI0014232_5'Flank	NM_005354	NP_005345	P17535	JUND_HUMAN	jun D proto-oncogene	121					regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0						GAGGAACTGTGAGCTCGTCGG	0.657													7	18	---	---	---	---	PASS
UPF1	5976	broad.mit.edu	37	19	18964156	18964156	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:18964156G>C	uc002nkg.2	+	8	1461	c.1186G>C	c.(1186-1188)GAT>CAT	p.D396H	UPF1_uc002nkf.2_Missense_Mutation_p.D385H	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1	396	Sufficient for interaction with RENT2.				cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2						CAAGGTCCCTGATAGTATCCT	0.587													9	50	---	---	---	---	PASS
HOMER3	9454	broad.mit.edu	37	19	19043761	19043761	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:19043761C>T	uc002nku.2	-	5	1158	c.505G>A	c.(505-507)GAG>AAG	p.E169K	HOMER3_uc002nko.1_RNA|HOMER3_uc002nkp.1_RNA|HOMER3_uc010eby.2_Missense_Mutation_p.E133K|HOMER3_uc010ebz.2_Missense_Mutation_p.E169K|HOMER3_uc002nkw.2_Missense_Mutation_p.E169K|HOMER3_uc002nkv.2_Missense_Mutation_p.E169K	NM_004838	NP_004829	Q9NSC5	HOME3_HUMAN	Homer, neuronal immediate early gene, 3 isoform	169					metabotropic glutamate receptor signaling pathway|protein targeting	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	protein binding				0			Epithelial(12;0.0107)			TTTAGCCGCTCGCGCTCTGTG	0.428													11	53	---	---	---	---	PASS
ZNF85	7639	broad.mit.edu	37	19	21131580	21131580	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:21131580G>C	uc002npg.3	+	4	387	c.260G>C	c.(259-261)TGG>TCG	p.W87S	ZNF85_uc010ecn.2_Missense_Mutation_p.W22S|ZNF85_uc010eco.2_Missense_Mutation_p.W35S|ZNF85_uc002npi.2_Missense_Mutation_p.W28S	NM_003429	NP_003420	Q03923	ZNF85_HUMAN	zinc finger protein 85	87						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1						CAAGACCTTTGGCCGGAGCAG	0.323													9	137	---	---	---	---	PASS
ZNF714	148206	broad.mit.edu	37	19	21299680	21299680	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:21299680G>A	uc002npo.3	+	5	570	c.210G>A	c.(208-210)GTG>GTA	p.V70V	ZNF714_uc002npl.2_5'UTR|ZNF714_uc010ecp.1_Silent_p.V22V|ZNF714_uc002npn.2_RNA	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	70					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTCAACAAGTGATACTGAGAA	0.353													8	77	---	---	---	---	PASS
ZNF708	7562	broad.mit.edu	37	19	21476864	21476864	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:21476864G>A	uc002npq.1	-	4	1102	c.904C>T	c.(904-906)CAT>TAT	p.H302Y	ZNF708_uc002npr.1_Missense_Mutation_p.H238Y|ZNF708_uc010ecs.1_Missense_Mutation_p.H238Y	NM_021269	NP_067092	P17019	ZN708_HUMAN	zinc finger protein 708	302	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(4)|skin(2)	6						TCTCCAGTATGAATTTTCTTG	0.378													7	100	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22941883	22941883	+	Splice_Site	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:22941883C>A	uc010xrh.1	-	5	556	c.556_splice	c.e5-1	p.I186_splice		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TATGAATTATCTTATGTTTCA	0.338													14	45	---	---	---	---	PASS
CCNE1	898	broad.mit.edu	37	19	30308042	30308042	+	Splice_Site	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:30308042A>G	uc002nsn.2	+	5	364	c.181_splice	c.e5-2	p.P61_splice	CCNE1_uc002nso.2_Splice_Site_p.P46_splice	NM_001238	NP_001229	P24864	CCNE1_HUMAN	cyclin E1 isoform 1						androgen receptor signaling pathway|cell division|positive regulation of transcription, DNA-dependent|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm	androgen receptor binding|protein kinase binding|transcription coactivator activity			lung(2)	2	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			TTTCATTTACAGCCTTGGGAC	0.443													29	96	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30934871	30934871	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:30934871C>A	uc002nsu.1	+	2	540	c.402C>A	c.(400-402)CTC>CTA	p.L134L	ZNF536_uc010edd.1_Silent_p.L134L	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	134	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					CGTGCCCACTCTGCGGCAAGC	0.627													26	55	---	---	---	---	PASS
TSHZ3	57616	broad.mit.edu	37	19	31767814	31767814	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:31767814C>T	uc002nsy.3	-	2	2950	c.2885G>A	c.(2884-2886)GGA>GAA	p.G962E		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	962					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					GAACTTTGTTCCACCTGTCCT	0.532													29	72	---	---	---	---	PASS
TSHZ3	57616	broad.mit.edu	37	19	31768045	31768045	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:31768045G>T	uc002nsy.3	-	2	2719	c.2654C>A	c.(2653-2655)TCG>TAG	p.S885*		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	885					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					GGCGGGCGTCGACTCCTCAGC	0.607													16	56	---	---	---	---	PASS
ZNF507	22847	broad.mit.edu	37	19	32844576	32844576	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:32844576C>G	uc002nte.2	+	3	1112	c.840C>G	c.(838-840)ATC>ATG	p.I280M	ZNF507_uc002ntc.2_Missense_Mutation_p.I280M|ZNF507_uc010xrn.1_Missense_Mutation_p.I280M|ZNF507_uc002ntd.2_Missense_Mutation_p.I280M	NM_001136156	NP_001129628	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	280					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(110;0.162)					CCTATCCAATCTTTGAAAATG	0.473													18	196	---	---	---	---	PASS
GPI	2821	broad.mit.edu	37	19	34890129	34890129	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:34890129C>A	uc002nvg.1	+	15	1390	c.1287C>A	c.(1285-1287)TTC>TTA	p.F429L	GPI_uc002nvf.2_Missense_Mutation_p.F468L|GPI_uc010xrv.1_Missense_Mutation_p.F440L|GPI_uc010xrw.1_Missense_Mutation_p.F401L|GPI_uc010edl.1_Missense_Mutation_p.F429L|GPI_uc002nvi.1_Missense_Mutation_p.F92L	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase	429					angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)					TGGCCAACTTCTTGGCCCAGA	0.587													5	40	---	---	---	---	PASS
GRAMD1A	57655	broad.mit.edu	37	19	35514178	35514178	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:35514178A>G	uc010xse.1	+	18	2029	c.1892A>G	c.(1891-1893)TAC>TGC	p.Y631C	GRAMD1A_uc002nxk.2_Missense_Mutation_p.Y620C|GRAMD1A_uc002nxl.2_Missense_Mutation_p.Y393C|GRAMD1A_uc010xsf.1_Missense_Mutation_p.Y632C|GRAMD1A_uc002nxm.1_RNA|GRAMD1A_uc002nxn.1_Missense_Mutation_p.Y242C	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	631						integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CTGCTCTTCTACCGCCTCTGG	0.582													154	188	---	---	---	---	PASS
CD22	933	broad.mit.edu	37	19	35832500	35832500	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:35832500G>A	uc010edt.2	+	8	1839	c.1762G>A	c.(1762-1764)GAA>AAA	p.E588K	CD22_uc010xst.1_Missense_Mutation_p.E416K|CD22_uc010edu.2_Missense_Mutation_p.E500K|CD22_uc010edv.2_Missense_Mutation_p.E588K|CD22_uc002nzb.3_Missense_Mutation_p.E411K|CD22_uc010edx.2_RNA	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule precursor	588	Extracellular (Potential).				cell adhesion		protein binding|sugar binding			ovary(5)|lung(3)|breast(1)	9	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)	CTGGACACTTGAAGTGCTGTG	0.597													27	61	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38689091	38689091	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:38689091G>T	uc002ohk.2	+	19	5412	c.4903G>T	c.(4903-4905)GAC>TAC	p.D1635Y		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1635					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GCGGCGCCTGGACCCTGGGCT	0.672													26	145	---	---	---	---	PASS
