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
ACAP3	116983	broad.mit.edu	37	1	1233244	1233244	+	Silent	SNP	G	A	A	rs144855997		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:1233244G>A	uc001aeb.2	-	14	1160	c.1086C>T	c.(1084-1086)ATC>ATT	p.I362I	ACAP3_uc001ady.2_Silent_p.I92I|ACAP3_uc001aea.2_Silent_p.I320I	NM_030649	NP_085152	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH	362	PH.				filopodium assembly|regulation of ARF GTPase activity|signal transduction		ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding				0						AGGCGGAGGCGATGCTGGCCT	0.682													10	5	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34052159	34052159	+	Silent	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:34052159C>G	uc001bxn.1	-	47	7031	c.7002G>C	c.(7000-7002)CTG>CTC	p.L2334L	CSMD2_uc001bxm.1_Silent_p.L2332L	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2334	Sushi 13.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTTTGCAGGTCAGAATTTCAT	0.493													13	25	---	---	---	---	PASS
EPHA10	284656	broad.mit.edu	37	1	38187350	38187350	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:38187350C>A	uc009vvi.2	-	11	2214	c.2128G>T	c.(2128-2130)GAG>TAG	p.E710*	EPHA10_uc001cbt.2_5'Flank|EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	710	Cytoplasmic (Potential).|Protein kinase.					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity	p.L710M(1)		breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACAACGCCCTCCAGCCGCACG	0.652													8	10	---	---	---	---	PASS
ZNF684	127396	broad.mit.edu	37	1	41006273	41006273	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:41006273C>A	uc001cft.1	+	3	282	c.31C>A	c.(31-33)CAG>AAG	p.Q11K		NM_152373	NP_689586	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	11	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			AGTGACATTCCAGGATGTGGC	0.428													5	55	---	---	---	---	PASS
EPS15	2060	broad.mit.edu	37	1	51871588	51871588	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:51871588G>T	uc001csq.1	-	16	1758	c.1666C>A	c.(1666-1668)CAG>AAG	p.Q556K	EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_Missense_Mutation_p.Q242K	NM_001981	NP_001972	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway	556					cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2						GGAGATTCCTGGTGTATGGGC	0.423			T	MLL	ALL								5	69	---	---	---	---	PASS
PARS2	25973	broad.mit.edu	37	1	55224198	55224198	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:55224198C>G	uc001cxy.2	-	2	720	c.637G>C	c.(637-639)GAC>CAC	p.D213H		NM_152268	NP_689481	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase (mitochondrial)(putative)	213					prolyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|proline-tRNA ligase activity			ovary(2)	2					L-Proline(DB00172)	GGGGAGGAGTCAAAGGTGTAC	0.557													21	28	---	---	---	---	PASS
LEPROT	54741	broad.mit.edu	37	1	65895678	65895678	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:65895678G>T	uc001dcf.2	+	3	315	c.226G>T	c.(226-228)GGA>TGA	p.G76*	LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc001dci.2_Intron|LEPR_uc009waq.2_Intron|LEPROT_uc009wap.2_Nonsense_Mutation_p.G85*	NM_017526	NP_059996	O15243	OBRG_HUMAN	leptin receptor gene-related protein	76	Helical; (Potential).					endosome membrane|Golgi membrane|integral to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		CTTCACTACTGGAATTGTTGT	0.448													6	147	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	97547958	97547958	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:97547958C>A	uc001drv.2	-	22	2972	c.2835G>T	c.(2833-2835)GTG>GTT	p.V945V		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	945	4Fe-4S ferredoxin-type 2.				'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	CAATCATAGCCACAACTTGCT	0.393													5	48	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118548056	118548056	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:118548056G>T	uc001ehk.2	-	32	4825	c.4757C>A	c.(4756-4758)CCT>CAT	p.P1586H		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1586						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GTTTCCCTCAGGATCCAGAAC	0.438													5	80	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118635898	118635898	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:118635898T>A	uc001ehk.2	-	8	1122	c.1054A>T	c.(1054-1056)ATG>TTG	p.M352L		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	352						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ATGTCATACATCAAGCAGGCA	0.373													10	13	---	---	---	---	PASS
PPIAL4G	644591	broad.mit.edu	37	1	143767766	143767766	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:143767766T>A	uc001ejt.2	-	1	116	c.83A>T	c.(82-84)AAG>ATG	p.K28M		NM_001123068	NP_001116540	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like	28	PPIase cyclophilin-type.				protein folding	cytoplasm	peptidyl-prolyl cis-trans isomerase activity				0						CTTTGGAATCTTGTCTGCAAA	0.468													29	199	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145532206	145532206	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:145532206G>A	uc001eoa.2	+	8	926	c.850G>A	c.(850-852)GAG>AAG	p.E284K	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.E153K|ITGA10_uc009wiw.2_Missense_Mutation_p.E141K|ITGA10_uc010oyw.1_Missense_Mutation_p.E229K	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	284	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TGATGGAGAGGAGCTTCCTGC	0.567													12	49	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152281652	152281652	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:152281652G>T	uc001ezu.1	-	3	5746	c.5710C>A	c.(5710-5712)CAA>AAA	p.Q1904K		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1904	Ser-rich.|Filaggrin 11.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTGATGATTGTCCCTGGCCC	0.587									Ichthyosis				51	174	---	---	---	---	PASS
INSRR	3645	broad.mit.edu	37	1	156823678	156823678	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:156823678A>G	uc010pht.1	-	2	757	c.503T>C	c.(502-504)GTG>GCG	p.V168A	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|INSRR_uc009wsj.1_Missense_Mutation_p.V168A	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	168					protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1)	20	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTTGTTGCCCACGATGTGGTT	0.642													5	20	---	---	---	---	PASS
C1orf92	149499	broad.mit.edu	37	1	156899076	156899076	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:156899076C>T	uc001fqm.2	+	10	1173	c.1001C>T	c.(1000-1002)TCC>TTC	p.S334F	C1orf92_uc001fql.2_Missense_Mutation_p.S119F	NM_144702	NP_653303	Q8N4P6	LRC71_HUMAN	hypothetical protein LOC149499	334											0	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCACAGCCCTCCTCCTCTCGA	0.552													4	19	---	---	---	---	PASS
ARHGAP30	257106	broad.mit.edu	37	1	161039355	161039355	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:161039355G>A	uc001fxl.2	-	1	406	c.60C>T	c.(58-60)TGC>TGT	p.C20C	ARHGAP30_uc001fxk.2_Silent_p.C20C|ARHGAP30_uc001fxm.2_5'UTR|ARHGAP30_uc009wtx.2_5'UTR|ARHGAP30_uc001fxn.1_5'UTR	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	20	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|upper_aerodigestive_tract(1)	3	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CCTGCAAGTCGCACCCAAAAA	0.637													22	43	---	---	---	---	PASS
FAM5B	57795	broad.mit.edu	37	1	177199026	177199026	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:177199026G>A	uc001glf.2	+	2	326	c.14G>A	c.(13-15)TGT>TAT	p.C5Y		NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	5						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						AGGTGGCAGTGTGGCACTCGG	0.652													6	17	---	---	---	---	PASS
TDRD5	163589	broad.mit.edu	37	1	179659920	179659920	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:179659920G>T	uc001gnf.1	+	17	3038	c.2788G>T	c.(2788-2790)GAC>TAC	p.D930Y	TDRD5_uc010pnp.1_Missense_Mutation_p.D984Y|TDRD5_uc001gnh.1_Missense_Mutation_p.D485Y	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	930					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						AGAATCTGTAGACCAGCTGTC	0.443													8	41	---	---	---	---	PASS
CDC73	79577	broad.mit.edu	37	1	193121513	193121513	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:193121513C>A	uc001gtb.2	+	10	1154	c.911C>A	c.(910-912)ACG>AAG	p.T304K		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	304					cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						TTCGTAGAAACGGAAGGCTTC	0.338									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				3	13	---	---	---	---	PASS
PTPRC	5788	broad.mit.edu	37	1	198678943	198678943	+	Silent	SNP	A	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:198678943A>C	uc001gur.1	+	11	1335	c.1155A>C	c.(1153-1155)ACA>ACC	p.T385T	PTPRC_uc001gus.1_Silent_p.T337T|PTPRC_uc001gut.1_Silent_p.T224T|PTPRC_uc009wzf.1_Silent_p.T273T|PTPRC_uc010ppg.1_Silent_p.T321T	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	385	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12						TTATTAAAACAGATTTTGGGA	0.269													18	39	---	---	---	---	PASS
ZNF281	23528	broad.mit.edu	37	1	200377463	200377463	+	Silent	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:200377463T>C	uc001gve.2	-	2	1478	c.1371A>G	c.(1369-1371)GAA>GAG	p.E457E	ZNF281_uc001gvf.1_Silent_p.E457E|ZNF281_uc001gvg.1_Silent_p.E421E	NM_012482	NP_036614	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	457					negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)	2						TCTTCTGCAGTTCATCTATTC	0.373													19	56	---	---	---	---	PASS
KCNH1	3756	broad.mit.edu	37	1	210856671	210856671	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:210856671C>A	uc001hib.2	-	11	3092	c.2922G>T	c.(2920-2922)TCG>TCT	p.S974S	KCNH1_uc001hic.2_Silent_p.S947S	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	974	Cytoplasmic (Potential).				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		ACTGTGGCCTCGATATTTCAA	0.438													5	123	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248202064	248202064	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr1:248202064C>A	uc001idw.2	+	1	591	c.495C>A	c.(493-495)ATC>ATA	p.I165I	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CACTCTGTATCCCATATTGCA	0.433													33	65	---	---	---	---	PASS
THUMPD2	80745	broad.mit.edu	37	2	39963957	39963957	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:39963957G>T	uc002rru.2	-	10	1467	c.1430C>A	c.(1429-1431)CCA>CAA	p.P477Q	THUMPD2_uc002rrv.2_RNA|THUMPD2_uc010ynt.1_Missense_Mutation_p.P368Q	NM_025264	NP_079540	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	477							methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)				GCATTCCACTGGTACCAAGGA	0.438													5	72	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61441365	61441365	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:61441365G>T	uc002sbe.2	-	68	8534	c.8512C>A	c.(8512-8514)CAT>AAT	p.H2838N		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2838					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)			TGATCATCATGGTCAGCAAGG	0.478													6	69	---	---	---	---	PASS
REG1A	5967	broad.mit.edu	37	2	79350303	79350303	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:79350303G>A	uc002snz.2	+	6	566	c.463G>A	c.(463-465)GAA>AAA	p.E155K	REG1A_uc010ysd.1_Missense_Mutation_p.E155K	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor	155	C-type lectin.				positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						TGTGCCTTGTGAAGACAAGTT	0.413													6	51	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141291599	141291599	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:141291599C>A	uc002tvj.1	-	47	8725	c.7753G>T	c.(7753-7755)GAT>TAT	p.D2585Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2585	Extracellular (Potential).|LDL-receptor class A 12.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCTTTACAATCTAATTCATCA	0.418										TSP Lung(27;0.18)			8	33	---	---	---	---	PASS
RBMS1	5937	broad.mit.edu	37	2	161141535	161141535	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:161141535G>T	uc002ubo.2	-	8	1221	c.777C>A	c.(775-777)TAC>TAA	p.Y259*	RBMS1_uc002ubj.2_Nonsense_Mutation_p.Y223*|RBMS1_uc002ubk.2_Nonsense_Mutation_p.Y223*|RBMS1_uc002ubl.2_Nonsense_Mutation_p.Y254*|RBMS1_uc002ubn.2_Nonsense_Mutation_p.Y256*|RBMS1_uc002ubi.3_Nonsense_Mutation_p.Y256*|RBMS1_uc002ubm.2_Nonsense_Mutation_p.Y226*|RBMS1_uc002ubp.2_Nonsense_Mutation_p.Y259*|RBMS1_uc010fox.2_Nonsense_Mutation_p.Y259*	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting	259					DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0						TAGTTGGGTCGTAAGTAAGTG	0.318													26	29	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168108054	168108054	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:168108054G>T	uc002udx.2	+	8	10170	c.10152G>T	c.(10150-10152)ACG>ACT	p.T3384T	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.T3209T|XIRP2_uc010fpq.2_Silent_p.T3162T|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	3209					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						TAGGAAACACGAGTTTTACAG	0.383													21	80	---	---	---	---	PASS
ABCB11	8647	broad.mit.edu	37	2	169780238	169780238	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:169780238G>T	uc002ueo.1	-	28	3986	c.3860C>A	c.(3859-3861)GCT>GAT	p.A1287D	ABCB11_uc010zda.1_Missense_Mutation_p.A705D|ABCB11_uc010zdb.1_Missense_Mutation_p.A763D	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	1287	Cytoplasmic (Potential).|ABC transporter 2.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	TGCCATGACAGCAATGATATC	0.532													10	61	---	---	---	---	PASS
CDCA7	83879	broad.mit.edu	37	2	174230295	174230295	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:174230295G>A	uc002uid.1	+	6	904	c.773G>A	c.(772-774)CGA>CAA	p.R258Q	CDCA7_uc002uic.1_Missense_Mutation_p.R337Q|CDCA7_uc010zej.1_Missense_Mutation_p.R293Q|CDCA7_uc010zek.1_Missense_Mutation_p.R216Q	NM_145810	NP_665809	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7 isoform 2	258	Mediates transcriptional activity.				regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.116)			AGCAATTCTCGAGAGAAGATA	0.478													7	33	---	---	---	---	PASS
TTC30A	92104	broad.mit.edu	37	2	178482680	178482680	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:178482680C>A	uc002ulo.2	-	1	1015	c.750G>T	c.(748-750)CTG>CTT	p.L250L		NM_152275	NP_689488	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	250					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			AGGCTTCCACCAGAGCAGTCT	0.537													5	73	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179411391	179411391	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:179411391A>T	uc010zfg.1	-	290	87284	c.87060T>A	c.(87058-87060)AAT>AAA	p.N29020K	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.N22715K|TTN_uc010zfi.1_Missense_Mutation_p.N22648K|TTN_uc010zfj.1_Missense_Mutation_p.N22523K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	29947							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)			CGCCTGCTGCATTCTTGGCTA	0.438													11	36	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179457260	179457260	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:179457260G>A	uc010zfg.1	-	250	51992	c.51768C>T	c.(51766-51768)GAC>GAT	p.D17256D	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.D10951D|TTN_uc010zfi.1_Silent_p.D10884D|TTN_uc010zfj.1_Silent_p.D10759D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18183							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)			GAGCATCTCTGTCTTCTTTTT	0.388													19	130	---	---	---	---	PASS
HECW2	57520	broad.mit.edu	37	2	197090571	197090571	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:197090571A>T	uc002utm.1	-	23	4124	c.3941T>A	c.(3940-3942)CTT>CAT	p.L1314H	HECW2_uc002utl.1_Missense_Mutation_p.L958H	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	1314	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						TGCAAGACCAAGGATCCTACC	0.423													5	33	---	---	---	---	PASS
NRP2	8828	broad.mit.edu	37	2	206562429	206562429	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:206562429G>T	uc002vaw.2	+	2	1026	c.235G>T	c.(235-237)GAG>TAG	p.E79*	NRP2_uc002vat.2_Nonsense_Mutation_p.E79*|NRP2_uc002vau.2_Nonsense_Mutation_p.E79*|NRP2_uc002vav.2_Nonsense_Mutation_p.E79*|NRP2_uc002vax.2_Nonsense_Mutation_p.E79*|NRP2_uc002vay.2_Nonsense_Mutation_p.E79*|NRP2_uc010fud.2_Nonsense_Mutation_p.E79*	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	79	Extracellular (Potential).|CUB 1.				angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4						CTTTGAAATCGAGAAGCACGA	0.552													9	289	---	---	---	---	PASS
UNC80	285175	broad.mit.edu	37	2	210654270	210654270	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:210654270C>A	uc010zjc.1	+	6	819	c.739C>A	c.(739-741)CCT>ACT	p.P247T	UNC80_uc002vdj.1_Missense_Mutation_p.P247T	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	247						integral to membrane					0						GAGAAGTTCTCCTATCAACAG	0.343													20	99	---	---	---	---	PASS
CCDC108	255101	broad.mit.edu	37	2	219869012	219869012	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:219869012C>A	uc002vjl.1	-	33	5301	c.5217G>T	c.(5215-5217)GAG>GAT	p.E1739D	uc010fvz.1_5'Flank|MIR375_hsa-mir-375|MI0000783_5'Flank	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1739						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTTCCCATCCTCCCAGCTGC	0.413													19	61	---	---	---	---	PASS