YIF1B	90522	broad.mit.edu	37	19	38799948	38799948	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:38799948G>A	uc002ohz.2	-	3	367	c.318C>T	c.(316-318)ATC>ATT	p.I106I	YIF1B_uc002ohw.2_Silent_p.I75I|YIF1B_uc002ohx.2_Silent_p.I91I|YIF1B_uc010xtx.1_Silent_p.I89I|YIF1B_uc010xty.1_Silent_p.I75I|YIF1B_uc002oia.2_Silent_p.I103I|YIF1B_uc002ohy.2_Silent_p.I103I|YIF1B_uc002oib.2_Silent_p.I103I	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5	106	Cytoplasmic (Potential).					integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TGAGCTTGGTGATGGGGATGA	0.607													35	142	---	---	---	---	PASS
ATP1A3	478	broad.mit.edu	37	19	42490037	42490037	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:42490037G>T	uc002osg.2	-	6	739	c.585C>A	c.(583-585)ATC>ATA	p.I195I	ATP1A3_uc010xwf.1_Silent_p.I206I|ATP1A3_uc010xwg.1_Silent_p.I165I|ATP1A3_uc010xwh.1_Silent_p.I208I|ATP1A3_uc002osh.2_Silent_p.I195I	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	195	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2						GGGCTGAGATGATCCGCAGGT	0.483													37	155	---	---	---	---	PASS
CIC	23152	broad.mit.edu	37	19	42794394	42794394	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:42794394C>T	uc002otf.1	+	10	1514	c.1474C>T	c.(1474-1476)CGG>TGG	p.R492W		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	492			R -> W (de novo variant found in a patient with mental retardation).		regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)				GGGCTTTGGTCGGAAGGTGTT	0.627			T	DUX4	soft tissue sarcoma								12	213	---	---	---	---	PASS
HIF3A	64344	broad.mit.edu	37	19	46811549	46811549	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:46811549G>C	uc002peh.2	+	4	464	c.435G>C	c.(433-435)CTG>CTC	p.L145L	HIF3A_uc002pef.1_Silent_p.L145L|HIF3A_uc002peg.3_Silent_p.L145L|HIF3A_uc010xxx.1_RNA|HIF3A_uc002pei.3_Silent_p.L89L|HIF3A_uc002pej.1_Silent_p.L76L|HIF3A_uc002pek.2_Silent_p.L89L|HIF3A_uc010xxy.1_Silent_p.L76L|HIF3A_uc002pel.2_Silent_p.L143L|HIF3A_uc010xxz.1_Silent_p.L94L	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	145	PAS 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		AGGACGCCCTGACCCCCCAGC	0.502													21	150	---	---	---	---	PASS
PRKD2	25865	broad.mit.edu	37	19	47197343	47197343	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:47197343G>A	uc002pfh.2	-	11	1707	c.1365C>T	c.(1363-1365)TTC>TTT	p.F455F	PRKD2_uc010ekt.2_5'Flank|PRKD2_uc002pfe.2_5'UTR|PRKD2_uc002pff.2_5'UTR|PRKD2_uc002pfg.2_Silent_p.F298F|PRKD2_uc002pfi.2_Silent_p.F455F|PRKD2_uc002pfj.2_Silent_p.F455F|PRKD2_uc010xye.1_Silent_p.F455F|PRKD2_uc002pfk.2_Silent_p.F298F	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A	455	PH.				cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		GCACAAGGCTGAAGTTCTGGG	0.607													10	96	---	---	---	---	PASS
GRLF1	2909	broad.mit.edu	37	19	47422077	47422077	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:47422077G>T	uc010ekv.2	+	1	145	c.145G>T	c.(145-147)GAG>TAG	p.E49*		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	49					axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		GAGTGCTGACGAGTTTCACTT	0.537													39	107	---	---	---	---	PASS
CRX	1406	broad.mit.edu	37	19	48342941	48342941	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:48342941C>T	uc002phq.3	+	4	821	c.617C>T	c.(616-618)TCC>TTC	p.S206F		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	206					organ morphogenesis|response to stimulus|visual perception		leucine zipper domain binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		TCTTCCCCCTCCGCCTATGGG	0.682													45	168	---	---	---	---	PASS
CRX	1406	broad.mit.edu	37	19	48343180	48343180	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:48343180C>T	uc002phq.3	+	4	1060	c.856C>T	c.(856-858)CTG>TTG	p.L286L		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	286					organ morphogenesis|response to stimulus|visual perception		leucine zipper domain binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		CATGGACCCTCTGGACTACAA	0.547													64	240	---	---	---	---	PASS
NUCB1	4924	broad.mit.edu	37	19	49409111	49409111	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:49409111C>G	uc002plb.3	+	4	417	c.345C>G	c.(343-345)CTC>CTG	p.L115L	NUCB1_uc002pla.2_Silent_p.L115L|NUCB1_uc002plc.2_Silent_p.L115L	NM_006184	NP_006175	Q02818	NUCB1_HUMAN	nucleobindin 1 precursor	115						ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		GGATGCTGCTCAAGGCCAAGA	0.672													29	36	---	---	---	---	PASS
NTF4	4909	broad.mit.edu	37	19	49564991	49564991	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:49564991C>G	uc002pmf.3	-	2	405	c.264G>C	c.(262-264)GCG>GCC	p.A88A	CGB7_uc010yah.1_Intron	NM_006179	NP_006170	P34130	NTF4_HUMAN	neurotrophin 5 preproprotein	88			A -> V.		adult locomotory behavior|epidermis development|ganglion mother cell fate determination|long-term memory|sensory organ boundary specification	endoplasmic reticulum lumen|extracellular region	growth factor activity				0		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CCCGACGACTCGCTGGTGCAG	0.692													3	29	---	---	---	---	PASS
PPFIA3	8541	broad.mit.edu	37	19	49637089	49637089	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:49637089C>T	uc002pmr.2	+	10	1530	c.1198C>T	c.(1198-1200)CGG>TGG	p.R400W	PPFIA3_uc010yai.1_RNA|PPFIA3_uc010emt.2_Missense_Mutation_p.R324W|PPFIA3_uc010yaj.1_RNA|PPFIA3_uc002pms.2_Missense_Mutation_p.R268W	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3	400	Potential.					cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GGAGCGGCTTCGGCAGCTGGA	0.627													11	30	---	---	---	---	PASS
PRR12	57479	broad.mit.edu	37	19	50099552	50099552	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:50099552C>T	uc002poo.3	+	4	1960	c.1960C>T	c.(1960-1962)CGG>TGG	p.R654W		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CAGCCCTCCTCGGACCTCAGG	0.706													8	21	---	---	---	---	PASS
AP2A1	160	broad.mit.edu	37	19	50306555	50306555	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:50306555C>T	uc002ppn.2	+	19	2543	c.2332C>T	c.(2332-2334)CTC>TTC	p.L778F	AP2A1_uc010enj.1_RNA|AP2A1_uc002ppo.2_Missense_Mutation_p.L756F|AP2A1_uc002ppp.1_3'UTR|AP2A1_uc010enk.2_5'Flank	NM_014203	NP_055018	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1	778					axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|Golgi to endosome transport|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|clathrin coat of trans-Golgi network vesicle|cytosol	protein binding|protein transporter activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		CCGCATGTATCTCTTCTATGG	0.602													8	68	---	---	---	---	PASS
ZNF468	90333	broad.mit.edu	37	19	53344268	53344268	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:53344268C>G	uc002qaf.2	-	4	1430	c.1279G>C	c.(1279-1281)GAA>CAA	p.E427Q	ZNF468_uc002qae.2_Missense_Mutation_p.E374Q	NM_001008801	NP_001008801	Q5VIY5	ZN468_HUMAN	zinc finger protein ZNF468 isoform 2	427	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0358)		CTGTGTCTTTCCAGGTTTGAT	0.418													32	200	---	---	---	---	PASS
MBOAT7	79143	broad.mit.edu	37	19	54677872	54677872	+	Missense_Mutation	SNP	T	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:54677872T>G	uc002qdq.2	-	9	1551	c.1285A>C	c.(1285-1287)ATC>CTC	p.I429L	TMC4_uc010erf.2_5'Flank|TMC4_uc002qdo.2_5'Flank|MBOAT7_uc010erg.2_Missense_Mutation_p.I113L|MBOAT7_uc010yem.1_Missense_Mutation_p.I411L|MBOAT7_uc002qdr.2_Missense_Mutation_p.I429L|MBOAT7_uc002qds.2_Missense_Mutation_p.I356L|MBOAT7_uc010yen.1_Missense_Mutation_p.I356L	NM_024298	NP_077274	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain	429	Helical; (Potential).				phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CAGAAGTAGATGGAGGCCCAG	0.642													12	131	---	---	---	---	PASS