SPEG	10290	broad.mit.edu	37	2	220309423	220309423	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:220309423G>A	uc010fwg.2	+	2	437	c.437G>A	c.(436-438)CGC>CAC	p.R146H	SPEG_uc002vlm.2_RNA|SPEG_uc010fwh.1_5'UTR|SPEG_uc002vln.1_5'UTR	NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	146					muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GGAACCCAGCGCCTGGAGCTT	0.632													9	37	---	---	---	---	PASS
COL4A4	1286	broad.mit.edu	37	2	227924170	227924170	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:227924170C>A	uc010zlt.1	-	28	2988	c.2334G>T	c.(2332-2334)GTG>GTT	p.V778V		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	778	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TTATCCCTGGCACTCCTGAAA	0.577													25	119	---	---	---	---	PASS
ATG16L1	55054	broad.mit.edu	37	2	234202917	234202917	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:234202917C>A	uc002vty.2	+	18	2002	c.1745C>A	c.(1744-1746)GCG>GAG	p.A582E	ATG16L1_uc002vtx.1_Missense_Mutation_p.A419E|ATG16L1_uc002vua.2_Missense_Mutation_p.A563E|ATG16L1_uc002vub.2_Missense_Mutation_p.A440E|ATG16L1_uc002vtz.2_Missense_Mutation_p.A403E|ATG16L1_uc002vud.3_Missense_Mutation_p.A498E	NM_030803	NP_110430	Q676U5	A16L1_HUMAN	APG16 autophagy 16-like isoform 1	582	WD 7.				autophagic vacuole assembly|protein homooligomerization|protein transport	autophagic vacuole|pre-autophagosomal structure membrane	protein binding				0		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		TCCATCAATGCGGTGGCGTGG	0.522													10	43	---	---	---	---	PASS
UGT1A9	54600	broad.mit.edu	37	2	234580705	234580705	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr2:234580705G>T	uc002vus.2	+	1	162	c.125G>T	c.(124-126)AGG>ATG	p.R42M	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Missense_Mutation_p.R42M	NM_021027	NP_066307	O60656	UD19_HUMAN	UDP glycosyltransferase 1 family, polypeptide A9	42					drug metabolic process|flavone metabolic process|negative regulation of fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding			ovary(3)|breast(1)|skin(1)	5		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Entacapone(DB00494)|Etodolac(DB00749)|Indomethacin(DB00328)|Irinotecan(DB00762)|Mycophenolic acid(DB01024)|Oxyphenonium(DB00219)|Propofol(DB00818)|Sorafenib(DB00398)	TTCACCATGAGGTCGGTGGTG	0.552													14	38	---	---	---	---	PASS
HRH1	3269	broad.mit.edu	37	3	11301422	11301422	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:11301422C>A	uc010hdr.2	+	2	1041	c.699C>A	c.(697-699)TCC>TCA	p.S233S	HRH1_uc010hds.2_Silent_p.S233S|HRH1_uc010hdt.2_Silent_p.S233S|HRH1_uc003bwb.3_Silent_p.S233S	NM_001098213	NP_001091683	P35367	HRH1_HUMAN	histamine receptor H1	233	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	CCCTCCCTTCCTTCTCAGAAA	0.537													5	74	---	---	---	---	PASS
TIMP4	7079	broad.mit.edu	37	3	12195893	12195893	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:12195893C>A	uc003bwo.2	-	4	718	c.411G>T	c.(409-411)TGG>TGT	p.W137C	SYN2_uc003bwl.1_Intron|SYN2_uc003bwm.2_Intron|SYN2_uc003bwn.2_Intron	NM_003256	NP_003247	Q99727	TIMP4_HUMAN	tissue inhibitor of metalloproteinase 4	137	NTR.						metal ion binding|metalloendopeptidase inhibitor activity				0						ACAGGTCCTCCCAGGGCTCGA	0.493													39	46	---	---	---	---	PASS
NEK10	152110	broad.mit.edu	37	3	27332856	27332856	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:27332856T>A	uc003cdt.1	-	19	1776	c.1502A>T	c.(1501-1503)GAA>GTA	p.E501V	NEK10_uc003cds.1_5'UTR	NM_199347	NP_955379	Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10 isoform 3	501	Potential.						ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						TTCAATATTTTCAGCAATTTG	0.343													18	25	---	---	---	---	PASS
GOLGA4	2803	broad.mit.edu	37	3	37292888	37292888	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:37292888G>T	uc003cgv.2	+	2	379	c.75G>T	c.(73-75)GCG>GCT	p.A25A	GOLGA4_uc010hgr.1_Silent_p.A25A|GOLGA4_uc003cgw.2_Silent_p.A25A|GOLGA4_uc010hgs.2_Silent_p.A25A|GOLGA4_uc003cgu.1_Silent_p.A25A	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	25					Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						AAATCTAGGCGTCCTCCAATT	0.388													15	19	---	---	---	---	PASS
SMARCC1	6599	broad.mit.edu	37	3	47734751	47734751	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:47734751C>A	uc003crq.2	-	12	1323	c.1205G>T	c.(1204-1206)GGA>GTA	p.G402V	SMARCC1_uc011bbd.1_Missense_Mutation_p.G293V	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated	402					chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		TACAGTTCCTCCTTTAACAGG	0.333													5	59	---	---	---	---	PASS
RBM5	10181	broad.mit.edu	37	3	50151525	50151525	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:50151525A>G	uc003cyg.2	+	19	1908	c.1760A>G	c.(1759-1761)GAG>GGG	p.E587G	RBM5_uc011bdj.1_Missense_Mutation_p.E531G|RBM5_uc011bdk.1_Missense_Mutation_p.E415G|RBM5_uc003cyh.2_Missense_Mutation_p.E44G	NM_005778	NP_005769	P52756	RBM5_HUMAN	RNA binding motif protein 5	587	Required for interaction with U2AF2.				apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCTCTCTTTGAGAAGAAGGTA	0.448													5	52	---	---	---	---	PASS
WNT5A	7474	broad.mit.edu	37	3	55513523	55513523	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:55513523G>T	uc003dhn.2	-	3	528	c.210C>A	c.(208-210)AGC>AGA	p.S70R	WNT5A_uc003dhm.2_Missense_Mutation_p.S55R|WNT5A_uc010hmw.2_Missense_Mutation_p.S55R|WNT5A_uc010hmx.2_Intron	NM_003392	NP_003383	P41221	WNT5A_HUMAN	wingless-type MMTV integration site family,	70					activation of JUN kinase activity|activation of protein kinase B activity|axon guidance|cartilage development|cellular protein localization|cellular response to calcium ion|cellular response to interferon-gamma|cellular response to lipopolysaccharide|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|cervix development|cochlea morphogenesis|convergent extension involved in organogenesis|dopaminergic neuron differentiation|dorsal/ventral axis specification|embryonic digit morphogenesis|embryonic skeletal system development|epithelial cell proliferation involved in mammary gland duct elongation|epithelial to mesenchymal transition|face development|genitalia development|heart looping|hemopoietic stem cell proliferation|keratinocyte differentiation|lateral sprouting involved in mammary gland duct morphogenesis|lens development in camera-type eye|male gonad development|mammary gland branching involved in thelarche|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of mesenchymal cell proliferation|negative regulation of transcription, DNA-dependent|neural tube closure|olfactory bulb interneuron development|optic cup formation involved in camera-type eye development|palate development|positive regulation of angiogenesis|positive regulation of cartilage development|positive regulation of cGMP metabolic process|positive regulation of chemokine biosynthetic process|positive regulation of cytokine secretion involved in immune response|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of macrophage activation|positive regulation of macrophage cytokine production|positive regulation of mesenchymal cell proliferation|positive regulation of neuron projection development|positive regulation of NF-kappaB transcription factor activity|positive regulation of ossification|positive regulation of protein catabolic process|positive regulation of protein kinase C signaling cascade|positive regulation of T cell chemotaxis|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|primitive streak formation|regulation of branching involved in mammary gland duct morphogenesis|somitogenesis|tail morphogenesis|type B pancreatic cell development|urinary bladder development|uterus development|vagina development|Wnt receptor signaling pathway, calcium modulating pathway|wound healing	extracellular space|membrane fraction|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|receptor tyrosine kinase-like orphan receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)		CTGCCAGTTGGCTGCAGAGAG	0.478													17	106	---	---	---	---	PASS
FLNB	2317	broad.mit.edu	37	3	58127599	58127599	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:58127599A>C	uc003djj.2	+	30	5289	c.5124A>C	c.(5122-5124)GAA>GAC	p.E1708D	FLNB_uc010hne.2_Missense_Mutation_p.E1739D|FLNB_uc003djk.2_Missense_Mutation_p.E1708D|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Missense_Mutation_p.E1539D|FLNB_uc003djm.2_Intron	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	1708	Hinge 1 (By similarity).				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CAGATGGGGAAGTCACAGCCG	0.507													24	33	---	---	---	---	PASS
PDZRN3	23024	broad.mit.edu	37	3	73433190	73433190	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:73433190T>C	uc003dpl.1	-	10	2623	c.2527A>G	c.(2527-2529)AGC>GGC	p.S843G	PDZRN3_uc011bgh.1_Missense_Mutation_p.S500G|PDZRN3_uc010hoe.1_Missense_Mutation_p.S541G|PDZRN3_uc011bgf.1_Missense_Mutation_p.S560G|PDZRN3_uc011bgg.1_Missense_Mutation_p.S563G	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	843							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CTCCCGTCGCTGGCTCTCCGC	0.657													11	20	---	---	---	---	PASS
NSUN3	63899	broad.mit.edu	37	3	93813893	93813893	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:93813893C>T	uc003drl.1	+	5	754	c.638C>T	c.(637-639)CCG>CTG	p.P213L		NM_022072	NP_071355	Q9H649	NSUN3_HUMAN	NOL1/NOP2/Sun domain family, member 3	213							methyltransferase activity			skin(1)	1						GTGGATGCTCCGTGTTCAAAT	0.408													12	34	---	---	---	---	PASS
OR5H15	403274	broad.mit.edu	37	3	97887996	97887996	+	Silent	SNP	T	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:97887996T>G	uc011bgu.1	+	1	453	c.453T>G	c.(451-453)GCT>GCG	p.A151A		NM_001005515	NP_001005515	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H,	151	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						CATATATAGCTGGTATTCTTC	0.373													23	22	---	---	---	---	PASS
ALCAM	214	broad.mit.edu	37	3	105250889	105250889	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:105250889C>A	uc003dvx.2	+	4	978	c.438C>A	c.(436-438)CTC>CTA	p.L146L	ALCAM_uc003dvw.1_Silent_p.L146L|ALCAM_uc003dvy.2_Silent_p.L146L|ALCAM_uc011bhh.1_Silent_p.L95L|ALCAM_uc010hpp.2_5'Flank	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	146	Extracellular (Potential).|Ig-like V-type 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3						CACTGTTTCTCGAAACAGAGC	0.348													6	128	---	---	---	---	PASS
LRRC58	116064	broad.mit.edu	37	3	120054684	120054684	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:120054684G>T	uc003edr.2	-	2	713	c.617C>A	c.(616-618)CCT>CAT	p.P206H		NM_001099678	NP_001093148	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	206	LRR 7.										0				GBM - Glioblastoma multiforme(114;0.147)		TGAAAGTTGAGGAGGTATGCT	0.343													6	72	---	---	---	---	PASS
SLC15A2	6565	broad.mit.edu	37	3	121649761	121649761	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:121649761A>G	uc003eep.2	+	18	1781	c.1628A>G	c.(1627-1629)TAT>TGT	p.Y543C	SLC15A2_uc011bjn.1_Missense_Mutation_p.Y512C	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	543					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)	GGTGAAGACTATGGTGTGTCT	0.368													16	41	---	---	---	---	PASS
PARP15	165631	broad.mit.edu	37	3	122353965	122353965	+	Silent	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:122353965C>G	uc003efm.2	+	11	1737	c.1671C>G	c.(1669-1671)CTC>CTG	p.L557L	PARP15_uc003efn.2_Silent_p.L362L|PARP15_uc003efo.1_Silent_p.L304L|PARP15_uc003efp.1_Silent_p.L323L|PARP15_uc011bjt.1_Silent_p.L254L	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	535	PARP catalytic.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)		AGAGACTCCTCTTCCATGGGA	0.418													24	37	---	---	---	---	PASS
C3orf58	205428	broad.mit.edu	37	3	143708453	143708453	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:143708453A>G	uc003evo.2	+	3	1598	c.1063A>G	c.(1063-1065)ACT>GCT	p.T355A	C3orf58_uc011bnl.1_Missense_Mutation_p.T146A	NM_173552	NP_775823	Q8NDZ4	CC058_HUMAN	hypothetical protein LOC205428 isoform a	355						COPI vesicle coat|extracellular region				ovary(1)	1						TGCTCGTGCCACTGTGGACCA	0.433													11	57	---	---	---	---	PASS
GPR171	29909	broad.mit.edu	37	3	150916412	150916412	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:150916412T>C	uc003eyq.3	-	3	1002	c.762A>G	c.(760-762)ATA>ATG	p.I254M	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_013308	NP_037440	O14626	GP171_HUMAN	G protein-coupled receptor 171	254	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGCAATCAGTTATGACTTCTG	0.463													16	51	---	---	---	---	PASS
SCHIP1	29970	broad.mit.edu	37	3	159606697	159606697	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:159606697A>T	uc003fcs.1	+	6	1349	c.1283A>T	c.(1282-1284)CAA>CTA	p.Q428L	SCHIP1_uc003fcq.1_Missense_Mutation_p.Q504L|SCHIP1_uc003fcr.1_Missense_Mutation_p.Q417L|SCHIP1_uc003fct.1_Missense_Mutation_p.Q415L|SCHIP1_uc010hvz.1_Missense_Mutation_p.Q388L|SCHIP1_uc003fcu.1_Missense_Mutation_p.Q185L|SCHIP1_uc003fcv.1_Missense_Mutation_p.Q201L	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1	428	Potential.					cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			GGGCAGCTACAAGTGATAGTC	0.378													6	58	---	---	---	---	PASS
BDH1	622	broad.mit.edu	37	3	197238877	197238877	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:197238877G>A	uc003fxr.2	-	8	1323	c.921C>T	c.(919-921)ACC>ACT	p.T307T	BDH1_uc003fxs.2_Silent_p.T307T|BDH1_uc003fxt.2_Silent_p.T220T|BDH1_uc003fxu.2_Silent_p.T307T	NM_203314	NP_976059	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	307					cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity			ovary(1)	1	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	NADH(DB00157)	GGGTGGTGGCGGTCAGGGCGT	0.562													15	69	---	---	---	---	PASS
TAPT1	202018	broad.mit.edu	37	4	16189952	16189952	+	Silent	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:16189952A>G	uc010ied.1	-	5	720	c.639T>C	c.(637-639)TTT>TTC	p.F213F	TAPT1_uc011bxd.1_RNA|TAPT1_uc011bxe.1_Silent_p.F102F	NM_153365	NP_699196	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation	213						integral to membrane	growth hormone-releasing hormone receptor activity				0						TGTCTTGTCCAAAAGATGAAA	0.323													9	17	---	---	---	---	PASS
MED28	80306	broad.mit.edu	37	4	17623209	17623209	+	Splice_Site	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:17623209G>T	uc003gpi.1	+	3	239	c.227_splice	c.e3-1	p.G76_splice	MED28_uc003gpj.2_Splice_Site	NM_025205	NP_079481	Q9H204	MED28_HUMAN	mediator complex subunit 28						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|membrane|nucleus	actin binding				0						TTTTTTTTAAGGTGTTGATCA	0.313													6	17	---	---	---	---	PASS
TBC1D1	23216	broad.mit.edu	37	4	38138765	38138765	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:38138765G>T	uc003gtb.2	+	20	3659	c.3316G>T	c.(3316-3318)GGT>TGT	p.G1106C	TBC1D1_uc011byd.1_Missense_Mutation_p.G1097C|TBC1D1_uc010ifd.2_Missense_Mutation_p.G893C|TBC1D1_uc003gtd.2_Missense_Mutation_p.G118C	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,	1106						nucleus	Rab GTPase activator activity			ovary(1)	1						GGTGGCAAATGGTAGGATCCA	0.527													6	181	---	---	---	---	PASS
PHOX2B	8929	broad.mit.edu	37	4	41750460	41750460	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:41750460G>T	uc003gwf.3	-	1	528	c.168C>A	c.(166-168)GGC>GGA	p.G56G		NM_003924	NP_003915	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	56					positive regulation of transcription from RNA polymerase II promoter	nuclear chromatin	RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1)	12						GGGAAGGGCAGCCGGACGTGG	0.622			Mis|F		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				6	44	---	---	---	---	PASS
GABRA2	2555	broad.mit.edu	37	4	46305516	46305516	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:46305516A>G	uc003gxc.3	-	7	1490	c.817T>C	c.(817-819)TGG>CGG	p.W273R	GABRA2_uc010igc.2_Missense_Mutation_p.W273R|GABRA2_uc011bzc.1_Missense_Mutation_p.W218R|GABRA2_uc003gxe.2_Missense_Mutation_p.W273R	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	273	Helical; (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|skin(2)	4					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	CTGTTAAGCCAGAATGAAACT	0.299													30	47	---	---	---	---	PASS
FIP1L1	81608	broad.mit.edu	37	4	54319142	54319142	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:54319142C>A	uc003gzy.2	+	16	1527	c.1341C>A	c.(1339-1341)ACC>ACA	p.T447T	PDGFRA_uc003haa.2_Intron|FIP1L1_uc011bzu.1_Silent_p.T441T|FIP1L1_uc003gzz.2_Silent_p.T373T|FIP1L1_uc003hab.2_Silent_p.T412T|FIP1L1_uc003hac.2_Silent_p.T201T|FIP1L1_uc010ign.2_RNA|FIP1L1_uc003had.2_Missense_Mutation_p.P32Q|FIP1L1_uc003hae.2_Missense_Mutation_p.P32Q	NM_030917	NP_112179	Q6UN15	FIP1_HUMAN	FIP1 like 1 isoform 1	447	Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing	nucleus	RNA binding			ovary(1)|skin(1)	2			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TTGTGGACACCAGCAAGCAGT	0.279			T	PDGFRA	idiopathic hypereosinophilic syndrome								5	94	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62453133	62453133	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:62453133G>C	uc010ihh.2	+	2	417	c.244G>C	c.(244-246)GAT>CAT	p.D82H	LPHN3_uc003hcq.3_Missense_Mutation_p.D82H|LPHN3_uc010ihg.1_Missense_Mutation_p.D150H	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	82	SUEL-type lectin.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						TTATCTGCCAGATGCCTATAA	0.373													8	11	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62845347	62845347	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:62845347G>A	uc010ihh.2	+	15	2841	c.2668G>A	c.(2668-2670)GTT>ATT	p.V890I	LPHN3_uc003hcq.3_Missense_Mutation_p.V890I|LPHN3_uc003hct.2_Missense_Mutation_p.V283I	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	877	Helical; Name=1; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						GCTGTCCCTTGTTTGTCTCCT	0.478													45	147	---	---	---	---	PASS