NLRP9	338321	broad.mit.edu	37	19	56235397	56235397	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:56235397C>G	uc002qly.2	-	4	2136	c.2108G>C	c.(2107-2109)AGA>ACA	p.R703T		NM_176820	NP_789790	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	703						cytoplasm	ATP binding			skin(4)|ovary(2)|breast(1)	7		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		ACACAGGTGTCTGATGTCAGA	0.473													21	118	---	---	---	---	PASS
USP29	57663	broad.mit.edu	37	19	57640692	57640692	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:57640692G>C	uc002qny.2	+	4	1005	c.649G>C	c.(649-651)GAA>CAA	p.E217Q		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	217					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGAGGATTTAGAAAAAGATAG	0.368													21	143	---	---	---	---	PASS
ZNF530	348327	broad.mit.edu	37	19	58118674	58118674	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:58118674G>T	uc002qpk.2	+	3	2001	c.1781G>T	c.(1780-1782)AGA>ATA	p.R594I	ZNF547_uc002qpm.3_Intron|ZNF530_uc002qpl.2_RNA	NM_020880	NP_065931	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	594	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTAAGACACAGAAGAGTTCAT	0.299													7	81	---	---	---	---	PASS
ZNF586	54807	broad.mit.edu	37	19	58288012	58288012	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:58288012G>C	uc002qqd.2	+	2	324	c.138G>C	c.(136-138)GAG>GAC	p.E46D	ZNF587_uc002qqb.2_Intron|ZNF586_uc002qqe.2_Intron|ZNF586_uc010euh.2_Missense_Mutation_p.E3D|ZNF586_uc002qqf.1_Intron	NM_017652	NP_060122	Q9NXT0	ZN586_HUMAN	zinc finger protein 586	46	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGATGCTGGAGACCTTGACAC	0.478													41	315	---	---	---	---	PASS
ZNF606	80095	broad.mit.edu	37	19	58490799	58490799	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:58490799G>C	uc002qqw.2	-	7	1867	c.1249C>G	c.(1249-1251)CAA>GAA	p.Q417E	ZNF606_uc010yhp.1_Missense_Mutation_p.Q327E	NM_025027	NP_079303	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	417	C2H2-type 3; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		TTCTTATGTTGAATAAGGTAA	0.393													20	121	---	---	---	---	PASS
ZNF274	10782	broad.mit.edu	37	19	58723025	58723025	+	Nonsense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr19:58723025G>T	uc002qrq.1	+	9	1411	c.952G>T	c.(952-954)GAG>TAG	p.E318*	ZNF274_uc002qrr.1_Nonsense_Mutation_p.E286*|ZNF274_uc002qrs.1_Nonsense_Mutation_p.E213*|ZNF274_uc010eum.1_Nonsense_Mutation_p.E77*	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c	318	KRAB 2.				viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		TGTGATGCTGGAGACCTTTGG	0.642													34	126	---	---	---	---	PASS
SPEF1	25876	broad.mit.edu	37	20	3760348	3760348	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:3760348G>C	uc002wjj.2	-	2	352	c.184C>G	c.(184-186)CTC>GTC	p.L62V		NM_015417	NP_056232	Q9Y4P9	SPEF1_HUMAN	calponin-homology and microtubule-associated	62						cilium axoneme|cytoplasm|cytoskeleton					0						TTCTGCTGGAGAGAGTTGGCG	0.527													10	64	---	---	---	---	PASS
CENPB	1059	broad.mit.edu	37	20	3766431	3766431	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:3766431C>A	uc002wjk.2	-	1	907	c.700G>T	c.(700-702)GAC>TAC	p.D234Y	CDC25B_uc010zqk.1_5'Flank|CDC25B_uc010zql.1_5'Flank|CDC25B_uc010zqm.1_5'Flank	NM_001810	NP_001801	P07199	CENPB_HUMAN	centromere protein B	234					regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	chromatin binding|satellite DNA binding				0						TCGCTGCCGTCGGCATTGGCG	0.726													19	29	---	---	---	---	PASS
SLC24A3	57419	broad.mit.edu	37	20	19662590	19662590	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:19662590G>A	uc002wrl.2	+	10	1053	c.856G>A	c.(856-858)GAT>AAT	p.D286N		NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24	286	Cytoplasmic (Potential).					integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						TGCTGAAATTGATGACAGCAG	0.378													6	58	---	---	---	---	PASS
RIN2	54453	broad.mit.edu	37	20	19945645	19945645	+	Silent	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:19945645C>G	uc002wro.1	+	5	549	c.513C>G	c.(511-513)CTC>CTG	p.L171L	RIN2_uc010gcu.1_Intron|RIN2_uc010gcv.1_Intron	NM_018993	NP_061866	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	171	SH2.				endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5						TATTCCGGCTCATTGCTTTCT	0.468													17	196	---	---	---	---	PASS
NKX2-2	4821	broad.mit.edu	37	20	21494134	21494134	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:21494134G>T	uc002wsi.2	-	1	531	c.174C>A	c.(172-174)AGC>AGA	p.S58R		NM_002509	NP_002500	O95096	NKX22_HUMAN	NK2 transcription factor related, locus 2	58					brain development|positive regulation of sequence-specific DNA binding transcription factor activity	nucleus	chromatin binding|core promoter proximal region DNA binding|transcription coactivator activity			pancreas(1)|skin(1)	2						TCAGGGGCAGGCTCTGCACCG	0.672													6	39	---	---	---	---	PASS
PAX1	5075	broad.mit.edu	37	20	21687680	21687680	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:21687680C>A	uc002wsj.2	+	2	945	c.891C>A	c.(889-891)GGC>GGA	p.G297G	PAX1_uc010zsl.1_Silent_p.G297G|PAX1_uc010zsm.1_Silent_p.G273G	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	297					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2						ACATCCTGGGCATCCGGACGT	0.662													15	48	---	---	---	---	PASS
CST4	1472	broad.mit.edu	37	20	23667745	23667745	+	Nonsense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:23667745C>A	uc002wto.1	-	2	378	c.322G>T	c.(322-324)GAA>TAA	p.E108*		NM_001899	NP_001890	P01036	CYTS_HUMAN	cystatin S precursor	108						extracellular region	cysteine-type endopeptidase inhibitor activity			breast(1)	1	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					TCTGGCTGTTCATGGAAGGCA	0.567													20	186	---	---	---	---	PASS
DEFB123	245936	broad.mit.edu	37	20	30037910	30037910	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:30037910G>C	uc002wvy.2	+	2	228	c.137G>C	c.(136-138)TGC>TCC	p.C46S		NM_153324	NP_697019	Q8N688	DB123_HUMAN	defensin, beta 123 precursor	46					defense response to bacterium	extracellular region					0	Lung NSC(7;0.000139)|all_lung(7;0.000197)|all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TATGTTTACTGCATAAATAAT	0.433													46	105	---	---	---	---	PASS
BPIL3	128859	broad.mit.edu	37	20	31629812	31629812	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:31629812C>A	uc010zuc.1	+	12	1179	c.1179C>A	c.(1177-1179)GGC>GGA	p.G393G	BPIL3_uc010zud.1_Silent_p.G332G	NM_174897	NP_777557	Q8NFQ5	BPIL3_HUMAN	bactericidal/permeability-increasing	393						extracellular region	lipid binding			ovary(1)|pancreas(1)	2						CATCGATTGGCAACTTCAATG	0.587													5	48	---	---	---	---	PASS
RALY	22913	broad.mit.edu	37	20	32664611	32664611	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:32664611G>T	uc002xab.2	+	7	946	c.648G>T	c.(646-648)AAG>AAT	p.K216N	RALY_uc002xac.2_Missense_Mutation_p.K200N|RALY_uc002xad.2_RNA|RALY_uc002xae.1_Missense_Mutation_p.K216N	NM_016732	NP_057951	Q9UKM9	RALY_HUMAN	RNA binding protein (autoantigenic,	216						catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(1)	1						CGGAGCAAAAGGCCAATCCAG	0.572													10	28	---	---	---	---	PASS
ITCH	83737	broad.mit.edu	37	20	33068455	33068455	+	Missense_Mutation	SNP	A	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:33068455A>G	uc010geu.1	+	20	2185	c.1993A>G	c.(1993-1995)AAG>GAG	p.K665E	ITCH_uc002xak.2_Missense_Mutation_p.K624E|ITCH_uc010zuj.1_Missense_Mutation_p.K514E	NM_031483	NP_113671	Q96J02	ITCH_HUMAN	itchy homolog E3 ubiquitin protein ligase	665	HECT.				apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6						ACCATTCTATAAGCGTATCTT	0.338													35	161	---	---	---	---	PASS
RBM39	9584	broad.mit.edu	37	20	34300964	34300964	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:34300964G>C	uc002xeb.2	-	12	1495	c.1151C>G	c.(1150-1152)TCT>TGT	p.S384C	RBM39_uc002xdz.2_Missense_Mutation_p.S360C|RBM39_uc002xea.2_Missense_Mutation_p.S227C|RBM39_uc010gfn.2_Missense_Mutation_p.S227C|RBM39_uc010zvm.1_Missense_Mutation_p.S362C|RBM39_uc002xeg.2_Missense_Mutation_p.S362C|RBM39_uc002xec.2_Missense_Mutation_p.S384C|RBM39_uc002xed.2_Missense_Mutation_p.S102C|RBM39_uc002xee.2_Missense_Mutation_p.S227C|RBM39_uc002xef.2_Missense_Mutation_p.S227C|RBM39_uc010zvn.1_Missense_Mutation_p.S227C	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	384	Interaction with ESR1 and ESR2 (By similarity).|Interaction with JUN (By similarity).				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					AAATGCCAAAGAGCCACTCAT	0.363													7	74	---	---	---	---	PASS
CHD6	84181	broad.mit.edu	37	20	40045984	40045984	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:40045984G>A	uc002xka.1	-	32	6311	c.6133C>T	c.(6133-6135)CCA>TCA	p.P2045S	CHD6_uc002xjz.1_5'Flank	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2045					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				TACTTCCCTGGATAATCTGGG	0.438													12	114	---	---	---	---	PASS
CSE1L	1434	broad.mit.edu	37	20	47701833	47701833	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:47701833G>C	uc002xty.2	+	16	1767	c.1633G>C	c.(1633-1635)GAA>CAA	p.E545Q	CSE1L_uc010zyg.1_Missense_Mutation_p.E328Q|CSE1L_uc010ghx.2_Missense_Mutation_p.E489Q|CSE1L_uc010ghy.2_Missense_Mutation_p.E166Q|CSE1L_uc010zyh.1_Missense_Mutation_p.E194Q	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein	545					apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TACAGCTGCAGAAATCGCACC	0.413													13	86	---	---	---	---	PASS
ZNFX1	57169	broad.mit.edu	37	20	47865809	47865809	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:47865809C>G	uc002xui.2	-	14	3999	c.3752G>C	c.(3751-3753)CGA>CCA	p.R1251P		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1251							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ATTGTTCTCTCGAAGTGTATG	0.517													23	129	---	---	---	---	PASS
FAM65C	140876	broad.mit.edu	37	20	49209624	49209624	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:49209624C>T	uc002xvm.2	-	18	2628	c.2310G>A	c.(2308-2310)CAG>CAA	p.Q770Q	FAM65C_uc010zyt.1_Silent_p.Q774Q|FAM65C_uc010zyu.1_RNA	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	770										ovary(2)	2						CGCTCTGCCTCTGCAGGTAGC	0.587													26	172	---	---	---	---	PASS
STMN3	50861	broad.mit.edu	37	20	62275232	62275232	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:62275232G>A	uc002yfr.1	-	3	250	c.168C>T	c.(166-168)GTC>GTT	p.V56V	STMN3_uc011abb.1_Silent_p.V56V	NM_015894	NP_056978	Q9NZ72	STMN3_HUMAN	SCG10-like-protein	56					cytoplasmic microtubule organization|intracellular signal transduction|negative regulation of Rac protein signal transduction|neuron projection development|regulation of cytoskeleton organization|regulation of Rac GTPase activity	cytoplasm	protein domain specific binding				0	all_cancers(38;2.31e-11)|all_epithelial(29;7.76e-13)		Epithelial(9;1.9e-09)|all cancers(9;1.22e-08)|BRCA - Breast invasive adenocarcinoma(10;8.86e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.00559)			ACTTGAGGATGACCTCGAAGC	0.617													26	153	---	---	---	---	PASS
PRPF6	24148	broad.mit.edu	37	20	62648166	62648166	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr20:62648166C>T	uc002yho.2	+	12	1783	c.1615C>T	c.(1615-1617)CGG>TGG	p.R539W	PRPF6_uc002yhp.2_Missense_Mutation_p.R539W	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	539					assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)					GGAGGAAGATCGGAAGCATAC	0.562													4	82	---	---	---	---	PASS
LIPI	149998	broad.mit.edu	37	21	15558281	15558281	+	Splice_Site	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:15558281C>A	uc002yjm.2	-	3	614	c.604_splice	c.e3+1	p.G202_splice	LIPI_uc010gkw.1_Splice_Site_p.G135_splice	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		aataattttaCCTGTTATTCT	0.254													6	125	---	---	---	---	PASS
GABPA	2551	broad.mit.edu	37	21	27117588	27117588	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:27117588G>C	uc002ylx.3	+	3	672	c.145G>C	c.(145-147)GGC>CGC	p.G49R	GABPA_uc002yly.3_Missense_Mutation_p.G49R	NM_002040	NP_002031	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha	49					positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2						TGAACCAATAGGCAATTTAAA	0.358													7	129	---	---	---	---	PASS
SYNJ1	8867	broad.mit.edu	37	21	34058125	34058125	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:34058125G>C	uc002yqh.2	-	9	1168	c.1168C>G	c.(1168-1170)CTT>GTT	p.L390V	SYNJ1_uc011ads.1_Missense_Mutation_p.L351V|SYNJ1_uc002yqf.2_Missense_Mutation_p.L351V|SYNJ1_uc002yqg.2_Missense_Mutation_p.L351V|SYNJ1_uc002yqi.2_Missense_Mutation_p.L390V	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	351	SAC.						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5						TGAGGTTTAAGAACACTATGT	0.338													33	79	---	---	---	---	PASS
GART	2618	broad.mit.edu	37	21	34897293	34897293	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:34897293G>C	uc002yrx.2	-	11	1216	c.1081C>G	c.(1081-1083)CAA>GAA	p.Q361E	GART_uc002yrz.2_Missense_Mutation_p.Q361E|GART_uc010gmd.2_Missense_Mutation_p.Q23E|GART_uc002yry.2_Missense_Mutation_p.Q361E|GART_uc002ysa.2_Missense_Mutation_p.Q361E	NM_000819	NP_000810	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase,	361					'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)	CCTAGAGCTTGAGCCTCAGGA	0.448													13	68	---	---	---	---	PASS
KCNJ6	3763	broad.mit.edu	37	21	39087405	39087405	+	Nonsense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:39087405G>A	uc011aej.1	-	3	108	c.55C>T	c.(55-57)CAG>TAG	p.Q19*	KCNJ6_uc002ywo.2_Nonsense_Mutation_p.Q19*	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6	19	Cytoplasmic (By similarity).				synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	TCGACGTCCTGATCCATGGAG	0.527													14	44	---	---	---	---	PASS
BRWD1	54014	broad.mit.edu	37	21	40568985	40568985	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:40568985C>T	uc002yxk.1	-	41	6149	c.6010G>A	c.(6010-6012)GAA>AAA	p.E2004K	BRWD1_uc010goc.1_Missense_Mutation_p.E647K|BRWD1_uc002yxl.2_Missense_Mutation_p.E2004K	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2004					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				GTACTACCTTCGGAGTCAGGA	0.418													31	163	---	---	---	---	PASS
TRPM2	7226	broad.mit.edu	37	21	45821777	45821777	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:45821777G>A	uc002zet.1	+	17	2748	c.2535G>A	c.(2533-2535)CGG>CGA	p.R845R	TRPM2_uc002zeu.1_Silent_p.R845R|TRPM2_uc002zew.1_Silent_p.R845R|TRPM2_uc010gpt.1_Silent_p.R845R|TRPM2_uc002zex.1_Silent_p.R631R|TRPM2_uc002zey.1_Silent_p.R358R	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	845	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						AGGAGATGCGGCAGGTACAGC	0.627													85	130	---	---	---	---	PASS