PPM1K	152926	broad.mit.edu	37	4	89189398	89189398	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:89189398C>A	uc003hrm.3	-	5	1186	c.796G>T	c.(796-798)GAT>TAT	p.D266Y		NM_152542	NP_689755	Q8N3J5	PPM1K_HUMAN	protein phosphatase 1K (PP2C domain containing)	266	PP2C-like.				protein dephosphorylation	mitochondrial matrix|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000192)		AGGTCCAAATCTCCAATACTT	0.428													16	63	---	---	---	---	PASS
MIR302D	442896	broad.mit.edu	37	4	113569220	113569220	+	RNA	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:113569220A>G	hsa-mir-302d|MI0000774	-			c.8A>G			LARP7_uc003iay.2_Intron|LARP7_uc003iaz.2_Intron|LARP7_uc003iba.2_Intron|LARP7_uc003ibb.2_Intron|uc011cfy.1_5'Flank|MIR367_hsa-mir-367|MI0000775_5'Flank																	0						TCCATGTTAAAGTAGAGGGGG	0.358													10	20	---	---	---	---	PASS
QRFPR	84109	broad.mit.edu	37	4	122254088	122254088	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:122254088C>A	uc010inj.1	-	4	1064	c.685G>T	c.(685-687)GTG>TTG	p.V229L	QRFPR_uc010ink.1_RNA|QRFPR_uc003ids.2_Splice_Site_p.M228_splice	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	229	Helical; Name=5; (Potential).			VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488).		plasma membrane	neuropeptide Y receptor activity				0						ATAAGCATCACCATAAGAGGC	0.428													13	38	---	---	---	---	PASS
FBXW7	55294	broad.mit.edu	37	4	153249410	153249410	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:153249410G>T	uc003ims.2	-	9	1517	c.1368C>A	c.(1366-1368)ACC>ACA	p.T456T	FBXW7_uc011cii.1_Silent_p.T456T|FBXW7_uc003imt.2_Silent_p.T456T|FBXW7_uc011cih.1_Silent_p.T280T|FBXW7_uc003imq.2_Silent_p.T376T|FBXW7_uc003imr.2_Silent_p.T338T	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform	456	WD 2.				interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GCCCATATAAGGTGTGTATAC	0.408			Mis|N|D|F		colorectal|endometrial|T-ALL								5	73	---	---	---	---	PASS
PDGFC	56034	broad.mit.edu	37	4	157693940	157693940	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:157693940G>C	uc003iph.1	-	4	1092	c.601C>G	c.(601-603)CGA>GGA	p.R201G	PDGFC_uc003ipi.1_Missense_Mutation_p.R38G|PDGFC_uc011cis.1_Missense_Mutation_p.R38G|PDGFC_uc011cir.1_Missense_Mutation_p.R45G	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor	201					central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		TCAAGATATCGAATAAGGTCT	0.438													4	17	---	---	---	---	PASS
FAM198B	51313	broad.mit.edu	37	4	159092200	159092200	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:159092200T>C	uc003ipp.3	-	2	780	c.328A>G	c.(328-330)ACC>GCC	p.T110A	uc003ipu.1_5'Flank|FAM198B_uc003ipq.3_Missense_Mutation_p.T110A|FAM198B_uc003ipr.3_Missense_Mutation_p.T110A|FAM198B_uc003ips.2_Missense_Mutation_p.T110A|uc003ipt.1_RNA	NM_016613	NP_057697	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 2	110	Extracellular (Potential).					Golgi membrane|integral to membrane					0						GAGCGTAGGGTAATGTACACC	0.622													5	51	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175897024	175897024	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:175897024C>A	uc003iuc.2	+	5	1018	c.348C>A	c.(346-348)CTC>CTA	p.L116L	ADAM29_uc003iud.2_Silent_p.L116L|ADAM29_uc010irr.2_Silent_p.L116L|ADAM29_uc011cki.1_Silent_p.L116L	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	116					proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TGGTTTCCCTCAGTACCTGTT	0.438													6	31	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183676047	183676047	+	Silent	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr4:183676047C>T	uc003ivd.1	+	21	4564	c.4527C>T	c.(4525-4527)AAC>AAT	p.N1509N	ODZ3_uc003ive.1_Silent_p.N922N	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	1509	Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		ACTCTATGAACTTCTATGAAG	0.413													11	49	---	---	---	---	PASS
MRPL36	64979	broad.mit.edu	37	5	1799040	1799040	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:1799040G>A	uc003jcx.3	-	2	73	c.10C>T	c.(10-12)CTT>TTT	p.L4F	NDUFS6_uc003jcy.2_5'Flank	NM_032479	NP_115868	Q9P0J6	RM36_HUMAN	mitochondrial ribosomal protein L36 precursor	4					translation	mitochondrial large ribosomal subunit	structural constituent of ribosome				0				GBM - Glioblastoma multiforme(108;0.241)		CTTATAAAAAGATTTGCCATG	0.448													5	91	---	---	---	---	PASS
ADCY2	108	broad.mit.edu	37	5	7789771	7789771	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:7789771G>T	uc003jdz.1	+	20	2553	c.2486G>T	c.(2485-2487)AGG>ATG	p.R829M	ADCY2_uc011cmo.1_Missense_Mutation_p.R649M|ADCY2_uc010itm.1_Missense_Mutation_p.R25M	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	829	Cytoplasmic (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	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						TATTACTGTAGGTTAGACTTC	0.438													6	137	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24593512	24593512	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:24593512G>T	uc003jgr.1	-	2	420	c.88C>A	c.(88-90)CCT>ACT	p.P30T	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	30					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)		TGTGGCACAGGCGTCCTTCTG	0.398										HNSCC(23;0.051)			26	41	---	---	---	---	PASS
CDH9	1007	broad.mit.edu	37	5	26915806	26915806	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:26915806A>C	uc003jgs.1	-	3	624	c.455T>G	c.(454-456)ATC>AGC	p.I152S	CDH9_uc010iug.2_Missense_Mutation_p.I152S	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	152	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						ATTGTCATTGATATCATGTAT	0.378													16	50	---	---	---	---	PASS
LMBRD2	92255	broad.mit.edu	37	5	36137453	36137453	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:36137453G>C	uc003jkb.1	-	5	874	c.459C>G	c.(457-459)ATC>ATG	p.I153M		NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	153	Helical; (Potential).					integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGCCATAGTAGATTGCATTCT	0.348													3	29	---	---	---	---	PASS
C5orf42	65250	broad.mit.edu	37	5	37120354	37120354	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:37120354A>C	uc011cpa.1	-	49	9343	c.9112T>G	c.(9112-9114)TCT>GCT	p.S3038A	C5orf42_uc003jko.1_Missense_Mutation_p.S69A|C5orf42_uc003jkp.1_RNA|C5orf42_uc011coy.1_Missense_Mutation_p.S1556A|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Missense_Mutation_p.S2131A	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	3038										ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TGCCCAAAAGACTTCCTCTTA	0.368													10	46	---	---	---	---	PASS
C6	729	broad.mit.edu	37	5	41142975	41142975	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:41142975A>T	uc003jmk.2	-	18	2967	c.2757T>A	c.(2755-2757)TGT>TGA	p.C919*	C6_uc003jml.1_Nonsense_Mutation_p.C919*	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	919	Complement control factor I module 2.|C5b-binding domain.|Kazal-like 2.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TCCTGTTTGCACATCTTATAG	0.433													20	116	---	---	---	---	PASS
CDC20B	166979	broad.mit.edu	37	5	54442562	54442562	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:54442562C>A	uc003jpo.1	-	3	424	c.249G>T	c.(247-249)AGG>AGT	p.R83S	CDC20B_uc003jpn.1_Missense_Mutation_p.R83S|CDC20B_uc010ivu.1_Missense_Mutation_p.R83S|CDC20B_uc010ivv.1_Missense_Mutation_p.R83S|CDC20B_uc003jpp.2_RNA	NM_152623	NP_689836	Q86Y33	CD20B_HUMAN	CDC20 cell division cycle 20 homolog B isoform	83											0		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			AGGACAGAGCCCTAGTTTGAC	0.522											OREG0016610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	37	54	---	---	---	---	PASS
DEPDC1B	55789	broad.mit.edu	37	5	59982955	59982955	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:59982955C>A	uc003jsh.2	-	2	221	c.148G>T	c.(148-150)GTG>TTG	p.V50L	DEPDC1B_uc011cqm.1_Missense_Mutation_p.V50L|DEPDC1B_uc011cqn.1_Missense_Mutation_p.V23L	NM_018369	NP_060839	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B isoform 1	50	DEP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)	1		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				AGCCAATCCACAGCTTCGGCC	0.498													18	17	---	---	---	---	PASS
KIF2A	3796	broad.mit.edu	37	5	61643888	61643888	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:61643888G>A	uc003jsy.3	+	3	484	c.173G>A	c.(172-174)AGC>AAC	p.S58N	KIF2A_uc003jsz.3_Missense_Mutation_p.S58N|KIF2A_uc010iwp.2_Missense_Mutation_p.S58N|KIF2A_uc003jsx.3_Missense_Mutation_p.S38N|KIF2A_uc010iwq.2_5'UTR	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1	58	Globular (Potential).				blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		GACCTGGAGAGCATCTTTTCA	0.363													45	82	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70798568	70798568	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:70798568A>G	uc003kbp.1	+	15	2454	c.2191A>G	c.(2191-2193)ATT>GTT	p.I731V	BDP1_uc003kbn.1_Missense_Mutation_p.I731V|BDP1_uc003kbo.2_Missense_Mutation_p.I731V	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	731					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		ACAGGAAGAAATTGGGGCCAA	0.418													19	31	---	---	---	---	PASS
AGGF1	55109	broad.mit.edu	37	5	76331382	76331382	+	Silent	SNP	G	T	T	rs146897885	by1000genomes	TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:76331382G>T	uc003ket.2	+	3	690	c.330G>T	c.(328-330)ACG>ACT	p.T110T	AGGF1_uc003kes.2_Silent_p.T110T|AGGF1_uc003keu.1_RNA	NM_018046	NP_060516	Q8N302	AGGF1_HUMAN	angiogenic factor VG5Q	110					angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		TTTATCAGACGTACTACAATG	0.294													3	15	---	---	---	---	PASS
ARSB	411	broad.mit.edu	37	5	78181566	78181566	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:78181566C>A	uc003kfq.2	-	5	2269	c.983G>T	c.(982-984)GGG>GTG	p.G328V	ARSB_uc003kfr.3_Missense_Mutation_p.G328V	NM_000046	NP_000037	P15848	ARSB_HUMAN	arylsulfatase B isoform 1 precursor	328					lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		AAAGCCCACCCCTCGGACGCC	0.577													35	63	---	---	---	---	PASS
STARD4	134429	broad.mit.edu	37	5	110843086	110843086	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:110843086T>C	uc003kph.1	-	2	130	c.46A>G	c.(46-48)AAC>GAC	p.N16D	STARD4_uc010jbw.1_5'UTR|STARD4_uc010jbx.1_Intron|STARD4_uc003kpi.1_RNA|STARD4_uc003kpj.2_Missense_Mutation_p.N16D	NM_139164	NP_631903	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain	16	START.				lipid transport		lipid binding			ovary(1)	1		all_cancers(142;0.00259)|all_epithelial(76;8.32e-05)|Prostate(80;0.0115)|Colorectal(10;0.0959)|Ovarian(225;0.156)|all_lung(232;0.18)|Lung NSC(167;0.248)		OV - Ovarian serous cystadenocarcinoma(64;4.91e-09)|Epithelial(69;1.39e-08)|all cancers(49;2.34e-06)|COAD - Colon adenocarcinoma(37;0.049)|Colorectal(14;0.138)		ATGAGAGTGTTTTTAAGTTTA	0.368													15	22	---	---	---	---	PASS
PCDHGA11	56105	broad.mit.edu	37	5	140802848	140802848	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:140802848C>G	uc003lkq.1	+	1	2312	c.2054C>G	c.(2053-2055)TCT>TGT	p.S685C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.S685C|PCDHGA11_uc003lkp.1_Intron	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	685	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCTAACTCTGAAACCTCA	0.637													19	39	---	---	---	---	PASS
PCDHGA11	56105	broad.mit.edu	37	5	140802857	140802857	+	Nonsense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:140802857C>G	uc003lkq.1	+	1	2321	c.2063C>G	c.(2062-2064)TCA>TGA	p.S688*	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Nonsense_Mutation_p.S688*|PCDHGA11_uc003lkp.1_Intron|PCDHGB8P_uc011daz.1_5'Flank	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	688	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGAAACCTCAGACCTCTCG	0.632													19	43	---	---	---	---	PASS
GABRG2	2566	broad.mit.edu	37	5	161580278	161580278	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:161580278C>G	uc003lyz.3	+	9	1666	c.1308C>G	c.(1306-1308)ATC>ATG	p.I436M	GABRG2_uc010jjc.2_Missense_Mutation_p.I484M|GABRG2_uc003lyy.3_Missense_Mutation_p.I444M|GABRG2_uc011dej.1_Missense_Mutation_p.I341M	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	436	Cytoplasmic (Probable).|Interaction with GABARAP (Potential).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)		GGATACATATCCGCATTGCCA	0.493													36	48	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170380642	170380642	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:170380642G>T	uc003mba.2	+	13	1526	c.1510G>T	c.(1510-1512)GGA>TGA	p.G504*	RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	504					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GACAGTTGTAGGAGGAAGATT	0.353			T	TRD@	ALL								11	20	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170380643	170380643	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:170380643G>T	uc003mba.2	+	13	1527	c.1511G>T	c.(1510-1512)GGA>GTA	p.G504V	RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	504					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACAGTTGTAGGAGGAAGATTA	0.353			T	TRD@	ALL								11	20	---	---	---	---	PASS
F12	2161	broad.mit.edu	37	5	176833016	176833016	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:176833016G>A	uc003mgo.3	-	3	211	c.162C>T	c.(160-162)CAC>CAT	p.H54H	F12_uc011dfy.1_5'Flank|F12_uc003mgn.3_5'Flank|F12_uc010jkl.2_RNA	NM_000505	NP_000496	P00748	FA12_HUMAN	coagulation factor XII precursor	54	Fibronectin type-II.				Factor XII activation|fibrinolysis|innate immune response|positive regulation of blood coagulation|positive regulation of fibrinolysis|positive regulation of plasminogen activation|protein autoprocessing|response to misfolded protein|zymogen activation	extracellular space|plasma membrane	serine-type endopeptidase activity				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGCTGCCGGTGGTACTGGA	0.602									Hereditary_Angioedema				17	42	---	---	---	---	PASS
TMEM170B	100113407	broad.mit.edu	37	6	11566033	11566033	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:11566033G>C	uc010jpa.2	+	2	232	c.232G>C	c.(232-234)GGA>CGA	p.G78R		NM_001100829	NP_001094299	Q5T4T1	T170B_HUMAN	transmembrane protein 170B	78	Helical; (Potential).					integral to membrane					0						AGTCAGCATTGGATTTCTGGC	0.438													19	87	---	---	---	---	PASS
HIST1H2AA	221613	broad.mit.edu	37	6	25726578	25726578	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:25726578T>C	uc003nfc.2	-	1	213	c.178A>G	c.(178-180)ACA>GCA	p.T60A	HIST1H2BA_uc003nfd.2_5'Flank	NM_170745	NP_734466	Q96QV6	H2A1A_HUMAN	histone cluster 1, H2aa	60					nucleosome assembly	nucleosome|nucleus	DNA binding				0						ATTTCTGCTGTGAGATACTCT	0.537													28	24	---	---	---	---	PASS
OR2J3	442186	broad.mit.edu	37	6	29080440	29080440	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:29080440C>A	uc011dll.1	+	1	773	c.773C>A	c.(772-774)GCC>GAC	p.A258D		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	258	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TTCATTCCGGCCATGTGCATG	0.453													26	42	---	---	---	---	PASS
TRIM39	56658	broad.mit.edu	37	6	30310025	30310025	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:30310025G>C	uc010jrz.2	+	9	1858	c.1546G>C	c.(1546-1548)GAT>CAT	p.D516H	TRIM39_uc003npz.2_Missense_Mutation_p.D486H|TRIM39_uc003nqb.2_Missense_Mutation_p.D486H|TRIM39_uc003nqc.2_Missense_Mutation_p.D486H|TRIM39_uc010jsa.1_Intron|RPP21_uc003nqd.1_5'Flank|RPP21_uc003nqe.1_5'Flank|RPP21_uc003nqf.1_5'Flank	NM_021253	NP_067076	Q9HCM9	TRI39_HUMAN	tripartite motif-containing 39 isoform 1	516					apoptosis	cytosol|mitochondrion	identical protein binding|zinc ion binding			ovary(3)	3						GCCCCCAACAGATTGGGAGTG	0.562													15	23	---	---	---	---	PASS
ITPR3	3710	broad.mit.edu	37	6	33634988	33634988	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:33634988A>G	uc011drk.1	+	15	1853	c.1634A>G	c.(1633-1635)AAG>AGG	p.K545R		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	545	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						TCAGACCAGAAGAACGCCCCC	0.637													9	22	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38851775	38851775	+	Splice_Site	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:38851775G>T	uc003ooe.1	+	54	8208	c.7608_splice	c.e54+1	p.Q2536_splice		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GGGAGATCAGGTATGGCTGAA	0.294													9	28	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38851776	38851776	+	Splice_Site	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:38851776T>A	uc003ooe.1	+	54	8208	c.7608_splice	c.e54+2	p.Q2536_splice		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GGAGATCAGGTATGGCTGAAA	0.294													9	27	---	---	---	---	PASS