MCM3AP	8888	broad.mit.edu	37	21	47685237	47685237	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:47685237C>T	uc002zir.1	-	12	3268	c.3232G>A	c.(3232-3234)GAG>AAG	p.E1078K	MCM3AP_uc002ziq.1_Missense_Mutation_p.E5K	NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3	1078					DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)					GTCCCTACCTCGTCAGAGTAC	0.607													7	39	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47783764	47783764	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:47783764G>A	uc002zji.3	+	14	2631	c.2524G>A	c.(2524-2526)GAG>AAG	p.E842K	PCNT_uc002zjj.2_Missense_Mutation_p.E724K	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	842					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					GTGTGGGCGGGAGCCGCCCAC	0.662													25	132	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47959842	47959842	+	Silent	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr21:47959842G>C	uc002zjo.2	+	17	2157	c.1974G>C	c.(1972-1974)CTG>CTC	p.L658L	DIP2A_uc011afy.1_Silent_p.L594L|DIP2A_uc011afz.1_Silent_p.L654L|DIP2A_uc002zjl.2_Silent_p.L658L|DIP2A_uc002zjm.2_Silent_p.L658L|DIP2A_uc010gql.2_Silent_p.L615L|DIP2A_uc002zjn.2_Silent_p.L658L|DIP2A_uc002zjp.1_Silent_p.L403L|DIP2A_uc002zjq.2_Silent_p.L50L	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	658					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		CCAGAGGTCTGAGGCCAGAGG	0.557													14	103	---	---	---	---	PASS
CECR5	27440	broad.mit.edu	37	22	17619180	17619180	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:17619180C>G	uc002zmf.2	-	8	1031	c.1003G>C	c.(1003-1005)GAT>CAT	p.D335H	CECR5_uc002zmd.2_Missense_Mutation_p.D146H|CECR5_uc002zme.2_Missense_Mutation_p.D127H|CECR5_uc002zmg.2_Missense_Mutation_p.D135H|CECR5_uc002zmh.2_Missense_Mutation_p.D305H	NM_033070	NP_149061	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	335							hydrolase activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				GGCGCCCCATCATGCGTTGCC	0.587													9	103	---	---	---	---	PASS
MICAL3	57553	broad.mit.edu	37	22	18374399	18374399	+	Splice_Site	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:18374399C>G	uc002zng.3	-	12	1900	c.1547_splice	c.e12-1	p.E516_splice	MICAL3_uc011agl.1_Splice_Site_p.E516_splice|MICAL3_uc002znh.2_Splice_Site_p.E516_splice|MICAL3_uc002znj.1_Splice_Site_p.E216_splice|MICAL3_uc002znk.1_Splice_Site_p.E516_splice|MICAL3_uc002znl.1_Splice_Site_p.E149_splice|MICAL3_uc002znm.2_Splice_Site_p.E17_splice|MICAL3_uc010grf.2_Splice_Site_p.E516_splice	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		GCTACAGACTCTAAAACAACA	0.458													4	39	---	---	---	---	PASS
SERPIND1	3053	broad.mit.edu	37	22	21141193	21141193	+	Missense_Mutation	SNP	G	A	A	rs142451096		TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:21141193G>A	uc002ztb.1	+	5	1406	c.1339G>A	c.(1339-1341)GAG>AAG	p.E447K	PI4KA_uc002zsz.3_Intron|SERPIND1_uc002ztc.2_Missense_Mutation_p.E475K	NM_000185	NP_000176	P05546	HEP2_HUMAN	heparin cofactor II precursor	447			E -> K (in HCF2D).		blood coagulation|chemotaxis|regulation of proteolysis	extracellular region	heparin binding|serine-type endopeptidase inhibitor activity				0	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)	CACAGTGAACGAGGAAGGCAC	0.517													16	115	---	---	---	---	PASS
MAPK1	5594	broad.mit.edu	37	22	22160160	22160160	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:22160160G>T	uc002zvn.2	-	3	711	c.471C>A	c.(469-471)CTC>CTA	p.L157L	MAPK1_uc002zvo.2_Silent_p.L157L|MAPK1_uc010gtk.1_Silent_p.L157L	NM_002745	NP_002736	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	157	Protein kinase.				activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription, DNA-dependent	cytosol|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)	AGGTGGTGTTGAGCAGCAGGT	0.393													20	178	---	---	---	---	PASS
APOL1	8542	broad.mit.edu	37	22	36661498	36661498	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:36661498G>T	uc003apf.2	+	6	784	c.616G>T	c.(616-618)GTA>TTA	p.V206L	APOL1_uc011amn.1_Missense_Mutation_p.V83L|APOL1_uc003apc.2_RNA|APOL1_uc003ape.2_Missense_Mutation_p.V222L|APOL1_uc011amo.1_Missense_Mutation_p.V83L|APOL1_uc011amp.1_Missense_Mutation_p.V206L|APOL1_uc011amq.1_Missense_Mutation_p.V188L|APOL1_uc010gwx.2_Missense_Mutation_p.V83L	NM_003661	NP_003652	O14791	APOL1_HUMAN	apolipoprotein L1 isoform a precursor	206					cholesterol metabolic process|cytolysis|innate immune response|killing of cells of other organism|lipid transport|lipoprotein metabolic process	high-density lipoprotein particle|very-low-density lipoprotein particle	chloride channel activity|lipid binding|protein binding			breast(2)|ovary(1)	3						AGGCAGCCTTGTACTCTTGGA	0.567													51	235	---	---	---	---	PASS
POLR3H	171568	broad.mit.edu	37	22	41926792	41926792	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:41926792C>A	uc003baf.2	-	6	520	c.460G>T	c.(460-462)GAC>TAC	p.D154Y	POLR3H_uc003bae.2_RNA|POLR3H_uc003bag.2_Missense_Mutation_p.D154Y|POLR3H_uc003bai.2_Missense_Mutation_p.D125Y	NM_138338	NP_612211	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	154					innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity			skin(1)	1						AAGCTCTCGTCCACCACCCGG	0.617													15	84	---	---	---	---	PASS
CYP2D6	1565	broad.mit.edu	37	22	42523977	42523977	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:42523977C>T	uc003bce.2	-	6	942	c.852G>A	c.(850-852)GGG>GGA	p.G284G	uc003bcd.1_Intron|CYP2D6_uc010gyu.2_Intron|CYP2D6_uc003bcf.2_Silent_p.G233G	NM_000106	NP_000097	Q6NWU0	Q6NWU0_HUMAN	cytochrome P450, family 2, subfamily D,	284							electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen			breast(1)|skin(1)	2						TCTCAGGGTTCCCCTTGGCCT	0.622													4	83	---	---	---	---	PASS
PKDREJ	10343	broad.mit.edu	37	22	46654808	46654808	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:46654808G>A	uc003bhh.2	-	1	4412	c.4412C>T	c.(4411-4413)TCA>TTA	p.S1471L		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1471	Cytoplasmic (Potential).				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ACTTGCTTCTGACATTAGAGG	0.443													5	197	---	---	---	---	PASS
CERK	64781	broad.mit.edu	37	22	47116103	47116103	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:47116103G>A	uc003bia.2	-	3	366	c.259C>T	c.(259-261)CAC>TAC	p.H87Y		NM_022766	NP_073603	Q8TCT0	CERK1_HUMAN	ceramide kinase	87	Required for binding to sulfatide and phosphoinositides.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TTTACACAGTGAACTGCACAG	0.517													11	65	---	---	---	---	PASS
TBC1D22A	25771	broad.mit.edu	37	22	47308002	47308002	+	Missense_Mutation	SNP	C	G	G			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:47308002C>G	uc003bib.2	+	8	1068	c.933C>G	c.(931-933)ATC>ATG	p.I311M	TBC1D22A_uc010haf.2_Missense_Mutation_p.I281M|TBC1D22A_uc003bic.2_Missense_Mutation_p.I252M|TBC1D22A_uc003bie.2_Missense_Mutation_p.I233M|TBC1D22A_uc003bid.2_RNA|TBC1D22A_uc010hag.2_RNA|TBC1D22A_uc003bif.2_Missense_Mutation_p.I264M	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	311	Rab-GAP TBC.					intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		TATGGGCGATCCGCCACCCAG	0.383													18	179	---	---	---	---	PASS
HDAC10	83933	broad.mit.edu	37	22	50684751	50684751	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr22:50684751G>C	uc003bkg.2	-	17	1999	c.1626C>G	c.(1624-1626)TTC>TTG	p.F542L	TUBGCP6_uc003bkb.1_5'Flank|TUBGCP6_uc010har.1_5'Flank|TUBGCP6_uc010has.1_5'Flank|TUBGCP6_uc010hau.1_5'Flank|HDAC10_uc003bke.2_Missense_Mutation_p.F268L|HDAC10_uc003bkf.2_Missense_Mutation_p.F268L|HDAC10_uc010hav.2_Missense_Mutation_p.F522L|HDAC10_uc003bkh.2_Missense_Mutation_p.F335L|HDAC10_uc003bki.2_Missense_Mutation_p.F492L|HDAC10_uc003bkj.2_RNA	NM_032019	NP_114408	Q969S8	HDA10_HUMAN	histone deacetylase 10 isoform 1	542					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nucleus	histone deacetylase activity|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGGAGACATGGAACATGGATA	0.597													14	158	---	---	---	---	PASS
ARSE	415	broad.mit.edu	37	X	2867672	2867672	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:2867672G>A	uc004crc.3	-	6	777	c.527C>T	c.(526-528)TCC>TTC	p.S176F	ARSE_uc011mhi.1_Missense_Mutation_p.S122F|ARSE_uc011mhh.1_Missense_Mutation_p.S201F	NM_000047	NP_000038	P51690	ARSE_HUMAN	arylsulfatase E precursor	176					skeletal system development	Golgi stack	arylsulfatase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCCATCAAGGAGAAAGGCAT	0.517													6	42	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3239840	3239840	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:3239840T>A	uc004crg.3	-	5	4043	c.3886A>T	c.(3886-3888)ATG>TTG	p.M1296L		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1296						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GTGGTTGTCATGTAATCTAAG	0.353													41	168	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3240621	3240621	+	Silent	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:3240621T>C	uc004crg.3	-	5	3262	c.3105A>G	c.(3103-3105)CAA>CAG	p.Q1035Q		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1035						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CTGTCAGTCCTTGTAGATGTG	0.448													45	166	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3241209	3241209	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:3241209T>A	uc004crg.3	-	5	2674	c.2517A>T	c.(2515-2517)GAA>GAT	p.E839D		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	839						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CTGAGGATTCTTCAGCACTGG	0.488													25	109	---	---	---	---	PASS
NLGN4X	57502	broad.mit.edu	37	X	6069167	6069167	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:6069167A>T	uc010ndh.2	-	2	842	c.341T>A	c.(340-342)CTG>CAG	p.L114Q	NLGN4X_uc004crp.2_Missense_Mutation_p.L114Q|NLGN4X_uc004crq.2_Missense_Mutation_p.L114Q|NLGN4X_uc010ndi.2_Missense_Mutation_p.L114Q|NLGN4X_uc004crr.2_Missense_Mutation_p.L114Q|NLGN4X_uc010ndj.2_Missense_Mutation_p.L114Q	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4 precursor	114	Extracellular (Potential).				brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4						TCTCTCATCCAGGTGCTGGGG	0.527													30	141	---	---	---	---	PASS
SHROOM2	357	broad.mit.edu	37	X	9905624	9905624	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:9905624G>C	uc004csu.1	+	7	4128	c.4038G>C	c.(4036-4038)TTG>TTC	p.L1346F	SHROOM2_uc004csv.2_Missense_Mutation_p.L181F|SHROOM2_uc011mic.1_Missense_Mutation_p.L181F|SHROOM2_uc004csw.1_Missense_Mutation_p.L181F	NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	1346	ASD2.				apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8		Hepatocellular(5;0.000888)				CTATGGACTTGATGGAAGGCA	0.557													15	44	---	---	---	---	PASS
TCEANC	170082	broad.mit.edu	37	X	13681157	13681157	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:13681157G>A	uc004cvk.2	+	2	760	c.530G>A	c.(529-531)TGC>TAC	p.C177Y	TCEANC_uc010nee.1_Missense_Mutation_p.C177Y|TCEANC_uc010nef.1_Missense_Mutation_p.C177Y|TCEANC_uc010neg.1_Missense_Mutation_p.C207Y|TCEANC_uc004cvl.2_RNA	NM_152634	NP_689847	Q8N8B7	TEANC_HUMAN	TFIIS central domain-containing protein 1	177	TFIIS central.				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			pancreas(1)	1						AGAACTAAATGCATAGAGCTT	0.428													29	138	---	---	---	---	PASS
CDKL5	6792	broad.mit.edu	37	X	18622327	18622327	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:18622327G>A	uc004cym.2	+	12	1536	c.1283G>A	c.(1282-1284)GGC>GAC	p.G428D	CDKL5_uc004cyn.2_Missense_Mutation_p.G428D	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	428					neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)					CCTTCAGAAGGCCCAGGGACA	0.448													33	161	---	---	---	---	PASS
CXorf23	256643	broad.mit.edu	37	X	19947938	19947938	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:19947938G>C	uc004czp.2	-	10	1984	c.1984C>G	c.(1984-1986)CAT>GAT	p.H662D	CXorf23_uc010nfn.2_RNA|CXorf23_uc011mjg.1_Intron|CXorf23_uc004czo.2_Missense_Mutation_p.H641D	NM_198279	NP_938020	A2AJT9	CX023_HUMAN	hypothetical protein LOC256643	691						mitochondrion				lung(1)|skin(1)	2						CTGAACTTATGAGTGATAAAT	0.353													43	223	---	---	---	---	PASS
KLHL15	80311	broad.mit.edu	37	X	24024735	24024735	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:24024735C>T	uc004dba.3	-	3	332	c.76G>A	c.(76-78)GAG>AAG	p.E26K		NM_030624	NP_085127	Q96M94	KLH15_HUMAN	kelch-like 15	26										ovary(1)|breast(1)	2						AATCCCTCCTCATACAGTGCT	0.468													7	63	---	---	---	---	PASS
POLA1	5422	broad.mit.edu	37	X	24761436	24761436	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:24761436C>A	uc004dbl.2	+	23	2561	c.2538C>A	c.(2536-2538)GAC>GAA	p.D846E	SCARNA23_uc004dbo.1_5'Flank	NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	846					cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	TGGTTTTGGACCCCAAAGTTG	0.383													10	51	---	---	---	---	PASS
POLA1	5422	broad.mit.edu	37	X	24761437	24761437	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:24761437C>A	uc004dbl.2	+	23	2562	c.2539C>A	c.(2539-2541)CCC>ACC	p.P847T	SCARNA23_uc004dbo.1_5'Flank	NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	847					cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	GGTTTTGGACCCCAAAGTTGG	0.383													10	51	---	---	---	---	PASS
IL1RAPL1	11141	broad.mit.edu	37	X	29938208	29938208	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:29938208C>A	uc004dby.2	+	8	1562	c.1054C>A	c.(1054-1056)CGA>AGA	p.R352R		NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	352	Extracellular (Potential).				innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5						CCTTCATAAACGAGGTGAGTG	0.403													21	70	---	---	---	---	PASS
CASK	8573	broad.mit.edu	37	X	41495861	41495861	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:41495861C>T	uc004dfl.3	-	9	931	c.885G>A	c.(883-885)CTG>CTA	p.L295L	CASK_uc004dfk.3_Silent_p.L110L|CASK_uc004dfm.3_Silent_p.L295L|CASK_uc004dfn.3_Silent_p.L295L	NM_003688	NP_003679	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein	295					cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6						TGAATTTCCTCAGCTGCTCTA	0.328													19	108	---	---	---	---	PASS
ELK1	2002	broad.mit.edu	37	X	47496454	47496454	+	Silent	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:47496454C>T	uc004dik.3	-	6	1468	c.1146G>A	c.(1144-1146)CTG>CTA	p.L382L	ELK1_uc010nhv.2_Silent_p.L382L|ELK1_uc010nhw.2_Silent_p.L272L|ELK1_uc004dil.3_Intron	NM_001114123	NP_001107595	P19419	ELK1_HUMAN	ELK1 protein	382	Sufficient for interaction with MAD2L2.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						CAATGGGACTCAGGGTGCTCC	0.602													10	31	---	---	---	---	PASS