SRF	6722	broad.mit.edu	37	6	43146615	43146615	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:43146615C>A	uc003oui.2	+	6	1901	c.1426C>A	c.(1426-1428)CAC>AAC	p.H476N	SRF_uc011dvf.1_Missense_Mutation_p.H272N	NM_003131	NP_003122	P11831	SRF_HUMAN	serum response factor (c-fos serum response	476					angiogenesis involved in wound healing|cell migration involved in sprouting angiogenesis|cellular senescence|heart looping|muscle cell homeostasis|neuron development|positive regulation of cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription via serum response element binding|regulation of smooth muscle cell differentiation|response to cytokine stimulus|response to hormone stimulus|response to toxin|transcription from RNA polymerase II promoter|trophectodermal cell differentiation	endoplasmic reticulum	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|serum response element binding|transcription factor binding			ovary(1)|breast(1)|central_nervous_system(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGTTCAGCTCCACCAGGTAGG	0.502													6	191	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54805755	54805755	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:54805755G>T	uc003pck.2	+	5	2102	c.1986G>T	c.(1984-1986)AGG>AGT	p.R662S		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	662										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					TACTTAAAAGGCGAAGTTTCC	0.338													8	62	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64389923	64389923	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:64389923G>T	uc003pep.1	+	2	293	c.267G>T	c.(265-267)ATG>ATT	p.M89I	PHF3_uc010kaf.1_Missense_Mutation_p.M89I|PHF3_uc003pem.2_Missense_Mutation_p.M42I|PHF3_uc010kag.1_Missense_Mutation_p.M1I|PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_Missense_Mutation_p.M1I|PHF3_uc011dxs.1_5'UTR|PHF3_uc003peo.2_Missense_Mutation_p.M89I	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	89					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			ACGATATTATGGATGAAGGAG	0.318													5	61	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69945025	69945025	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:69945025G>C	uc003pev.3	+	19	3157	c.2709G>C	c.(2707-2709)TGG>TGC	p.W903C	BAI3_uc010kak.2_Missense_Mutation_p.W903C|BAI3_uc011dxx.1_Missense_Mutation_p.W109C|BAI3_uc003pex.1_Missense_Mutation_p.W33C	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	903	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				CAGCATTATGGAGGTAAGTAA	0.378													5	20	---	---	---	---	PASS
SENP6	26054	broad.mit.edu	37	6	76333641	76333641	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:76333641G>A	uc003pid.3	+	3	791	c.172G>A	c.(172-174)GAA>AAA	p.E58K	SENP6_uc003pie.3_Missense_Mutation_p.E58K|SENP6_uc003pic.2_Missense_Mutation_p.E58K	NM_015571	NP_056386	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6 isoform 1	58					proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)				CAGTGTGGATGAAGATGAGGA	0.313													4	29	---	---	---	---	PASS
PHIP	55023	broad.mit.edu	37	6	79688325	79688325	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:79688325G>T	uc003pir.2	-	24	3099	c.2873C>A	c.(2872-2874)CCA>CAA	p.P958Q	PHIP_uc003piq.2_5'UTR|PHIP_uc011dyp.1_Missense_Mutation_p.P957Q	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	958	Mediates interaction with IRS1 (By similarity).				insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		ACCCATCTGTGGCACAAATGG	0.358													4	28	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90442427	90442427	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:90442427C>G	uc003pnn.1	-	34	4907	c.4791G>C	c.(4789-4791)AAG>AAC	p.K1597N		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	1597					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)		TGACCACACACTTTCTGCCAA	0.443													15	56	---	---	---	---	PASS
TRAF3IP2	10758	broad.mit.edu	37	6	111887689	111887689	+	Silent	SNP	G	A	A	rs144166946	by1000genomes	TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:111887689G>A	uc011ebc.1	-	8	2049	c.1434C>T	c.(1432-1434)GAC>GAT	p.D478D	TRAF3IP2_uc011ebb.1_Silent_p.D22D|TRAF3IP2_uc003pvd.2_Silent_p.D70D|TRAF3IP2_uc003pvg.2_Silent_p.D477D|TRAF3IP2_uc003pvf.2_Silent_p.D478D	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	487	SEFIR.				intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		GCTCATCCTCGTCCAGCTGCG	0.507													19	62	---	---	---	---	PASS
TRDN	10345	broad.mit.edu	37	6	123698878	123698878	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:123698878G>C	uc003pzj.1	-	18	1251	c.1229C>G	c.(1228-1230)CCA>CGA	p.P410R	TRDN_uc003pzk.1_Missense_Mutation_p.P411R|TRDN_uc003pzl.1_Missense_Mutation_p.P411R|TRDN_uc010kem.1_5'UTR	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	410	Lumenal.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		TTCTTTCTTTGGTGACTTTGC	0.343													10	46	---	---	---	---	PASS
ENPP3	5169	broad.mit.edu	37	6	132014720	132014720	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:132014720C>A	uc003qcu.3	+	16	1715	c.1368C>A	c.(1366-1368)ATC>ATA	p.I456I	ENPP3_uc010kfq.2_RNA|ENPP3_uc003qcv.2_Silent_p.I456I	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	456	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		ACGTCAGAATCGACAAAGTTC	0.398													4	49	---	---	---	---	PASS
TAAR2	9287	broad.mit.edu	37	6	132939037	132939037	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:132939037C>G	uc003qdl.1	-	2	308	c.308G>C	c.(307-309)AGA>ACA	p.R103T	TAAR2_uc010kfr.1_Missense_Mutation_p.R58T	NM_001033080	NP_001028252	Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2 isoform 1	103	Extracellular (Potential).					plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		CTCCACCGATCTGATCATACT	0.413													12	45	---	---	---	---	PASS
EYA4	2070	broad.mit.edu	37	6	133827274	133827274	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:133827274C>G	uc003qec.3	+	14	1680	c.1222C>G	c.(1222-1224)CGC>GGC	p.R408G	EYA4_uc011ecq.1_Missense_Mutation_p.R354G|EYA4_uc011ecr.1_Missense_Mutation_p.R360G|EYA4_uc003qed.3_Missense_Mutation_p.R408G|EYA4_uc003qee.3_Missense_Mutation_p.R385G|EYA4_uc011ecs.1_Missense_Mutation_p.R414G|uc003qef.1_RNA|uc003qeg.1_RNA	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a	408					anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		CCTTGGACTCCGCATGGAAGA	0.323													6	22	---	---	---	---	PASS
HIVEP2	3097	broad.mit.edu	37	6	143094585	143094585	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:143094585G>A	uc003qjd.2	-	5	2034	c.1291C>T	c.(1291-1293)CGG>TGG	p.R431W		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	431					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GGACTAAGCCGACAGTATTTT	0.448													21	74	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144808798	144808798	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:144808798G>A	uc003qkt.2	+	28	4029	c.3937G>A	c.(3937-3939)GCT>ACT	p.A1313T		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	1313	Spectrin 9.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAAACTGGAGGCTTTCAACAG	0.498													6	48	---	---	---	---	PASS
SHPRH	257218	broad.mit.edu	37	6	146256083	146256083	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:146256083G>T	uc003qlf.2	-	13	3349	c.2950C>A	c.(2950-2952)CCA>ACA	p.P984T	SHPRH_uc003qld.2_Missense_Mutation_p.P984T|SHPRH_uc003qle.2_Missense_Mutation_p.P984T|SHPRH_uc003qlg.1_Missense_Mutation_p.P540T|SHPRH_uc003qlj.1_Missense_Mutation_p.P873T|SHPRH_uc003qlh.2_5'Flank	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	984					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ACAGCCTGTGGGTGACAGCAG	0.438													23	40	---	---	---	---	PASS
ARID1B	57492	broad.mit.edu	37	6	157502211	157502211	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:157502211G>A	uc003qqn.2	+	12	3342	c.3190G>A	c.(3190-3192)GAG>AAG	p.E1064K	ARID1B_uc003qqo.2_Missense_Mutation_p.E1024K|ARID1B_uc003qqp.2_Missense_Mutation_p.E1011K|ARID1B_uc010kjl.2_Missense_Mutation_p.E209K	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1069	ARID.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CTTCATGGAAGAGAGAGGCTC	0.577													6	33	---	---	---	---	PASS
WTAP	9589	broad.mit.edu	37	6	160164807	160164807	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:160164807G>A	uc003qsl.2	+	5	478	c.256G>A	c.(256-258)GAG>AAG	p.E86K	WTAP_uc010kjx.2_Missense_Mutation_p.E86K|WTAP_uc003qsk.2_Missense_Mutation_p.E86K|WTAP_uc003qsm.1_RNA|WTAP_uc003qsn.2_Missense_Mutation_p.E86K	NM_004906	NP_004897	Q15007	FL2D_HUMAN	Wilms' tumour 1-associating protein isoform 1	86					cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		CAAGGAACAAGAGATGCAAGA	0.358													6	33	---	---	---	---	PASS
KDELR2	11014	broad.mit.edu	37	7	6505702	6505702	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:6505702C>A	uc003sqe.3	-	4	765	c.604G>T	c.(604-606)GTA>TTA	p.V202L	DAGLB_uc003sqd.3_Intron|KDELR2_uc003sqf.3_Intron	NM_006854	NP_006845	P33947	ERD22_HUMAN	KDEL receptor 2 isoform 1	202	Cytoplasmic (Potential).				intracellular protein transport|protein retention in ER lumen|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	KDEL sequence binding|protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		CCCAACATACCTTTTGTAATG	0.488													6	150	---	---	---	---	PASS
TMEM195	392636	broad.mit.edu	37	7	15430477	15430477	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:15430477C>A	uc003stb.1	-	7	900	c.730G>T	c.(730-732)GAT>TAT	p.D244Y		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	244					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						AAAATTTTATCCCAAATAATA	0.254													4	7	---	---	---	---	PASS
C7orf16	10842	broad.mit.edu	37	7	31746859	31746859	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:31746859G>T	uc003tcl.2	+	5	588	c.430G>T	c.(430-432)GAA>TAA	p.E144*	C7orf16_uc011kaf.1_Nonsense_Mutation_p.E93*	NM_006658	NP_006649	O96001	GSUB_HUMAN	G-substrate isoform 1	144					behavior|central nervous system development|intracellular protein kinase cascade|protein phosphorylation	soluble fraction				ovary(2)|central_nervous_system(1)	3			GBM - Glioblastoma multiforme(11;0.216)			AGCAATCGTGGAAGATGACGA	0.428													16	37	---	---	---	---	PASS
TARP	445347	broad.mit.edu	37	7	38299746	38299746	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:38299746G>T	uc003tge.1	-	7	1268	c.891C>A	c.(889-891)ATC>ATA	p.I297I	uc003tfx.1_5'Flank|uc003tfz.1_Intron|TARP_uc003tgb.2_Silent_p.I93I|TARP_uc003tgc.1_Silent_p.I93I|TARP_uc003tgd.1_Silent_p.I93I			A2JGV3	A2JGV3_HUMAN	Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.	Error:Variant_position_missing_in_A2JGV3_after_alignment											0						AGCAGGTGATGATGGCAAAAT	0.458													6	58	---	---	---	---	PASS
UPP1	7378	broad.mit.edu	37	7	48147012	48147012	+	Missense_Mutation	SNP	C	T	T	rs138630287		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:48147012C>T	uc003toj.2	+	9	1230	c.701C>T	c.(700-702)GCG>GTG	p.A234V	UPP1_uc003tok.2_Missense_Mutation_p.A234V|UPP1_uc003tol.2_Missense_Mutation_p.A234V|UPP1_uc011kch.1_Missense_Mutation_p.A27V|UPP1_uc003ton.2_Missense_Mutation_p.A97V|UPP1_uc003too.2_Missense_Mutation_p.A97V	NM_181597	NP_853628	Q16831	UPP1_HUMAN	uridine phosphorylase 1	234					nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage	cytosol	uridine phosphorylase activity				0						GACAAGCAGGCGTATCTGGAG	0.602													8	30	---	---	---	---	PASS
WBSCR28	135886	broad.mit.edu	37	7	73279346	73279346	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:73279346C>A	uc003tzk.2	+	2	132	c.96C>A	c.(94-96)CTC>CTA	p.L32L	RFC2_uc011kfa.1_Intron|WBSCR28_uc003tzl.2_5'UTR	NM_182504	NP_872310	Q6UE05	WBS28_HUMAN	hypothetical protein LOC135886	32						integral to membrane				breast(1)	1		Lung NSC(55;0.159)				GAGATCACCTCTATAATTTCC	0.537													8	401	---	---	---	---	PASS
RSBN1L	222194	broad.mit.edu	37	7	77325946	77325946	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:77325946C>A	uc010ldt.1	+	1	204	c.160C>A	c.(160-162)CGG>AGG	p.R54R	RSBN1L_uc003ugm.2_5'Flank|uc003ugj.1_RNA	NM_198467	NP_940869	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	54						nucleus				ovary(1)	1						GAAGGCACCGCGGAGAGTGAA	0.652													6	22	---	---	---	---	PASS
MAGI2	9863	broad.mit.edu	37	7	77756572	77756572	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:77756572T>C	uc003ugx.2	-	19	3619	c.3365A>G	c.(3364-3366)TAC>TGC	p.Y1122C	MAGI2_uc003ugy.2_Missense_Mutation_p.Y1108C|MAGI2_uc010ldx.1_Missense_Mutation_p.Y715C	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	1122						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)				GTGCTGCCTGTAGTCCAGTAG	0.637													14	55	---	---	---	---	PASS
SEMA3E	9723	broad.mit.edu	37	7	83014748	83014748	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:83014748C>A	uc003uhy.1	-	16	2203	c.1737G>T	c.(1735-1737)GGG>GGT	p.G579G		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor	579					axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				CCAAAGCATCCCCTACAACAG	0.358													58	39	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91709280	91709280	+	Silent	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:91709280A>G	uc003ulg.2	+	31	8058	c.7833A>G	c.(7831-7833)TTA>TTG	p.L2611L	AKAP9_uc003ulf.2_Silent_p.L2603L|AKAP9_uc003uli.2_Silent_p.L2234L|AKAP9_uc003ulj.2_Silent_p.L381L	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2623	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATCAGAATTAGAAAGCCAGG	0.308			T	BRAF	papillary thyroid								5	61	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103214585	103214585	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:103214585C>G	uc003vca.2	-	30	4625	c.4465G>C	c.(4465-4467)GGG>CGG	p.G1489R	RELN_uc010liz.2_Missense_Mutation_p.G1489R	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1489					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)		TCCCTTTTCCCAGGGCCATTG	0.473													16	67	---	---	---	---	PASS
LRRN3	54674	broad.mit.edu	37	7	110763735	110763735	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:110763735C>T	uc003vft.3	+	4	1953	c.907C>T	c.(907-909)CTT>TTT	p.L303F	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.L303F|LRRN3_uc003vfs.3_Missense_Mutation_p.L303F	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	303	Extracellular (Potential).|LRR 10.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		CATCGATAGTCTTGCTGTGGA	0.373													13	35	---	---	---	---	PASS
LRRN3	54674	broad.mit.edu	37	7	110763895	110763895	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:110763895C>G	uc003vft.3	+	4	2113	c.1067C>G	c.(1066-1068)TCT>TGT	p.S356C	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.S356C|LRRN3_uc003vfs.3_Missense_Mutation_p.S356C	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	356	Extracellular (Potential).|LRR 12.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		ACCATTGAGTCTCTGCCAAAC	0.458													6	38	---	---	---	---	PASS
PAX4	5078	broad.mit.edu	37	7	127255120	127255120	+	Silent	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:127255120T>C	uc010lld.1	-	2	356	c.150A>G	c.(148-150)CTA>CTG	p.L50L	PAX4_uc003vmf.2_Silent_p.L48L|PAX4_uc003vmg.1_Silent_p.L50L|PAX4_uc003vmh.2_Silent_p.L48L	NM_006193	NP_006184	O43316	PAX4_HUMAN	paired box 4	58	Paired.				cell differentiation|endocrine pancreas development|organ morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AGTAACGCCCTAGGATCTTGC	0.582													14	72	---	---	---	---	PASS
OR2A5	393046	broad.mit.edu	37	7	143748242	143748242	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:143748242C>A	uc011ktw.1	+	1	748	c.748C>A	c.(748-750)CTC>ATC	p.L250I		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	250	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)					CATGGTGGGACTCTTCTTTGG	0.592													28	87	---	---	---	---	PASS
GIMAP8	155038	broad.mit.edu	37	7	150164145	150164145	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:150164145T>G	uc003whj.2	+	2	689	c.359T>G	c.(358-360)GTG>GGG	p.V120G		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	120						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		ATCCAACAAGTGTTTGGAGCT	0.483													9	45	---	---	---	---	PASS
AGAP3	116988	broad.mit.edu	37	7	150840947	150840947	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:150840947G>T	uc003wjg.1	+	18	2656	c.2653G>T	c.(2653-2655)GGC>TGC	p.G885C	AGAP3_uc003wje.1_Missense_Mutation_p.G554C|AGAP3_uc003wjj.1_Missense_Mutation_p.G384C|AGAP3_uc003wjk.1_Missense_Mutation_p.G303C	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	849					regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3						GGAGGGCTGTGGCTTAGCGCC	0.647													11	33	---	---	---	---	PASS
AGAP3	116988	broad.mit.edu	37	7	150840948	150840948	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr7:150840948G>T	uc003wjg.1	+	18	2657	c.2654G>T	c.(2653-2655)GGC>GTC	p.G885V	AGAP3_uc003wje.1_Missense_Mutation_p.G554V|AGAP3_uc003wjj.1_Missense_Mutation_p.G384V|AGAP3_uc003wjk.1_Missense_Mutation_p.G303V	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	849					regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3						GAGGGCTGTGGCTTAGCGCCT	0.647													12	32	---	---	---	---	PASS
GSR	2936	broad.mit.edu	37	8	30539494	30539494	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:30539494G>A	uc003xih.1	-	11	1329	c.1238C>T	c.(1237-1239)ACT>ATT	p.T413I		NM_000637	NP_000628	P00390	GSHR_HUMAN	glutathione reductase precursor	413					cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)	GAAGACCACAGTTGGGATGTT	0.428													8	33	---	---	---	---	PASS
ADAM18	8749	broad.mit.edu	37	8	39525607	39525607	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:39525607C>G	uc003xni.2	+	14	1417	c.1417C>G	c.(1417-1419)CCT>GCT	p.P473A	ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Missense_Mutation_p.P449A	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18	473	Disintegrin.|Extracellular (Potential).				cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TAATTGTGTTCCTGACACTTA	0.418													29	38	---	---	---	---	PASS
HGSNAT	138050	broad.mit.edu	37	8	43037324	43037324	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:43037324A>T	uc003xpx.3	+	11	1097	c.1049A>T	c.(1048-1050)CAG>CTG	p.Q350L		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	378	Helical; (Potential).				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GGTGTGCTGCAGCGATTGGGA	0.483													110	504	---	---	---	---	PASS