SSX4	6759	broad.mit.edu	37	X	48270302	48270302	+	Missense_Mutation	SNP	G	C	C	rs143022814	byFrequency	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:48270302G>C	uc004djh.1	-	3	133	c.75C>G	c.(73-75)TTC>TTG	p.F25L	SSX4_uc004dji.1_Missense_Mutation_p.F25L	NM_001034832	NP_001030004	O60224	SSX4_HUMAN	synovial sarcoma, X breakpoint 4B isoform a	25	KRAB-related.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding		SS18/SSX4(12)	soft_tissue(12)	12						CAATATCATCGAAGGCCTGGA	0.423			T	SS18	synovial sarcoma								20	120	---	---	---	---	PASS
SLC38A5	92745	broad.mit.edu	37	X	48317959	48317959	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:48317959G>T	uc010nid.2	-	16	1458	c.1280C>A	c.(1279-1281)TCT>TAT	p.S427Y	SLC38A5_uc004djk.3_Missense_Mutation_p.S376Y	NM_033518	NP_277053	Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	427	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane				ovary(3)	3						CTCCACCTCAGAGGGTACAAT	0.567													4	18	---	---	---	---	PASS
GATA1	2623	broad.mit.edu	37	X	48652236	48652236	+	Nonsense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:48652236C>T	uc004dkq.3	+	6	998	c.907C>T	c.(907-909)CAG>TAG	p.Q303*		NM_002049	NP_002040	P15976	GATA1_HUMAN	GATA binding protein 1	303					basophil differentiation|eosinophil differentiation|erythrocyte development|megakaryocyte differentiation|platelet aggregation|platelet formation|positive regulation of anti-apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|regulation of glycoprotein biosynthetic process|transcription from RNA polymerase II promoter	nuclear membrane|nucleolus|nucleoplasm	C2H2 zinc finger domain binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(246)|lung(2)	248						GGATGGTATTCAGACTCGAAA	0.572			Mis|F		megakaryoblastic leukemia of Downs Syndrome								4	25	---	---	---	---	PASS
BMP15	9210	broad.mit.edu	37	X	50658840	50658840	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:50658840C>T	uc011mnw.1	+	2	412	c.412C>T	c.(412-414)CGC>TGC	p.R138C		NM_005448	NP_005439	O95972	BMP15_HUMAN	bone morphogenetic protein 15 precursor	138			R -> H (in POF4; leads to marked reduction of mature protein production; does not generate a complete recovery of wild-type activity in granulosa cell line transfected with defective mutant and with equal amount of wild-type protein).		female gamete generation|granulosa cell development|ovarian follicle development	extracellular space	cytokine activity|growth factor activity			ovary(2)	2	Ovarian(276;0.236)					TGTGGTTTACCGCCATCATCT	0.507													21	65	---	---	---	---	PASS
WNK3	65267	broad.mit.edu	37	X	54334465	54334465	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:54334465C>T	uc004dtd.1	-	5	1418	c.979G>A	c.(979-981)GAA>AAA	p.E327K	WNK3_uc004dtc.1_Missense_Mutation_p.E327K	NM_001002838	NP_001002838	Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3 isoform 2	327	Protein kinase.				intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11						TCTACGGATTCATCATAGTGT	0.403													20	57	---	---	---	---	PASS
ZXDA	7789	broad.mit.edu	37	X	57935958	57935958	+	Silent	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:57935958G>T	uc004dve.2	-	1	1110	c.897C>A	c.(895-897)CCC>CCA	p.P299P		NM_007156	NP_009087	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	299	Required for interaction with ZXDC.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						GGCATTTGAAGGGCCTCTGGC	0.632													5	21	---	---	---	---	PASS
OPHN1	4983	broad.mit.edu	37	X	67316832	67316832	+	Silent	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:67316832G>A	uc004dww.3	-	19	1860	c.1566C>T	c.(1564-1566)TCC>TCT	p.S522S	OPHN1_uc011mpg.1_Silent_p.S522S	NM_002547	NP_002538	O60890	OPHN1_HUMAN	oligophrenin 1	522	Rho-GAP.				axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2						CTCCCATGTTGGAGGGGGTCA	0.473													20	70	---	---	---	---	PASS
ARR3	407	broad.mit.edu	37	X	69498434	69498434	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:69498434G>T	uc004dyb.2	+	12	916	c.848G>T	c.(847-849)GGC>GTC	p.G283V	ARR3_uc004dya.2_Missense_Mutation_p.G283V	NM_004312	NP_004303	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	283					signal transduction|visual perception	cytoplasm|soluble fraction				large_intestine(2)|ovary(2)	4						CAGAAACGGGGCCTGGCACTG	0.498													9	58	---	---	---	---	PASS
KIF4A	24137	broad.mit.edu	37	X	69561721	69561721	+	Missense_Mutation	SNP	A	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:69561721A>T	uc004dyg.2	+	11	1333	c.1206A>T	c.(1204-1206)TTA>TTT	p.L402F	KIF4A_uc010nkw.2_Missense_Mutation_p.L402F|KIF4A_uc004dyf.1_Missense_Mutation_p.L402F	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	402	Potential.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4						ATGAAAAATTAAGTCGTGGTC	0.413													21	125	---	---	---	---	PASS
ZMYM3	9203	broad.mit.edu	37	X	70472625	70472625	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:70472625C>T	uc004dzh.1	-	2	568	c.481G>A	c.(481-483)GAG>AAG	p.E161K	BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Missense_Mutation_p.E161K|ZMYM3_uc004dzj.1_Missense_Mutation_p.E161K|ZMYM3_uc011mpu.1_5'Flank|ZMYM3_uc004dzk.3_Missense_Mutation_p.E161K|ZMYM3_uc004dzl.3_Missense_Mutation_p.E161K|ZMYM3_uc004dzm.3_Missense_Mutation_p.E161K	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	161					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)					GAGGTGGTCTCCTCCTCTTCA	0.587													15	49	---	---	---	---	PASS
ZNF711	7552	broad.mit.edu	37	X	84525778	84525778	+	Missense_Mutation	SNP	G	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:84525778G>C	uc004eeo.2	+	9	1577	c.1230G>C	c.(1228-1230)ATG>ATC	p.M410I	ZNF711_uc004eep.2_Missense_Mutation_p.M410I|ZNF711_uc004eeq.2_Missense_Mutation_p.M456I|ZNF711_uc011mqy.1_Missense_Mutation_p.M9I	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	410					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4						ATCATTTAATGAGAAAAAAAT	0.358													9	35	---	---	---	---	PASS
ZNF711	7552	broad.mit.edu	37	X	84526676	84526676	+	Missense_Mutation	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:84526676G>A	uc004eeo.2	+	9	2475	c.2128G>A	c.(2128-2130)GAA>AAA	p.E710K	ZNF711_uc004eep.2_Missense_Mutation_p.E710K|ZNF711_uc004eeq.2_Missense_Mutation_p.E756K|ZNF711_uc011mqy.1_Missense_Mutation_p.E309K	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	710	C2H2-type 11.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4						TGAGTATTGTGAATACAGCAC	0.378													25	97	---	---	---	---	PASS
GPRASP1	9737	broad.mit.edu	37	X	101908955	101908955	+	Silent	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:101908955C>A	uc004ejj.3	+	5	915	c.114C>A	c.(112-114)CCC>CCA	p.P38P	GPRASP1_uc004eji.3_Silent_p.P38P|GPRASP1_uc010nod.2_Silent_p.P38P	NM_014710	NP_055525	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting	38						cytoplasm	protein binding			ovary(1)|lung(1)	2						TGGTCAGACCCAAGGTTAGGA	0.537													38	242	---	---	---	---	PASS
ALG13	79868	broad.mit.edu	37	X	110951368	110951368	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:110951368C>A	uc011msy.1	+	4	531	c.497C>A	c.(496-498)TCC>TAC	p.S166Y	ALG13_uc011msw.1_Missense_Mutation_p.S88Y|ALG13_uc011msx.1_Missense_Mutation_p.S62Y|ALG13_uc011msz.1_Missense_Mutation_p.S88Y|ALG13_uc011mta.1_Missense_Mutation_p.S62Y|ALG13_uc011mtb.1_Missense_Mutation_p.S62Y			Q9NP73	ALG13_HUMAN	SubName: Full=Asparagine-linked glycosylation 13 homolog (S. cerevisiae);	166					dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	carbohydrate binding|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity			lung(1)	1						GGGCTGCTTTCCGGATACCTG	0.537													14	56	---	---	---	---	PASS
ZCCHC16	340595	broad.mit.edu	37	X	111698022	111698022	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:111698022T>A	uc004epo.1	+	3	507	c.66T>A	c.(64-66)AAT>AAA	p.N22K		NM_001004308	NP_001004308	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	22							nucleic acid binding|zinc ion binding			ovary(1)	1						AGGCAGAGAATCTGATTCTGC	0.498													26	117	---	---	---	---	PASS
DOCK11	139818	broad.mit.edu	37	X	117749672	117749672	+	Missense_Mutation	SNP	A	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:117749672A>C	uc004eqp.2	+	30	3353	c.3290A>C	c.(3289-3291)CAA>CCA	p.Q1097P	DOCK11_uc004eqq.2_Missense_Mutation_p.Q863P	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1097					blood coagulation	cytosol	GTP binding			ovary(3)	3						CAGCGGGTTCAAGGCATGTAT	0.363													9	37	---	---	---	---	PASS
KIAA1210	57481	broad.mit.edu	37	X	118222335	118222335	+	Missense_Mutation	SNP	G	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:118222335G>T	uc004era.3	-	11	2858	c.2858C>A	c.(2857-2859)CCA>CAA	p.P953Q		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	953										ovary(4)|skin(1)	5						GTTCACCCATGGCTGGAAAGG	0.483													14	62	---	---	---	---	PASS
GRIA3	2892	broad.mit.edu	37	X	122598715	122598715	+	Splice_Site	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:122598715G>A	uc004etq.3	+	14	2370	c.2077_splice	c.e14-1	p.R693_splice	GRIA3_uc004etr.3_Splice_Site_p.R693_splice|GRIA3_uc004ets.3_Splice_Site	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)	CTTTGGTGCAGAGATCCAAAA	0.373													17	131	---	---	---	---	PASS
FAM127B	26071	broad.mit.edu	37	X	134186115	134186115	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:134186115C>T	uc004eyf.2	-	1	107	c.24G>A	c.(22-24)ATG>ATA	p.M8I	FAM127B_uc004eyg.3_Missense_Mutation_p.M8I	NM_001078172	NP_001071640	Q9BWD3	F127B_HUMAN	family with sequence similarity 127, member B	8											0	Acute lymphoblastic leukemia(192;0.000127)					GGAGGGCCTTCATCAGCTGCA	0.706													6	54	---	---	---	---	PASS
SLC9A6	10479	broad.mit.edu	37	X	135080640	135080640	+	Splice_Site	SNP	G	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:135080640G>A	uc004ezj.2	+	4	584	c.508_splice	c.e4-1	p.R170_splice	SLC9A6_uc004ezk.2_Splice_Site_p.R202_splice|SLC9A6_uc011mvx.1_Splice_Site_p.R150_splice	NM_006359	NP_006350	Q92581	SL9A6_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TTTTTTGTCAGAGACATTTTT	0.299													7	81	---	---	---	---	PASS
MAP7D3	79649	broad.mit.edu	37	X	135312673	135312673	+	Missense_Mutation	SNP	T	C	C			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:135312673T>C	uc004ezt.2	-	10	1712	c.1621A>G	c.(1621-1623)AAA>GAA	p.K541E	MAP7D3_uc004ezs.2_Missense_Mutation_p.K505E|MAP7D3_uc011mwc.1_Missense_Mutation_p.K523E|MAP7D3_uc010nsa.1_Missense_Mutation_p.K499E	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	541						cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)					GGCATTATTTTATAAGGAAAA	0.373													34	173	---	---	---	---	PASS
AFF2	2334	broad.mit.edu	37	X	148037466	148037466	+	Missense_Mutation	SNP	C	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:148037466C>A	uc004fcp.2	+	11	2370	c.1891C>A	c.(1891-1893)CCC>ACC	p.P631T	AFF2_uc004fcq.2_Missense_Mutation_p.P621T|AFF2_uc004fcr.2_Missense_Mutation_p.P592T|AFF2_uc011mxb.1_Missense_Mutation_p.P596T|AFF2_uc004fcs.2_Missense_Mutation_p.P598T|AFF2_uc011mxc.1_Missense_Mutation_p.P272T	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	631					brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					GAAAAAACAGCCCAAAAAAGT	0.433													23	129	---	---	---	---	PASS
MAMLD1	10046	broad.mit.edu	37	X	149638334	149638334	+	Nonsense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:149638334T>A	uc004fee.1	+	3	565	c.489T>A	c.(487-489)TAT>TAA	p.Y163*	MAMLD1_uc011mxt.1_Nonsense_Mutation_p.Y125*|MAMLD1_uc011mxu.1_Nonsense_Mutation_p.Y138*|MAMLD1_uc011mxv.1_Nonsense_Mutation_p.Y138*|MAMLD1_uc011mxw.1_Nonsense_Mutation_p.Y90*	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	163					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)					TTCCTTACTATGAGAAAATCA	0.478													26	85	---	---	---	---	PASS
HCFC1	3054	broad.mit.edu	37	X	153220573	153220573	+	Missense_Mutation	SNP	T	A	A			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:153220573T>A	uc004fjp.2	-	17	3805	c.3277A>T	c.(3277-3279)ACC>TCC	p.T1093S		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	1093	HCF repeat 2.			T->A: Inactivates cleavage at HCF repeat.	cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					gaggtggcggtggtggcggtg	0.537													10	23	---	---	---	---	PASS
LAGE3	8270	broad.mit.edu	37	X	153706634	153706634	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:153706634C>T	uc004fln.1	-	2	647	c.305G>A	c.(304-306)AGG>AAG	p.R102K		NM_006014	NP_006005	Q14657	LAGE3_HUMAN	L antigen family, member 3	102							protein binding				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GACCAGGATCCTGCCACTCAC	0.627													11	112	---	---	---	---	PASS
LAGE3	8270	broad.mit.edu	37	X	153706719	153706719	+	Missense_Mutation	SNP	C	T	T			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chrX:153706719C>T	uc004fln.1	-	2	562	c.220G>A	c.(220-222)GAG>AAG	p.E74K		NM_006014	NP_006005	Q14657	LAGE3_HUMAN	L antigen family, member 3	74							protein binding				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ATTTCCGCCTCCAAGGGGGTC	0.592													7	118	---	---	---	---	PASS
SOS1	6654	broad.mit.edu	37	2	39222389	39222390	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:39222389_39222390delTC	uc002rrk.3	-	20	3261_3262	c.3220_3221delGA	c.(3220-3222)GAAfs	p.E1074fs	SOS1_uc002rrj.3_Frame_Shift_Del_p.E688fs	NM_005633	NP_005624	Q07889	SOS1_HUMAN	son of sevenless homolog 1	1074					apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)				TGCTGTACTTTCTGTTTCACTT	0.475									Noonan_syndrome				129	77	---	---	---	---	
MYO7B	4648	broad.mit.edu	37	2	128366337	128366337	+	Frame_Shift_Del	DEL	A	-	-			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:128366337delA	uc002top.2	+	22	2751	c.2698delA	c.(2698-2700)AAGfs	p.K900fs		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	900						apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		TCTCCCTGCCAAGAAGCGCAG	0.652													28	18	---	---	---	---	
HDLBP	3069	broad.mit.edu	37	2	242176058	242176059	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr2:242176058_242176059delTT	uc002waz.2	-	21	3103_3104	c.2875_2876delAA	c.(2875-2877)AAGfs	p.K959fs	HDLBP_uc002wba.2_Frame_Shift_Del_p.K959fs|HDLBP_uc002wbb.2_Frame_Shift_Del_p.K911fs	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	959	KH 11.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		AGCCTCACACTTTTCTTTCCGG	0.614													67	57	---	---	---	---	
RECQL5	9400	broad.mit.edu	37	17	73626918	73626919	+	Splice_Site	INS	-	TG	TG	rs142406301	by1000genomes	TCGA-39-5031-01A-01D-1441-08	TCGA-39-5031-11A-01D-1441-08									Somatic	Phase_I	Capture				Illumina GAIIx	3eab4096-8e8e-459d-a2bb-6ef03f414315	b4d9f9a2-e65f-443b-866c-50bb8e491be7	g.chr17:73626918_73626919insTG	uc010dgl.2	-	12	1742	c.1586_splice	c.e12-1	p.D529_splice	RECQL5_uc010dgk.2_Splice_Site_p.D502_splice|RECQL5_uc002jot.3_5'Flank|LOC643008_uc002jow.2_5'Flank	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1						DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			CAGTTCTCATCTGTGGGGGGGG	0.644								Other_identified_genes_with_known_or_suspected_DNA_repair_function					3	6	---	---	---	---