SNTG1	54212	broad.mit.edu	37	8	51664659	51664659	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:51664659G>C	uc010lxy.1	+	19	1754	c.1383G>C	c.(1381-1383)CAG>CAC	p.Q461H	SNTG1_uc003xqs.1_Missense_Mutation_p.Q461H|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	461					cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				ATACTAAACAGATTGAAGCAA	0.373													3	21	---	---	---	---	PASS
CYP7A1	1581	broad.mit.edu	37	8	59404141	59404141	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:59404141T>A	uc003xtm.3	-	6	1471	c.1408A>T	c.(1408-1410)ATA>TTA	p.I470L		NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,	470					bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				TGGCCCTCTATAAGCTCCAAT	0.408									Neonatal_Giant_Cell_Hepatitis				11	48	---	---	---	---	PASS
NCOA2	10499	broad.mit.edu	37	8	71082563	71082563	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:71082563C>A	uc003xyn.1	-	6	577	c.415G>T	c.(415-417)GTG>TTG	p.V139L		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	139	PAS.				cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TTCTCTGACACAAACACAACG	0.408			T	RUNXBP2	AML								11	25	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77763640	77763640	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:77763640C>A	uc003yav.2	+	10	4735	c.4348C>A	c.(4348-4350)CAC>AAC	p.H1450N	ZFHX4_uc003yau.1_Missense_Mutation_p.H1495N|ZFHX4_uc003yaw.1_Missense_Mutation_p.H1450N	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1450						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TGAGGTGGACCACGAAGGGAA	0.507										HNSCC(33;0.089)			5	55	---	---	---	---	PASS
DCAF4L2	138009	broad.mit.edu	37	8	88885863	88885863	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:88885863G>A	uc003ydz.2	-	1	434	c.337C>T	c.(337-339)CGG>TGG	p.R113W		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	113										ovary(1)	1						GGGTATACCCGGAGCTCAGGG	0.537													28	64	---	---	---	---	PASS
RBM12B	389677	broad.mit.edu	37	8	94746211	94746211	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:94746211C>A	uc003yfz.2	-	3	2621	c.2428G>T	c.(2428-2430)GAC>TAC	p.D810Y		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	810							nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			CCCCTGAAGTCTTCATCTGGT	0.577													16	85	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100513915	100513915	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:100513915G>C	uc003yiv.2	+	26	3982	c.3871G>C	c.(3871-3873)GGA>CGA	p.G1291R	VPS13B_uc003yiw.2_Missense_Mutation_p.G1291R|VPS13B_uc003yiu.1_Missense_Mutation_p.G1291R|VPS13B_uc003yix.1_Missense_Mutation_p.G761R	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1291					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)			CTCATCCCAGGGAGATTCTAT	0.308													6	63	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113668571	113668571	+	Splice_Site	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:113668571C>A	uc003ynu.2	-	18	2976	c.2817_splice	c.e18-1	p.R939_splice	CSMD3_uc003yns.2_Splice_Site_p.R211_splice|CSMD3_uc003ynt.2_Splice_Site_p.R899_splice|CSMD3_uc011lhx.1_Splice_Site_p.R835_splice	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							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						AGTCTGAAATCTAAGATTAAA	0.338										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	15	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	114111088	114111088	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:114111088C>A	uc003ynu.2	-	5	973	c.814G>T	c.(814-816)GTA>TTA	p.V272L	CSMD3_uc003ynt.2_Missense_Mutation_p.V232L|CSMD3_uc011lhx.1_Missense_Mutation_p.V272L|CSMD3_uc010mcx.1_Missense_Mutation_p.V272L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	272	Extracellular (Potential).|CUB 2.					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						GGCTCTGCTACAATGGTCCAA	0.408										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			5	13	---	---	---	---	PASS
NOV	4856	broad.mit.edu	37	8	120431549	120431549	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:120431549G>T	uc003yoq.2	+	4	962	c.741G>T	c.(739-741)CGG>CGT	p.R247R		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	247	TSP type-1.				regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GCATGGTGCGGCCCTGTGAAC	0.562													26	110	---	---	---	---	PASS
ZHX2	22882	broad.mit.edu	37	8	123964442	123964442	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:123964442G>T	uc003ypk.1	+	3	1259	c.692G>T	c.(691-693)GGG>GTG	p.G231V		NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	231	Required for homodimerization.					cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			AGACTCGGCGGGGTGGAGCTC	0.577													37	105	---	---	---	---	PASS
KHDRBS3	10656	broad.mit.edu	37	8	136594138	136594138	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr8:136594138C>A	uc003yuv.2	+	6	1023	c.629C>A	c.(628-630)ACA>AAA	p.T210K	KHDRBS3_uc003yuw.2_Missense_Mutation_p.T210K|KHDRBS3_uc010mek.2_RNA	NM_006558	NP_006549	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal	210					regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			GGAGGAGTTACAGCCCGGCCA	0.493													24	43	---	---	---	---	PASS
SLC1A1	6505	broad.mit.edu	37	9	4576030	4576030	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:4576030C>T	uc003zij.1	+	9	1141	c.905C>T	c.(904-906)CCG>CTG	p.P302L	C9orf68_uc003zik.2_Intron	NM_004170	NP_004161	P43005	EAA3_HUMAN	solute carrier family 1, member 1	302	Helical; (Potential).				D-aspartate import|L-glutamate import|synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)	GTAATTCTCCCGCTGATATAT	0.413													25	31	---	---	---	---	PASS
GLDC	2731	broad.mit.edu	37	9	6550883	6550883	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:6550883G>T	uc003zkc.2	-	21	2682	c.2489C>A	c.(2488-2490)ACG>AAG	p.T830K		NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	830					glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	CGCAGTTTCCGTGGCTTGTTT	0.423													98	59	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8486189	8486189	+	Silent	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:8486189T>C	uc003zkk.2	-	27	3339	c.2628A>G	c.(2626-2628)AAA>AAG	p.K876K	PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Silent_p.K867K|PTPRD_uc003zkm.2_Silent_p.K863K|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	876	Fibronectin type-III 6.|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)		AGTGATCTTCTTTTTCAGAGA	0.498										TSP Lung(15;0.13)			158	33	---	---	---	---	PASS
CER1	9350	broad.mit.edu	37	9	14720184	14720184	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:14720184C>A	uc003zlj.2	-	2	753	c.708G>T	c.(706-708)GTG>GTT	p.V236V		NM_005454	NP_005445	O95813	CER1_HUMAN	cerberus 1 precursor	236	CTCK.				BMP signaling pathway	extracellular space	cytokine activity				0				GBM - Glioblastoma multiforme(50;3.16e-06)		GGCACTCCTCCACCAGCATCA	0.522													6	97	---	---	---	---	PASS
FANCG	2189	broad.mit.edu	37	9	35079502	35079502	+	Missense_Mutation	SNP	G	A	A	rs35984312	byFrequency	TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:35079502G>A	uc003zwb.1	-	1	512	c.20C>T	c.(19-21)TCT>TTT	p.S7F	FANCG_uc003zwa.1_5'Flank|FANCG_uc010mkj.1_5'UTR|FANCG_uc011lot.1_Missense_Mutation_p.S7F	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	7					cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GGAGCCCACAGAGGTGGTCTG	0.647			Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				8	46	---	---	---	---	PASS
FANCG	2189	broad.mit.edu	37	9	35079503	35079503	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:35079503A>T	uc003zwb.1	-	1	511	c.19T>A	c.(19-21)TCT>ACT	p.S7T	FANCG_uc003zwa.1_5'Flank|FANCG_uc010mkj.1_5'UTR|FANCG_uc011lot.1_Missense_Mutation_p.S7T	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	7					cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GAGCCCACAGAGGTGGTCTGG	0.647			Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				8	45	---	---	---	---	PASS
TLN1	7094	broad.mit.edu	37	9	35720477	35720477	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:35720477T>A	uc003zxt.2	-	12	1590	c.1236A>T	c.(1234-1236)GAA>GAT	p.E412D		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	412	Interaction with LAYN (By similarity).				axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CCTCATCTCCTTCCAGCCCAA	0.488													87	113	---	---	---	---	PASS
ZCCHC7	84186	broad.mit.edu	37	9	37126431	37126431	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:37126431A>T	uc003zzq.2	+	2	275	c.102A>T	c.(100-102)CAA>CAT	p.Q34H	ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Missense_Mutation_p.Q33H|ZCCHC7_uc010mlt.2_Missense_Mutation_p.Q33H|ZCCHC7_uc003zzs.1_Missense_Mutation_p.Q33H	NM_032226	NP_115602	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	34							nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)		TGGAATTTCAACTCTATAGCC	0.398													10	72	---	---	---	---	PASS
VPS13A	23230	broad.mit.edu	37	9	79968365	79968365	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:79968365A>G	uc004akr.2	+	54	7720	c.7460A>G	c.(7459-7461)TAT>TGT	p.Y2487C	VPS13A_uc004akp.3_Missense_Mutation_p.Y2487C|VPS13A_uc004akq.3_Missense_Mutation_p.Y2487C|VPS13A_uc004aks.2_Missense_Mutation_p.Y2448C	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	2487					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						AAGACAATATATTTAGTTTCA	0.299													4	25	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107645435	107645435	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:107645435C>A	uc004bcl.2	-	5	619	c.306G>T	c.(304-306)GTG>GTT	p.V102V	ABCA1_uc004bcm.2_Silent_p.V42V	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	102	Extracellular.				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	ACAGGCGAGCCACACTGTAAA	0.493													17	73	---	---	---	---	PASS
TLR4	7099	broad.mit.edu	37	9	120476154	120476154	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:120476154G>T	uc004bjz.2	+	3	2039	c.1748G>T	c.(1747-1749)TGT>TTT	p.C583F	TLR4_uc004bka.2_Missense_Mutation_p.C543F|TLR4_uc004bkb.2_Missense_Mutation_p.C383F	NM_138554	NP_612564	O00206	TLR4_HUMAN	toll-like receptor 4 precursor	583	LRRCT.|Extracellular (Potential).				activation of MAPK activity|cellular response to mechanical stimulus|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm	lipopolysaccharide receptor activity|transmembrane receptor activity			lung(10)|ovary(4)|breast(1)|skin(1)	16						GACTTTGCTTGTACTTGTGAA	0.408													15	29	---	---	---	---	PASS
NELF	26012	broad.mit.edu	37	9	140347593	140347593	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr9:140347593G>T	uc004cna.2	-	9	1194	c.962C>A	c.(961-963)GCC>GAC	p.A321D	C9orf167_uc011mew.1_Intron|NELF_uc011mex.1_Missense_Mutation_p.A118D|NELF_uc010nci.2_Missense_Mutation_p.A65D|NELF_uc011mey.1_RNA|NELF_uc011mez.1_Missense_Mutation_p.A298D|NELF_uc004cmz.2_Missense_Mutation_p.A319D|NELF_uc004cnc.2_Missense_Mutation_p.A296D|NELF_uc004cnb.2_Missense_Mutation_p.A291D	NM_001130969	NP_001124441	Q6X4W1	NELF_HUMAN	nasal embryonic LHRH factor isoform a	321						nucleus|plasma membrane					0	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000222)|Epithelial(140;0.000888)		GTCCTCGAAGGCCTCGTCCAG	0.657													4	34	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5789240	5789240	+	Silent	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:5789240C>T	uc001iij.2	+	15	4481	c.3856C>T	c.(3856-3858)CTA>TTA	p.L1286L	C10orf18_uc001iik.2_Silent_p.L130L	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	1286										ovary(1)|central_nervous_system(1)	2						TGACTTAGCTCTAACAATATC	0.418													26	124	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55582261	55582261	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:55582261G>A	uc001jju.1	-	33	5620	c.5225C>T	c.(5224-5226)CCT>CTT	p.P1742L	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.P1739L|PCDH15_uc010qhw.1_Missense_Mutation_p.P1702L|PCDH15_uc010qhx.1_Missense_Mutation_p.P1673L|PCDH15_uc010qhy.1_Missense_Mutation_p.P1749L|PCDH15_uc010qhz.1_Missense_Mutation_p.P1744L|PCDH15_uc010qia.1_Missense_Mutation_p.P1722L|PCDH15_uc010qib.1_Missense_Mutation_p.P1719L	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1742	Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				aCAGGCAGAAGGAGAGATGTT	0.209										HNSCC(58;0.16)			3	17	---	---	---	---	PASS
TET1	80312	broad.mit.edu	37	10	70451506	70451506	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:70451506A>G	uc001jok.3	+	12	6851	c.6346A>G	c.(6346-6348)AAT>GAT	p.N2116D		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	2116					DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9						AACCCATGACAATGTTGTCAC	0.453													20	64	---	---	---	---	PASS
COL13A1	1305	broad.mit.edu	37	10	71690217	71690217	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:71690217A>G	uc001jpr.1	+	28	2095	c.1559A>G	c.(1558-1560)GAT>GGT	p.D520G	COL13A1_uc001jqj.1_Missense_Mutation_p.D520G|COL13A1_uc001jps.1_Missense_Mutation_p.D491G|COL13A1_uc001jpt.1_Missense_Mutation_p.D479G|COL13A1_uc001jpu.1_Missense_Mutation_p.D501G|COL13A1_uc001jpv.1_Missense_Mutation_p.D520G|COL13A1_uc001jpx.1_Missense_Mutation_p.D498G|COL13A1_uc001jpw.1_Missense_Mutation_p.D467G|COL13A1_uc001jpy.1_Missense_Mutation_p.D458G|COL13A1_uc001jpz.1_Missense_Mutation_p.D463G|COL13A1_uc001jqa.1_Missense_Mutation_p.D460G|COL13A1_uc001jqc.1_Missense_Mutation_p.D520G|COL13A1_uc001jqb.1_Missense_Mutation_p.D469G|COL13A1_uc001jql.2_Missense_Mutation_p.D520G|COL13A1_uc001jqd.1_Missense_Mutation_p.D508G|COL13A1_uc001jqe.1_Missense_Mutation_p.D503G|COL13A1_uc001jqf.1_Missense_Mutation_p.D501G|COL13A1_uc001jqg.1_Missense_Mutation_p.D498G|COL13A1_uc001jqh.1_Missense_Mutation_p.D520G|COL13A1_uc001jqi.1_Missense_Mutation_p.D520G|COL13A1_uc010qjf.1_Missense_Mutation_p.D310G	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1	520	Extracellular (Potential).|Triple-helical region 3 (COL3).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	CCAGGAAAGGATGGACCTCCA	0.567													5	9	---	---	---	---	PASS
LRRC20	55222	broad.mit.edu	37	10	72100443	72100443	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:72100443T>A	uc001jqx.1	-	3	320	c.98A>T	c.(97-99)AAG>ATG	p.K33M	LRRC20_uc001jqy.1_Missense_Mutation_p.K33M|LRRC20_uc001jqz.1_Intron	NM_207119	NP_997002	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20 isoform 1	33											0						GGAGACCAGCTTGCACTCGGC	0.547													8	36	---	---	---	---	PASS
LRIT1	26103	broad.mit.edu	37	10	85993948	85993948	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:85993948C>A	uc001kcz.1	-	3	798	c.776G>T	c.(775-777)GGA>GTA	p.G259V		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	259	Lumenal (Potential).					integral to endoplasmic reticulum membrane					0						GCTGGCCACTCCTGGATGGAG	0.617													19	62	---	---	---	---	PASS
SORBS1	10580	broad.mit.edu	37	10	97098986	97098986	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:97098986C>A	uc001kkp.2	-	27	2814	c.2769G>T	c.(2767-2769)GTG>GTT	p.V923V	SORBS1_uc001kkk.2_Silent_p.V417V|SORBS1_uc001kkl.2_Silent_p.V525V|SORBS1_uc001kkn.2_Silent_p.V688V|SORBS1_uc001kkm.2_Silent_p.V723V|SORBS1_uc001kko.2_Silent_p.V945V|SORBS1_uc001kkq.2_Silent_p.V774V|SORBS1_uc001kkr.2_Silent_p.V629V|SORBS1_uc001kks.2_Silent_p.V573V|SORBS1_uc001kkt.2_RNA|SORBS1_uc001kku.2_Silent_p.V670V|SORBS1_uc001kkv.2_Silent_p.V705V|SORBS1_uc001kkw.2_Silent_p.V877V|SORBS1_uc010qoe.1_Silent_p.V638V	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	923	SH3 2.				focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGATCACATCCACGTAGGTGA	0.562													5	68	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115365986	115365986	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:115365986C>G	uc001laj.2	-	33	3922	c.3758G>C	c.(3757-3759)GGT>GCT	p.G1253A	NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Missense_Mutation_p.G1218A|NRAP_uc001lal.3_Missense_Mutation_p.G1253A	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	1253	Nebulin 33.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTCGGGCAGACCCAGGGTCAT	0.438													9	33	---	---	---	---	PASS
CASP7	840	broad.mit.edu	37	10	115486137	115486137	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:115486137C>A	uc001lan.2	+	6	800	c.626C>A	c.(625-627)CCT>CAT	p.P209H	CASP7_uc001lam.2_Missense_Mutation_p.L198I|CASP7_uc001lao.2_Missense_Mutation_p.P242H|CASP7_uc001lap.2_Missense_Mutation_p.P209H|CASP7_uc001laq.2_Missense_Mutation_p.P209H|CASP7_uc010qsa.1_Missense_Mutation_p.P294H|CASP7_uc010qsb.1_Missense_Mutation_p.P184H	NM_033339	NP_203125	P55210	CASP7_HUMAN	caspase 7 isoform alpha	209					activation of caspase activity by cytochrome c|cellular component disassembly involved in apoptosis|induction of apoptosis by intracellular signals|proteolysis	cytosol|endoplasmic reticulum membrane|mitochondrial membrane|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)		GATGCTAATCCTCGATACAAG	0.498													5	66	---	---	---	---	PASS
KCNK18	338567	broad.mit.edu	37	10	118960727	118960727	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:118960727G>T	uc010qsr.1	+	2	281	c.281G>T	c.(280-282)TGG>TTG	p.W94L		NM_181840	NP_862823	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	94						integral to membrane|plasma membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;0.19)		all cancers(201;0.0211)		AAGCCTCAGTGGTTTAACAGG	0.527													41	105	---	---	---	---	PASS
CUZD1	50624	broad.mit.edu	37	10	124597003	124597003	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:124597003C>G	uc001lgq.2	-	4	848	c.516G>C	c.(514-516)AAG>AAC	p.K172N	CUZD1_uc001lgp.2_5'UTR|CUZD1_uc009yad.2_5'UTR|CUZD1_uc009yaf.2_Intron|CUZD1_uc001lgr.2_5'UTR|CUZD1_uc010qty.1_5'UTR|CUZD1_uc009yae.2_5'UTR|CUZD1_uc001lgs.2_Missense_Mutation_p.K172N|CUZD1_uc010qtz.1_Missense_Mutation_p.K172N	NM_022034	NP_071317	Q86UP6	CUZD1_HUMAN	CUB and zona pellucida-like domains 1 precursor	172	Extracellular (Potential).|CUB 2.				cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		CAGGATGCGGCTTTGGGTAAT	0.443													24	59	---	---	---	---	PASS
IKZF5	64376	broad.mit.edu	37	10	124758038	124758038	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr10:124758038C>T	uc001lha.2	-	3	403	c.104G>A	c.(103-105)GGG>GAG	p.G35E		NM_022466	NP_071911	Q9H5V7	IKZF5_HUMAN	zinc finger protein, subfamily 1A, 5	35					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		TTCTTTGTCCCCACTAACTGA	0.408													5	45	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093582	1093582	+	Missense_Mutation	SNP	G	C	C	rs55641679		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:1093582G>C	uc001lsx.1	+	31	12514	c.12487G>C	c.(12487-12489)GCA>CCA	p.A4163P		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4163				P -> A (in Ref. 4).		inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tacGGTGACCGCAACCCCAAC	0.338													4	22	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1157747	1157747	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:1157747G>T	uc009ycr.1	+	9	940	c.814G>T	c.(814-816)GGC>TGC	p.G272C		NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	268	VWFD 1.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCTCCTGCACGGCCAGCTGTT	0.637													9	18	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1271174	1271174	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:1271174C>G	uc009ycr.1	+	51	14609	c.14483C>G	c.(14482-14484)TCC>TGC	p.S4828C	MUC5B_uc001ltb.2_Missense_Mutation_p.S4358C	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	4355	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CACCCCTCCTCCACTCCGGAG	0.657													26	51	---	---	---	---	PASS
TRIM21	6737	broad.mit.edu	37	11	4408217	4408217	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:4408217C>A	uc001lyy.1	-	5	852	c.739G>T	c.(739-741)GTG>TTG	p.V247L		NM_003141	NP_003132	P19474	RO52_HUMAN	tripartite motif protein 21	247					cell cycle|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein deubiquitination|positive regulation of cell cycle|protein autoubiquitination|protein destabilization|protein monoubiquitination|protein polyubiquitination|protein trimerization	cytoplasmic mRNA processing body|nucleus	DNA binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		ACAATTATCACCTCCTGAGGA	0.458													4	8	---	---	---	---	PASS
OR52B2	255725	broad.mit.edu	37	11	6190909	6190909	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:6190909G>T	uc010qzy.1	-	1	648	c.648C>A	c.(646-648)ATC>ATA	p.I216I		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	216	Helical; Name=5; (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)		AAGACACAGCGATGAGGATAA	0.512													20	37	---	---	---	---	PASS
CTR9	9646	broad.mit.edu	37	11	10776627	10776627	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:10776627G>T	uc001mja.2	+	3	416	c.267G>T	c.(265-267)TTG>TTT	p.L89F		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	89					histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGGATACATTGGCAGCGTATT	0.378													7	153	---	---	---	---	PASS
HPS5	11234	broad.mit.edu	37	11	18303747	18303747	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:18303747C>A	uc001mod.1	-	22	3357	c.3079G>T	c.(3079-3081)GAG>TAG	p.E1027*	HPS5_uc001moe.1_Nonsense_Mutation_p.E913*|HPS5_uc001mof.1_Nonsense_Mutation_p.E913*	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a	1027						cytosol				ovary(1)|pancreas(1)|skin(1)	3						TTCCATTCCTCCACGGTCTCT	0.517									Hermansky-Pudlak_syndrome				5	53	---	---	---	---	PASS
COMMD9	29099	broad.mit.edu	37	11	36296266	36296266	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:36296266C>A	uc001mwn.3	-	6	550	c.513G>T	c.(511-513)GTG>GTT	p.V171V	COMMD9_uc009ykj.2_Silent_p.V129V|COMMD9_uc009yki.1_5'Flank	NM_014186	NP_054905	Q9P000	COMD9_HUMAN	COMM domain containing 9 isoform 1	171	COMM.									ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)				TGCTCAGCTCCACGGTGACAG	0.542													5	97	---	---	---	---	PASS
LRP4	4038	broad.mit.edu	37	11	46900684	46900684	+	Silent	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:46900684C>T	uc001ndn.3	-	21	3143	c.2997G>A	c.(2995-2997)CGG>CGA	p.R999R		NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	999	Extracellular (Potential).				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		CACCTGGGGGCCGGCGGCGGT	0.607													28	95	---	---	---	---	PASS
OR4C13	283092	broad.mit.edu	37	11	49974260	49974260	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:49974260A>T	uc010rhz.1	+	1	286	c.286A>T	c.(286-288)ATG>TTG	p.M96L		NM_001001955	NP_001001955	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C,	96	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(1)	4						CAATGGATGTATGACTCAAGT	0.413													25	49	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55135552	55135552	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:55135552G>A	uc010rif.1	+	1	193	c.193G>A	c.(193-195)GTG>ATG	p.V65M		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	65	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						AATCTACATGGTGACGATAAT	0.418													8	36	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55136373	55136373	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:55136373G>A	uc010rif.1	+	1	1014	c.1014G>A	c.(1012-1014)GGG>GGA	p.G338G		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	338	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						GCTTAGCTGGGAAATGGCTGT	0.368													10	45	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587161	55587161	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:55587161C>A	uc010rin.1	+	1	56	c.56C>A	c.(55-57)TCA>TAA	p.S19*		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	19	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				TTGGGCTTCTCAGATTACCCA	0.428													21	27	---	---	---	---	PASS
OR8H3	390152	broad.mit.edu	37	11	55890170	55890170	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:55890170G>T	uc001nii.1	+	1	322	c.322G>T	c.(322-324)GGT>TGT	p.G108C		NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					TGTCTTCTTGGGTACTGCTGA	0.453													9	238	---	---	---	---	PASS
OR8H3	390152	broad.mit.edu	37	11	55890505	55890505	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:55890505G>A	uc001nii.1	+	1	657	c.657G>A	c.(655-657)GTG>GTA	p.V219V		NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					CATCCTATGTGTCCATTCTCT	0.438													13	68	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55944289	55944289	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:55944289C>G	uc010rjb.1	+	1	196	c.196C>G	c.(196-198)CTT>GTT	p.L66V		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	66	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					ACTCAGCTGTCTTTCATTTGT	0.443													23	87	---	---	---	---	PASS
OR5T1	390155	broad.mit.edu	37	11	56043645	56043645	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:56043645C>A	uc001nio.1	+	1	531	c.531C>A	c.(529-531)AGC>AGA	p.S177R		NM_001004745	NP_001004745	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T,	177	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00448)					CTACATTTAGCCTGTCCTTCT	0.418													8	116	---	---	---	---	PASS
OR4D6	219983	broad.mit.edu	37	11	59224488	59224488	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:59224488C>A	uc010rku.1	+	1	55	c.55C>A	c.(55-57)CGT>AGT	p.R19S		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	19	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						GGAACTTACACGTTCCCGAGA	0.443													34	93	---	---	---	---	PASS
TM7SF2	7108	broad.mit.edu	37	11	64880868	64880868	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:64880868G>C	uc001oct.2	+	4	628	c.481G>C	c.(481-483)GCA>CCA	p.A161P	TM7SF2_uc010rny.1_Missense_Mutation_p.A45P|TM7SF2_uc001ocu.2_Missense_Mutation_p.A161P|TM7SF2_uc001ocv.2_Missense_Mutation_p.A182P	NM_003273	NP_003264	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	161					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane	delta14-sterol reductase activity			ovary(1)	1						TTCGGCCCTGGCACCTGGGGG	0.587											OREG0021072	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	81	---	---	---	---	PASS
DPP3	10072	broad.mit.edu	37	11	66254031	66254031	+	Silent	SNP	C	T	T	rs76983925	by1000genomes	TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:66254031C>T	uc001oig.1	+	4	443	c.381C>T	c.(379-381)ATC>ATT	p.I127I	DPP3_uc001oif.1_Silent_p.I127I|DPP3_uc010rpe.1_Silent_p.I116I	NM_005700	NP_005691	Q9NY33	DPP3_HUMAN	dipeptidyl peptidase III	127					proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2						AACGGGTGATCCTAGGGAGTG	0.602													21	114	---	---	---	---	PASS
RBM4	5936	broad.mit.edu	37	11	66411414	66411414	+	Silent	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:66411414A>T	uc009yrj.2	+	3	1394	c.906A>T	c.(904-906)TCA>TCT	p.S302S	RBM4_uc009yrk.2_Silent_p.S277S|RBM4_uc001oiw.1_Silent_p.S302S|RBM4_uc001oix.1_Intron|RBM4_uc010rpj.1_Intron|RBM4_uc001oiy.1_Silent_p.S302S|RBM4_uc001oiz.1_Silent_p.S302S	NM_002896	NP_002887	Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	302	Interaction with TNPO3.				circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|negative regulation of translation in response to stress|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|positive regulation of muscle cell differentiation|regulation of alternative nuclear mRNA splicing, via spliceosome|regulation of nucleocytoplasmic transport|RNA splicing|stress-activated MAPK cascade	nuclear speck|nucleolus|stress granule	miRNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|zinc ion binding			ovary(1)	1				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		ctTCCACTTCATATTACGGGC	0.438													8	28	---	---	---	---	PASS
AIP	9049	broad.mit.edu	37	11	67258318	67258318	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:67258318G>C	uc001olv.2	+	6	972	c.847G>C	c.(847-849)GAG>CAG	p.E283Q		NM_003977	NP_003968	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein	283	TPR 2.				protein maturation by protein folding|protein targeting to mitochondrion	nucleus	signal transducer activity|transcription coactivator activity|transcription factor binding|unfolded protein binding				0						GAATGCCCAGGAGGCCCAGGC	0.667									Familial_Isolated_Pituitary_Adenoma_				4	25	---	---	---	---	PASS
GAL	51083	broad.mit.edu	37	11	68453099	68453099	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:68453099G>T	uc001oob.2	+	3	337	c.119G>T	c.(118-120)GGC>GTC	p.G40V		NM_015973	NP_057057	P22466	GALA_HUMAN	galanin preproprotein	40					growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)		AACAGCGCGGGCTACCTGCTG	0.632													6	60	---	---	---	---	PASS
CPT1A	1374	broad.mit.edu	37	11	68574951	68574951	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:68574951G>A	uc001oog.3	-	4	607	c.437C>T	c.(436-438)GCC>GTC	p.A146V	CPT1A_uc001oof.3_Missense_Mutation_p.A146V|CPT1A_uc009ysj.2_Missense_Mutation_p.A146V	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform	146	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)	GATCTTGGTGGCACGACTCAT	0.597													5	93	---	---	---	---	PASS
ANO1	55107	broad.mit.edu	37	11	70007429	70007429	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:70007429G>A	uc001opj.2	+	17	2046	c.1741G>A	c.(1741-1743)GAG>AAG	p.E581K	ANO1_uc001opk.1_Missense_Mutation_p.E523K|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Missense_Mutation_p.E290K	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	581	Helical; (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						CCTCCTGGACGAGGTGTATGG	0.463													19	245	---	---	---	---	PASS
CTTN	2017	broad.mit.edu	37	11	70255985	70255985	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:70255985G>T	uc001opv.3	+	5	416	c.210G>T	c.(208-210)AAG>AAT	p.K70N	CTTN_uc001opu.2_Missense_Mutation_p.K70N|CTTN_uc001opw.3_Missense_Mutation_p.K70N	NM_005231	NP_005222	Q14247	SRC8_HUMAN	cortactin isoform a	70						cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		AGACCCTTAAGGAGAAGGAAC	0.463													12	925	---	---	---	---	PASS
ARRB1	408	broad.mit.edu	37	11	74994459	74994459	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:74994459G>A	uc001owe.1	-	5	448	c.226C>T	c.(226-228)CGC>TGC	p.R76C	ARRB1_uc001owf.1_Missense_Mutation_p.R76C	NM_004041	NP_004032	P49407	ARRB1_HUMAN	arrestin beta 1 isoform A	76	Interaction with CHRM2 (By similarity).|Interaction with SRC (By similarity).				G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2						AGGTCCTTGCGAAAGGTCAGG	0.642													39	32	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108224510	108224510	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:108224510G>A	uc001pkb.1	+	60	9074	c.8689G>A	c.(8689-8691)GGC>AGC	p.G2897S	ATM_uc009yxr.1_Missense_Mutation_p.G2897S|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.G1549S	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2897	PI3K/PI4K.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TTTTGAACAGGGCAAAATCCT	0.408			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			29	52	---	---	---	---	PASS
CBL	867	broad.mit.edu	37	11	119155953	119155953	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:119155953C>A	uc001pwe.2	+	11	1756	c.1618C>A	c.(1618-1620)CGA>AGA	p.R540R		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	540	Pro-rich.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TCCCACACTTCGAGATCTTCC	0.532									CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome		OREG0021401	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	68	---	---	---	---	PASS
IGSF9B	22997	broad.mit.edu	37	11	133805642	133805642	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:133805642C>G	uc001qgx.3	-	7	1068	c.837G>C	c.(835-837)AGG>AGC	p.R279S	IGSF9B_uc001qgy.1_Missense_Mutation_p.R121S	NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	279	Extracellular (Potential).|Ig-like 3.					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGATGCGCACCCTCAGCTTCA	0.632													5	7	---	---	---	---	PASS
GLB1L2	89944	broad.mit.edu	37	11	134228991	134228991	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr11:134228991C>A	uc001qhp.2	+	7	877	c.689C>A	c.(688-690)ACT>AAT	p.T230N	GLB1L2_uc009zdg.1_RNA	NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor	230					carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|pancreas(1)|skin(1)	3	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		CTGCTCCTGACTTCAGACAAC	0.612													4	78	---	---	---	---	PASS
C12orf5	57103	broad.mit.edu	37	12	4461510	4461510	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:4461510G>T	uc001qmp.2	+	6	545	c.466G>T	c.(466-468)GGA>TGA	p.G156*		NM_020375	NP_065108	Q9NQ88	TIGAR_HUMAN	TP53-induced glycolysis and apoptosis regulator	156						intracellular	fructose-2,6-bisphosphate 2-phosphatase activity			skin(1)	1			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			GTTTTCCCAAGGATCTCCAAG	0.363													10	33	---	---	---	---	PASS
ZNF705A	440077	broad.mit.edu	37	12	8329842	8329842	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:8329842G>T	uc001qud.1	+	5	638	c.566G>T	c.(565-567)CGG>CTG	p.R189L	FAM66C_uc001que.3_5'Flank|FAM66C_uc001quf.3_5'Flank|FAM66C_uc009zgc.2_5'Flank|FAM66C_uc001qug.3_5'Flank	NM_001004328	NP_001004328	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	189	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				Kidney(36;0.0877)		CGCCTTAGACGGCACAAGATG	0.393													37	74	---	---	---	---	PASS
GUCY2C	2984	broad.mit.edu	37	12	14832636	14832636	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:14832636C>A	uc001rcd.2	-	6	922	c.785G>T	c.(784-786)CGA>CTA	p.R262L	GUCY2C_uc009zhz.2_Missense_Mutation_p.R262L	NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C precursor	262	Extracellular (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(2)	6						AGCCACTGCTCGGTCACCCTT	0.418													4	63	---	---	---	---	PASS
WBP11	51729	broad.mit.edu	37	12	14947584	14947584	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:14947584G>T	uc001rci.2	-	7	769	c.608C>A	c.(607-609)CCC>CAC	p.P203H		NM_016312	NP_057396	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	203	Pro-rich.				mRNA processing|RNA splicing|rRNA processing	cytoplasm	single-stranded DNA binding|WW domain binding			ovary(1)|lung(1)	2						TGGACCAGGGGGAGGGCCAGG	0.512													7	162	---	---	---	---	PASS
STK38L	23012	broad.mit.edu	37	12	27450705	27450705	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:27450705C>T	uc001rhr.2	+	2	251	c.52C>T	c.(52-54)CGG>TGG	p.R18W	STK38L_uc001rhs.2_RNA|STK38L_uc010sjm.1_Intron	NM_015000	NP_055815	Q9Y2H1	ST38L_HUMAN	serine/threonine kinase 38 like	18					intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)					CAACCATACCCGGGAAAGAGT	0.403													11	53	---	---	---	---	PASS
NELL2	4753	broad.mit.edu	37	12	45173639	45173639	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:45173639A>T	uc001rog.2	-	4	1097	c.502T>A	c.(502-504)TGC>AGC	p.C168S	NELL2_uc001rof.3_Missense_Mutation_p.C167S|NELL2_uc001roh.2_Missense_Mutation_p.C168S|NELL2_uc009zkd.2_Missense_Mutation_p.C167S|NELL2_uc010skz.1_Missense_Mutation_p.C218S|NELL2_uc010sla.1_Missense_Mutation_p.C191S|NELL2_uc001roi.1_Missense_Mutation_p.C168S|NELL2_uc010slb.1_Missense_Mutation_p.C167S|NELL2_uc001roj.2_Missense_Mutation_p.C168S	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	168	TSP N-terminal.				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		TACTTATTGCAGTCAATGTGT	0.398													13	61	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49443771	49443771	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:49443771G>C	uc001rta.3	-	11	3600	c.3600C>G	c.(3598-3600)ATC>ATG	p.I1200M		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1200					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						TGTCGGATTTGATGAGAGTGG	0.592			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			16	41	---	---	---	---	PASS
BIN2	51411	broad.mit.edu	37	12	51685860	51685860	+	Missense_Mutation	SNP	C	A	A	rs150210505		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:51685860C>A	uc001ryg.2	-	10	1082	c.1030G>T	c.(1030-1032)GCC>TCC	p.A344S	BIN2_uc009zlz.2_Missense_Mutation_p.A312S|BIN2_uc001ryh.2_Missense_Mutation_p.A220S|BIN2_uc010sng.1_Missense_Mutation_p.A318S	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2	344						cytoplasm	protein binding			ovary(1)	1						TGGGCCTGGGCGGGGCCATTG	0.577													3	22	---	---	---	---	PASS
MIR616	693201	broad.mit.edu	37	12	57913018	57913018	+	RNA	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:57913018G>C	hsa-mir-616|MI0003629	-			c.25G>C			DDIT3_uc001soi.2_Intron|DDIT3_uc009zps.2_Intron|DDIT3_uc009zpt.2_Intron																	0						gtcactgaagggttttgagtg	0.000													4	24	---	---	---	---	PASS
FRS2	10818	broad.mit.edu	37	12	69968637	69968637	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:69968637G>T	uc001suy.2	+	10	1939	c.1429G>T	c.(1429-1431)GAG>TAG	p.E477*	FRS2_uc001suz.2_Nonsense_Mutation_p.E477*|FRS2_uc009zrj.2_Nonsense_Mutation_p.E477*|FRS2_uc009zrk.2_Nonsense_Mutation_p.E477*	NM_006654	NP_006645	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	477					activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			GATAGACATCGAGAGAACTGC	0.493													5	113	---	---	---	---	PASS
SLC41A2	84102	broad.mit.edu	37	12	105282956	105282956	+	Splice_Site	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:105282956C>A	uc001tla.2	-	4	903	c.736_splice	c.e4-1	p.V246_splice		NM_032148	NP_115524	Q96JW4	S41A2_HUMAN	solute carrier family 41, member 2							integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			ovary(1)|skin(1)	2						TTGCCTGAACCTAAAATTTTT	0.299													6	14	---	---	---	---	PASS
IFT81	28981	broad.mit.edu	37	12	110656005	110656005	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:110656005G>T	uc001tqi.2	+	19	2135	c.2005G>T	c.(2005-2007)GGT>TGT	p.G669C	IFT81_uc001tqh.2_Missense_Mutation_p.G669C|IFT81_uc001tqj.2_RNA	NM_001143779	NP_001137251	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81-like isoform 1	669					cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1						AATTCAGGAGGGTGGGGAGGA	0.388													18	56	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117672370	117672370	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:117672370C>A	uc001twm.1	-	21	3921	c.3235G>T	c.(3235-3237)GGT>TGT	p.G1079C		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1079	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	GGAATGTTACCTAAAGCCGTG	0.592													5	29	---	---	---	---	PASS
MPHOSPH8	54737	broad.mit.edu	37	13	20240600	20240600	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:20240600C>A	uc001umh.2	+	10	2064	c.2055C>A	c.(2053-2055)CTC>CTA	p.L685L	MPHOSPH8_uc001umg.2_Silent_p.L685L	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	685	ANK 3.				cell cycle	cytoplasm|nucleus					0		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		TCGTACGACTCGTAATTGAAT	0.443													6	259	---	---	---	---	PASS
SOHLH2	54937	broad.mit.edu	37	13	36747888	36747888	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:36747888G>A	uc001uvj.2	-	9	1030	c.941C>T	c.(940-942)ACG>ATG	p.T314M	SOHLH2_uc010tei.1_Missense_Mutation_p.T391M	NM_017826	NP_060296	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic	314					cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		ATTCCAGCACGTATTAGTCAG	0.483													7	72	---	---	---	---	PASS
COG3	83548	broad.mit.edu	37	13	46077414	46077414	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:46077414G>T	uc001vak.2	+	14	1625	c.1524G>T	c.(1522-1524)AAG>AAT	p.K508N	COG3_uc001vaj.1_Missense_Mutation_p.K508N|COG3_uc010tfv.1_Missense_Mutation_p.K345N|COG3_uc010aci.2_Missense_Mutation_p.K284N	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3	508					ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AACAGAAGAAGGTACCTTCAG	0.378													5	50	---	---	---	---	PASS
SLAIN1	122060	broad.mit.edu	37	13	78335084	78335084	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:78335084G>T	uc010thy.1	+	6	1087	c.1044G>T	c.(1042-1044)ATG>ATT	p.M348I	SLAIN1_uc001vkk.1_Missense_Mutation_p.M271I|SLAIN1_uc001vkl.1_Missense_Mutation_p.M227I|SLAIN1_uc010thz.1_Missense_Mutation_p.M226I|SLAIN1_uc010aex.1_Missense_Mutation_p.M113I|SLAIN1_uc010aey.1_Missense_Mutation_p.M113I|SLAIN1_uc001vkm.2_Missense_Mutation_p.M227I	NM_144595	NP_653196	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1 B	490										ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		GCAGTAACATGCCTTTATCAA	0.522													16	43	---	---	---	---	PASS
LIG4	3981	broad.mit.edu	37	13	108863508	108863508	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:108863508T>A	uc001vqn.2	-	2	382	c.109A>T	c.(109-111)AGA>TGA	p.R37*	LIG4_uc001vqo.2_Nonsense_Mutation_p.R37*|LIG4_uc010agg.1_5'UTR|LIG4_uc010agf.2_Nonsense_Mutation_p.R37*|LIG4_uc001vqp.2_Nonsense_Mutation_p.R37*	NM_002312	NP_002303	P49917	DNLI4_HUMAN	DNA ligase IV	37					cell cycle|cell division|cell proliferation|central nervous system development|chromosome organization|DNA ligation involved in DNA recombination|DNA ligation involved in DNA repair|DNA replication|double-strand break repair via nonhomologous end joining|in utero embryonic development|initiation of viral infection|isotype switching|negative regulation of neuron apoptosis|neuron apoptosis|nucleotide-excision repair, DNA gap filling|positive regulation of fibroblast proliferation|positive regulation of neurogenesis|pro-B cell differentiation|provirus integration|response to gamma radiation|response to X-ray|single strand break repair|somatic stem cell maintenance|T cell differentiation in thymus|T cell receptor V(D)J recombination	condensed chromosome|cytoplasm|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|focal adhesion|nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding|protein C-terminus binding				0	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					CTGAAGTGTCTGATTTTTTCT	0.363								NHEJ					10	17	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109859134	109859134	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:109859134G>T	uc001vqt.1	+	35	5653	c.5527G>T	c.(5527-5529)GGG>TGG	p.G1843W	MYO16_uc010agk.1_Missense_Mutation_p.G1865W	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	1843					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)			GAAGCCGGAAGGGGCCTCCTG	0.582													21	14	---	---	---	---	PASS
OR4M1	441670	broad.mit.edu	37	14	20248579	20248579	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:20248579C>A	uc010tku.1	+	1	98	c.98C>A	c.(97-99)TCC>TAC	p.S33Y		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	33	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATATTTCTATCCTTCTATTTG	0.413													61	81	---	---	---	---	PASS
RNASE12	493901	broad.mit.edu	37	14	21058511	21058511	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:21058511G>T	uc001vxt.2	-	1	472	c.372C>A	c.(370-372)TCC>TCA	p.S124S	RNASE11_uc010ahv.2_5'Flank|RNASE11_uc010ahx.2_5'Flank|RNASE11_uc010ahw.2_5'Flank|RNASE11_uc001vxs.2_5'Flank|uc001vxu.1_5'Flank	NM_001024822	NP_001019993	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	124						extracellular region	nucleic acid binding|pancreatic ribonuclease activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		CCTCTGTGGGGGAATAGTGGT	0.458													7	98	---	---	---	---	PASS
CDH24	64403	broad.mit.edu	37	14	23519129	23519129	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:23519129C>T	uc001wil.2	-	10	1761	c.1501G>A	c.(1501-1503)GTG>ATG	p.V501M	CDH24_uc001wik.3_RNA|CDH24_uc010akf.2_Missense_Mutation_p.V463M	NM_022478	NP_071923	Q86UP0	CAD24_HUMAN	cadherin-like 24 isoform 1	501	Cadherin 4.|Extracellular (Potential).				adherens junction organization|cell junction assembly|cell-cell adhesion|homophilic cell adhesion	cell-cell junction|cell-cell junction|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|delta-catenin binding			central_nervous_system(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		GCCACTTGCACGCGCGAGGCC	0.542													41	38	---	---	---	---	PASS
PRKD1	5587	broad.mit.edu	37	14	30068938	30068938	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:30068938C>G	uc001wqh.2	-	14	2172	c.1991G>C	c.(1990-1992)GGA>GCA	p.G664A		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	664	Protein kinase.				cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CAGCATGTCTCCATGGAGTTT	0.378													9	39	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42357069	42357069	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:42357069C>A	uc001wvm.2	+	3	2439	c.1241C>A	c.(1240-1242)ACT>AAT	p.T414N	LRFN5_uc010ana.2_Missense_Mutation_p.T414N	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	414	Extracellular (Potential).|Fibronectin type-III.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		AATGGTGATACTAAATTGAGT	0.353										HNSCC(30;0.082)			9	16	---	---	---	---	PASS
MIR329-1	574408	broad.mit.edu	37	14	101493144	101493144	+	RNA	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:101493144G>T	hsa-mir-329-1|MI0001725	+			c.23G>T			MIR329-2_hsa-mir-329-2|MI0001726_5'Flank|MIR494_hsa-mir-494|MI0003134_5'Flank|uc010txm.1_5'Flank																	0						GAGGTTTTCTGGGTTTCTGTT	0.448													29	56	---	---	---	---	PASS
GPR132	29933	broad.mit.edu	37	14	105518036	105518036	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:105518036G>T	uc001yqd.2	-	4	1337	c.438C>A	c.(436-438)TAC>TAA	p.Y146*	GPR132_uc001yqc.2_5'UTR|GPR132_uc001yqe.2_Nonsense_Mutation_p.Y137*	NM_013345	NP_037477	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	146	Cytoplasmic (Potential).				response to stress	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		TCTCCAGCGCGTACACCACGG	0.622													19	28	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106967470	106967470	+	RNA	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr14:106967470C>T	uc010tyt.1	-	201		c.8971G>A								Parts of antibodies, mostly variable regions.												0						AGAAGACCCTCCAGGTCCAGT	0.498													36	51	---	---	---	---	PASS
PYGO1	26108	broad.mit.edu	37	15	55838299	55838299	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr15:55838299G>T	uc010bfl.1	-	3	1238	c.1182C>A	c.(1180-1182)ACC>ACA	p.T394T	PYGO1_uc002adf.1_Silent_p.T394T	NM_015617	NP_056432	Q9Y3Y4	PYGO1_HUMAN	pygopus homolog 1	394	PHD-type.				Wnt receptor signaling pathway	nucleus	zinc ion binding			ovary(1)|skin(1)	2				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		CAGCCATACAGGTATCACAGC	0.443													13	51	---	---	---	---	PASS
ALDH1A2	8854	broad.mit.edu	37	15	58256106	58256106	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr15:58256106G>T	uc002aex.2	-	9	1121	c.1063C>A	c.(1063-1065)CCC>ACC	p.P355T	ALDH1A2_uc002aey.2_Missense_Mutation_p.P317T|ALDH1A2_uc010ugv.1_Missense_Mutation_p.P334T|ALDH1A2_uc010ugw.1_Missense_Mutation_p.P326T|ALDH1A2_uc002aew.2_Missense_Mutation_p.P259T	NM_003888	NP_003879	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 1	355					negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	TCAGTGGTGGGGTCAAAGGGA	0.527													21	32	---	---	---	---	PASS
CILP	8483	broad.mit.edu	37	15	65489533	65489533	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr15:65489533C>A	uc002aon.2	-	9	3272	c.3091G>T	c.(3091-3093)GGC>TGC	p.G1031C		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	1031					negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix				ovary(4)|pancreas(2)|skin(1)	7						CGGCAGCTGCCCTGGGGGATG	0.577													13	32	---	---	---	---	PASS
TLE3	7090	broad.mit.edu	37	15	70347520	70347520	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr15:70347520G>A	uc002asm.2	-	15	2574	c.1455C>T	c.(1453-1455)CAC>CAT	p.H485H	TLE3_uc002ask.2_Silent_p.H412H|TLE3_uc002asl.2_Silent_p.H485H|TLE3_uc010ukd.1_Silent_p.H475H|TLE3_uc010bik.1_Silent_p.H66H|TLE3_uc010bil.1_Silent_p.H482H|TLE3_uc002asn.2_Silent_p.H473H|TLE3_uc002asp.2_Silent_p.H477H|TLE3_uc002aso.2_Silent_p.H480H	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a	485	WD 1.				organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						CCACCTCCCCGTGGCTGAGTG	0.662													16	37	---	---	---	---	PASS
FLYWCH2	114984	broad.mit.edu	37	16	2946558	2946558	+	Silent	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:2946558C>T	uc002csa.2	+	3	479	c.108C>T	c.(106-108)CCC>CCT	p.P36P	FLYWCH2_uc010uwj.1_Silent_p.P36P|FLYWCH2_uc010uwk.1_Silent_p.P36P	NM_138439	NP_612448	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	36											0						CCAGGAAGCCCAGAAAGTTCT	0.642													15	75	---	---	---	---	PASS
CIITA	4261	broad.mit.edu	37	16	10996609	10996609	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:10996609G>A	uc002dai.3	+	8	856	c.723G>A	c.(721-723)TGG>TGA	p.W241*	CIITA_uc002daj.3_Nonsense_Mutation_p.W242*|CIITA_uc002dak.3_Nonsense_Mutation_p.W192*|CIITA_uc002dag.2_Nonsense_Mutation_p.W241*|CIITA_uc002dah.2_Nonsense_Mutation_p.W193*|CIITA_uc010bup.1_Nonsense_Mutation_p.W241*	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	241					interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1						ATGGGCTCTGGCAAATCTCTG	0.582			T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								10	51	---	---	---	---	PASS
RRN3	54700	broad.mit.edu	37	16	15180227	15180227	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:15180227T>C	uc002dde.2	-	4	405	c.337A>G	c.(337-339)ATA>GTA	p.I113V	PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Missense_Mutation_p.I14V|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Missense_Mutation_p.I113V	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor	113					regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1						CTTACTAATATAATACTGATA	0.299													12	40	---	---	---	---	PASS
ANKS4B	257629	broad.mit.edu	37	16	21245162	21245162	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:21245162C>A	uc010bwp.1	+	1	147	c.104C>A	c.(103-105)CCT>CAT	p.P35H		NM_145865	NP_665872	Q8N8V4	ANS4B_HUMAN	harmonin-interacting ankyrin-repeat containing	35	ANK 1.									ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0565)		GGCATGACTCCTACTCTCTTG	0.463													7	168	---	---	---	---	PASS
PLK1	5347	broad.mit.edu	37	16	23695281	23695281	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:23695281G>T	uc002dlz.1	+	5	960	c.907G>T	c.(907-909)GAG>TAG	p.E303*		NM_005030	NP_005021	P53350	PLK1_HUMAN	polo-like kinase 1	303	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding	centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole	anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding			lung(1)|skin(1)	2				GBM - Glioblastoma multiforme(48;0.0156)		GCTTAATGACGAGTTCTTTAC	0.567													6	280	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30745064	30745064	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:30745064C>A	uc002dze.1	+	29	6824	c.6439C>A	c.(6439-6441)CAG>AAG	p.Q2147K	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.Q1942K	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	2147	Helicase C-terminal.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			CATGGATGCTCAGGCCCAGGA	0.527													15	50	---	---	---	---	PASS
FAM192A	80011	broad.mit.edu	37	16	57207687	57207687	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:57207687C>A	uc010vhk.1	-	2	339	c.80G>T	c.(79-81)AGG>ATG	p.R27M	FAM192A_uc002ekz.3_Missense_Mutation_p.R27M|FAM192A_uc002ekv.3_Translation_Start_Site|FAM192A_uc002ekw.3_Missense_Mutation_p.R27M|FAM192A_uc002ekx.3_Missense_Mutation_p.R27M|FAM192A_uc002eky.3_Missense_Mutation_p.R27M|FAM192A_uc010ccx.2_Missense_Mutation_p.R27M	NM_024946	NP_079222	Q9GZU8	F192A_HUMAN	NEFA-interacting nuclear protein NIP30	27						nucleus					0						TTCTTGCCTCCTTTTGCGCCG	0.363													7	80	---	---	---	---	PASS
JPH3	57338	broad.mit.edu	37	16	87723839	87723839	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr16:87723839C>T	uc002fkd.2	+	4	2127	c.1873C>T	c.(1873-1875)CCC>TCC	p.P625S	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	625	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GGAGACGCATCCCCAGAAAAG	0.657													4	8	---	---	---	---	PASS
NLRP1	22861	broad.mit.edu	37	17	5421068	5421068	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:5421068G>T	uc002gci.2	-	15	4610	c.4055C>A	c.(4054-4056)CCA>CAA	p.P1352Q	NLRP1_uc002gcg.1_Missense_Mutation_p.P1356Q|NLRP1_uc002gck.2_Missense_Mutation_p.P1308Q|NLRP1_uc002gcj.2_Missense_Mutation_p.P1322Q|NLRP1_uc002gcl.2_Missense_Mutation_p.P1278Q|NLRP1_uc002gch.3_Missense_Mutation_p.P1308Q	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	1352					defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)				GGATTTACCTGGTTTCACCAA	0.398													5	69	---	---	---	---	PASS
NEURL4	84461	broad.mit.edu	37	17	7224163	7224163	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:7224163C>A	uc002gga.1	-	21	3447	c.3440G>T	c.(3439-3441)GGG>GTG	p.G1147V	NEURL4_uc002gfy.1_5'Flank|GPS2_uc002gfz.1_5'Flank|NEURL4_uc002ggb.1_Missense_Mutation_p.G1145V	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	1147	NHR 6.						protein binding			upper_aerodigestive_tract(1)|ovary(1)	2						CGTACGGTTCCCATTAGACAA	0.562													7	150	---	---	---	---	PASS
EIF4A1	1973	broad.mit.edu	37	17	7480801	7480801	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:7480801G>T	uc002gho.1	+	15	2089	c.764G>T	c.(763-765)CGA>CTA	p.R255L	EIF4A1_uc002ghr.1_Missense_Mutation_p.R255L|EIF4A1_uc002ghq.1_Missense_Mutation_p.R255L|EIF4A1_uc002ghp.1_Missense_Mutation_p.R255L|SNORA67_uc010cml.1_5'Flank|CD68_uc002ghv.2_5'Flank|CD68_uc002ghu.2_5'Flank	NM_001416	NP_001407	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A	255	Helicase C-terminal.				nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1						AACGTGGAACGAGAGGTGGGG	0.557													4	39	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578407	7578407	+	Missense_Mutation	SNP	G	C	C	rs138729528		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:7578407G>C	uc002gim.2	-	5	717	c.523C>G	c.(523-525)CGC>GGC	p.R175G	TP53_uc002gig.1_Missense_Mutation_p.R175G|TP53_uc002gih.2_Missense_Mutation_p.R175G|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R43G|TP53_uc010cng.1_Missense_Mutation_p.R43G|TP53_uc002gii.1_Missense_Mutation_p.R43G|TP53_uc010cnh.1_Missense_Mutation_p.R175G|TP53_uc010cni.1_Missense_Mutation_p.R175G|TP53_uc002gij.2_Missense_Mutation_p.R175G|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R82G|TP53_uc002gio.2_Missense_Mutation_p.R43G|TP53_uc010vug.1_Missense_Mutation_p.R136G	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	175	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in sporadic cancers; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		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.R175H(721)|p.R175L(19)|p.R175C(12)|p.R175G(11)|p.0?(7)|p.R175P(5)|p.R175S(5)|p.R175R(4)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.R175fs*5(2)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.K164_P219del(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*6(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R175fs*72(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.S149fs*72(1)|p.R174_E180>K(1)|p.R174fs*3(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)		TGGGGGCAGCGCCTCACAACC	0.657		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)			10	25	---	---	---	---	PASS
SCO1	6341	broad.mit.edu	37	17	10596167	10596167	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:10596167C>A	uc002gmr.3	-	3	537	c.476G>T	c.(475-477)TGG>TTG	p.W159L	SCO1_uc002gms.3_Intron	NM_004589	NP_004580	O75880	SCO1_HUMAN	cytochrome oxidase deficient homolog 1	159					cellular copper ion homeostasis|copper ion transport|generation of precursor metabolites and energy|respiratory chain complex IV assembly	mitochondrial inner membrane	copper ion binding				0						AATCAATAACCACTGACCCAA	0.458													5	56	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18023401	18023401	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:18023401G>A	uc010vxh.1	+	2	1625	c.1287G>A	c.(1285-1287)ATG>ATA	p.M429I		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	429	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)					CCCACGCCATGGATGACATCG	0.652													17	21	---	---	---	---	PASS
CCDC144NL	339184	broad.mit.edu	37	17	20799191	20799191	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:20799191C>A	uc002gyf.2	-	1	263	c.143G>T	c.(142-144)GGC>GTC	p.G48V	uc002gyg.1_Intron|uc002gyh.1_Intron	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,	48											0						GTAGGAGAAGCCCAAGGACCA	0.617													19	64	---	---	---	---	PASS
MMP28	79148	broad.mit.edu	37	17	34100371	34100371	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:34100371C>A	uc002hjy.1	-	4	676	c.417G>T	c.(415-417)CTG>CTT	p.L139L	MMP28_uc002hjw.1_RNA|MMP28_uc002hjz.1_RNA	NM_024302	NP_077278	Q9H239	MMP28_HUMAN	matrix metalloproteinase 28 isoform 1	139					proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GCCAGTTCACCAGGCGGTAGG	0.637													5	2	---	---	---	---	PASS
GGNBP2	79893	broad.mit.edu	37	17	34937844	34937844	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:34937844G>T	uc002hnb.2	+	9	1340	c.1091G>T	c.(1090-1092)CGA>CTA	p.R364L	GGNBP2_uc002hna.2_Missense_Mutation_p.R364L|GGNBP2_uc002hnc.1_Missense_Mutation_p.R193L	NM_024835	NP_079111	Q9H3C7	GGNB2_HUMAN	zinc finger protein 403	364					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		GAAGAGGAACGAGTAAGAGAA	0.368													4	83	---	---	---	---	PASS
KRT9	3857	broad.mit.edu	37	17	39724766	39724766	+	Silent	SNP	G	T	T	rs139934315		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:39724766G>T	uc002hxe.3	-	5	1230	c.1164C>A	c.(1162-1164)CTC>CTA	p.L388L	JUP_uc010wfs.1_Intron	NM_000226	NP_000217	P35527	K1C9_HUMAN	keratin 9	388	Rod.|Coil 2.				intermediate filament organization|skin development		protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Breast(137;0.000307)				CAACCTTGCTGAGCTGAGACT	0.552													7	239	---	---	---	---	PASS
AARSD1	80755	broad.mit.edu	37	17	41103875	41103875	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:41103875C>G	uc002icc.2	-	11	1048	c.1045G>C	c.(1045-1047)GGT>CGT	p.G349R	AARSD1_uc002icd.2_Missense_Mutation_p.G462R|AARSD1_uc002ice.2_Missense_Mutation_p.G432R|AARSD1_uc002icf.2_Missense_Mutation_p.G523R|AARSD1_uc010whg.1_Missense_Mutation_p.G523R	NM_025267	NP_079543	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	349					alanyl-tRNA aminoacylation	cytoplasm	alanine-tRNA ligase activity|ATP binding|metal ion binding|nucleic acid binding				0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		AGTCCACCACCTTTCTCATCG	0.522													15	19	---	---	---	---	PASS
OR4D2	124538	broad.mit.edu	37	17	56247485	56247485	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:56247485A>C	uc010wnp.1	+	1	469	c.469A>C	c.(469-471)ATT>CTT	p.I157L		NM_001004707	NP_001004707	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D,	157	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						TGTCCACTCTATTGTCCAGCT	0.567													14	54	---	---	---	---	PASS
TBC1D16	125058	broad.mit.edu	37	17	77925290	77925290	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:77925290G>T	uc002jxj.2	-	5	1164	c.1048C>A	c.(1048-1050)CAG>AAG	p.Q350K	TBC1D16_uc002jxh.2_5'Flank|TBC1D16_uc002jxi.2_5'Flank|TBC1D16_uc002jxk.1_5'Flank	NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	350						intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			TTCCACTGCTGGAACACGTCA	0.632													5	79	---	---	---	---	PASS
METTL4	64863	broad.mit.edu	37	18	2539011	2539011	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr18:2539011C>A	uc002klh.3	-	9	2187	c.1407G>T	c.(1405-1407)GAG>GAT	p.E469D	METTL4_uc010dkj.2_3'UTR	NM_022840	NP_073751	Q8N3J2	METL4_HUMAN	methyltransferase like 4	469					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		methyltransferase activity|nucleic acid binding			kidney(1)|skin(1)	2						AGCTTCCAGACTCCACAGCAA	0.353													14	40	---	---	---	---	PASS
KLHL14	57565	broad.mit.edu	37	18	30350180	30350180	+	Silent	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr18:30350180C>A	uc002kxm.1	-	2	763	c.375G>T	c.(373-375)CTG>CTT	p.L125L		NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14	125	BTB.					cytosol|endoplasmic reticulum membrane				ovary(1)	1						CCTGCAGCACCAGGTTGTTGA	0.567													5	64	---	---	---	---	PASS
DTNA	1837	broad.mit.edu	37	18	32438301	32438301	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr18:32438301C>G	uc010dmn.1	+	15	1505	c.1504C>G	c.(1504-1506)CAG>GAG	p.Q502E	DTNA_uc010xbx.1_Missense_Mutation_p.Q252E|DTNA_uc002kxv.3_Missense_Mutation_p.Q445E|DTNA_uc002kxw.2_Missense_Mutation_p.Q445E|DTNA_uc010dmj.2_Missense_Mutation_p.Q442E|DTNA_uc002kxz.2_Missense_Mutation_p.Q442E|DTNA_uc002kxy.2_Missense_Mutation_p.Q442E|DTNA_uc010dml.2_Missense_Mutation_p.Q442E|DTNA_uc002kyb.3_Missense_Mutation_p.Q499E|DTNA_uc010dmm.2_Missense_Mutation_p.Q502E|DTNA_uc010xby.1_Missense_Mutation_p.Q192E|DTNA_uc010dmo.2_Missense_Mutation_p.Q124E|DTNA_uc002kyd.3_Missense_Mutation_p.Q124E|DTNA_uc010xbz.1_Missense_Mutation_p.Q211E|DTNA_uc010xca.1_Missense_Mutation_p.Q154E|DTNA_uc002kye.2_Missense_Mutation_p.Q150E	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	502	Potential.				neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						ACAAGCTTCTCAGCCCACGCC	0.512													20	22	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56149153	56149153	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr18:56149153T>A	uc002lhj.3	-	13	6629	c.6415A>T	c.(6415-6417)AAA>TAA	p.K2139*		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	2139							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						TGCTTCTGTTTCTGGTTGTTG	0.428													15	41	---	---	---	---	PASS
CDH20	28316	broad.mit.edu	37	18	59174738	59174738	+	Missense_Mutation	SNP	C	A	A	rs148517362		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr18:59174738C>A	uc010dps.1	+	5	974	c.962C>A	c.(961-963)GCC>GAC	p.A321D	CDH20_uc002lif.2_Missense_Mutation_p.A315D	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	321	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				GGTGCAGATGCCTTTGACATT	0.423													12	33	---	---	---	---	PASS
SAFB2	9667	broad.mit.edu	37	19	5621405	5621405	+	Silent	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:5621405C>T	uc002mcd.2	-	2	401	c.189G>A	c.(187-189)GCG>GCA	p.A63A	SAFB_uc010xiq.1_5'Flank|SAFB_uc002mcf.2_5'Flank|SAFB_uc002mcg.2_5'Flank|SAFB_uc002mce.3_5'Flank|SAFB_uc010xir.1_5'Flank|SAFB_uc010xis.1_5'Flank|SAFB_uc010xit.1_5'Flank|SAFB_uc010xiu.1_5'Flank|SAFB2_uc010xio.1_Silent_p.A63A|SAFB2_uc010xip.1_RNA	NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	63	SAP.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CTTCTTTAACCGCCTATTAGG	0.443													13	397	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9026256	9026256	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:9026256C>A	uc002mkp.2	-	14	36934	c.36730G>T	c.(36730-36732)GAG>TAG	p.E12244*		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12246	SEA 2.|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						ATGTCCTCCTCGTACTGCAGG	0.532													6	180	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9072230	9072230	+	Silent	SNP	G	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:9072230G>C	uc002mkp.2	-	3	15420	c.15216C>G	c.(15214-15216)CTC>CTG	p.L5072L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5074	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						GGCCAGAGGTGAGAAGTGAAG	0.478													28	98	---	---	---	---	PASS
ZNF625	90589	broad.mit.edu	37	19	12256633	12256633	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:12256633A>C	uc002mth.2	-	4	750	c.400T>G	c.(400-402)TTG>GTG	p.L134V	ZNF20_uc002mtg.1_Intron|ZNF625_uc010dyn.1_RNA|ZNF625_uc010dyo.1_Missense_Mutation_p.L168V	NM_145233	NP_660276	Q96I27	ZN625_HUMAN	zinc finger protein 625	134	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGACACATCAAGGCTTTCCCA	0.408													39	41	---	---	---	---	PASS
FBXW9	84261	broad.mit.edu	37	19	12800824	12800824	+	Silent	SNP	G	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:12800824G>A	uc010dyx.2	-	6	1044	c.1044C>T	c.(1042-1044)ACC>ACT	p.T348T	FBXW9_uc010xmp.1_RNA|uc002mul.1_3'UTR|FBXW9_uc002mum.1_Silent_p.T328T|FBXW9_uc002mun.1_Silent_p.T165T	NM_032301	NP_115677	Q5XUX1	FBXW9_HUMAN	F-box and WD-40 domain protein 9	358	WD 4.						protein binding			ovary(1)	1						CCACCACCAGGGTGTGGTCCT	0.682													9	18	---	---	---	---	PASS
OR7A17	26333	broad.mit.edu	37	19	14991543	14991543	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:14991543C>G	uc010xob.1	-	1	625	c.625G>C	c.(625-627)GGT>CGT	p.G209R		NM_030901	NP_112163	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Ovarian(108;0.203)					ACAAGGGGACCACCAGCCAGC	0.483													14	50	---	---	---	---	PASS
LPAR2	9170	broad.mit.edu	37	19	19735130	19735130	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:19735130C>A	uc002nnb.3	-	3	1130	c.991G>T	c.(991-993)GGA>TGA	p.G331*	LPAR2_uc002nna.3_Nonsense_Mutation_p.G331*|LPAR2_uc002nnc.3_Nonsense_Mutation_p.G331*	NM_004720	NP_004711	Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	331	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration	cell surface|integral to plasma membrane	LIM domain binding|lipid binding			ovary(1)|breast(1)	2						CTGGCACCTCCCTGGGCAGAG	0.622													6	106	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30935742	30935742	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:30935742A>T	uc002nsu.1	+	2	1411	c.1273A>T	c.(1273-1275)AAC>TAC	p.N425Y	ZNF536_uc010edd.1_Missense_Mutation_p.N425Y	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	425					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)					GGCCCACGCCAACCTGTACTC	0.637													8	21	---	---	---	---	PASS
SPTBN4	57731	broad.mit.edu	37	19	41071430	41071430	+	Missense_Mutation	SNP	G	C	C	rs139699793	byFrequency	TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:41071430G>C	uc002ony.2	+	28	6103	c.6017G>C	c.(6016-6018)CGA>CCA	p.R2006P	SPTBN4_uc002onz.2_Missense_Mutation_p.R2006P|SPTBN4_uc010egx.2_Missense_Mutation_p.R749P	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	2006	Spectrin 17.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GAGCTGGGGCGATCTCTGCTG	0.632													10	8	---	---	---	---	PASS
ZNF234	10780	broad.mit.edu	37	19	44660428	44660428	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:44660428G>T	uc002oym.2	+	6	566	c.259G>T	c.(259-261)GAG>TAG	p.E87*	ZNF234_uc002oyl.3_Nonsense_Mutation_p.E87*	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	87	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				AAGTGAGGTGGAGACTGTTCC	0.428													6	116	---	---	---	---	PASS
POLD1	5424	broad.mit.edu	37	19	50909578	50909578	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:50909578A>T	uc002psb.3	+	11	1438	c.1382A>T	c.(1381-1383)CAG>CTG	p.Q461L	POLD1_uc002psc.3_Missense_Mutation_p.Q461L|POLD1_uc010enx.2_RNA|POLD1_uc010eny.2_Missense_Mutation_p.Q461L	NM_002691	NP_002682	P28340	DPOD1_HUMAN	DNA-directed DNA polymerase delta 1	461					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|response to UV|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm|nucleotide-excision repair complex	3'-5'-exodeoxyribonuclease activity|chromatin binding|DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding|protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GACATGCTGCAGGTATGGGCG	0.662								DNA_polymerases_(catalytic_subunits)					5	18	---	---	---	---	PASS
SIGLEC6	946	broad.mit.edu	37	19	52023372	52023372	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:52023372G>T	uc002pwy.2	-	8	1488	c.1326C>A	c.(1324-1326)ACC>ACA	p.T442T	SIGLEC6_uc002pwz.2_Silent_p.T426T|SIGLEC6_uc002pxa.2_3'UTR|SIGLEC6_uc010ydb.1_Silent_p.T379T|SIGLEC6_uc010ydc.1_3'UTR|SIGLEC6_uc010eoz.1_3'UTR	NM_001245	NP_001236	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6 isoform 1	442	Cytoplasmic (Potential).				cell adhesion|cell-cell signaling	cytoplasm|extracellular region|integral to plasma membrane|membrane fraction|nucleus				ovary(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		ACTCAGTGTCGGTGACCTTTG	0.473													38	65	---	---	---	---	PASS
GP6	51206	broad.mit.edu	37	19	55539070	55539070	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr19:55539070C>A	uc002qik.2	-	4	514	c.486G>T	c.(484-486)AGG>AGT	p.R162S	GP6_uc002qil.2_Missense_Mutation_p.R162S|GP6_uc010esq.2_Missense_Mutation_p.R162S|RDH13_uc010esr.1_RNA	NM_016363	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet) isoform 2	162	Ig-like C2-type 2.|Extracellular (Potential).				enzyme linked receptor protein signaling pathway|leukocyte migration|platelet activation	integral to plasma membrane	collagen binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		GAAAACTAGCCCTGTACCATC	0.572													16	44	---	---	---	---	PASS
NRSN2	80023	broad.mit.edu	37	20	333854	333854	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr20:333854A>G	uc002wdi.3	+	4	728	c.190A>G	c.(190-192)ATC>GTC	p.I64V	NRSN2_uc002wdj.2_RNA|NRSN2_uc002wdl.2_Intron	NM_024958	NP_079234	Q9GZP1	NRSN2_HUMAN	neurensin 2	64						integral to membrane|plasma membrane|transport vesicle					0		all_cancers(10;0.0834)				TTCTCCCTAGATCAGCCTGTC	0.622													8	44	---	---	---	---	PASS
XRN2	22803	broad.mit.edu	37	20	21367572	21367572	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr20:21367572G>T	uc002wsf.1	+	29	2810	c.2715G>T	c.(2713-2715)CAG>CAT	p.Q905H	XRN2_uc002wsg.1_Missense_Mutation_p.Q829H|XRN2_uc010zsk.1_Missense_Mutation_p.Q851H|XRN2_uc002wsh.1_Missense_Mutation_p.Q43H	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	905					cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						CAGCCTTCCAGCCAAACCAGT	0.527													4	49	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47269940	47269940	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr20:47269940C>G	uc002xtw.1	-	20	2328	c.2305G>C	c.(2305-2307)GAG>CAG	p.E769Q	PREX1_uc002xtv.1_Missense_Mutation_p.E66Q	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	769					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TGGAAGTGCTCCAGGACCTCA	0.597													49	94	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62595205	62595205	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr20:62595205G>T	uc002yhl.1	-	9	1596	c.1542C>A	c.(1540-1542)ACC>ACA	p.T514T		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	514					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CCACGTTGCAGGTGGGGCAGA	0.652													6	86	---	---	---	---	PASS
TUBA8	51807	broad.mit.edu	37	22	18609318	18609318	+	Silent	SNP	C	A	A	rs150232320		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr22:18609318C>A	uc002znv.1	+	4	646	c.573C>A	c.(571-573)ACC>ACA	p.T191T	TUBA8_uc002znr.2_Silent_p.T125T|TUBA8_uc002znw.1_Silent_p.T215T|TUBA8_uc002znx.1_Silent_p.T38T	NM_018943	NP_061816	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	191					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0						TCCTGACCACCCACACCACAC	0.527													6	108	---	---	---	---	PASS
CLDN5	7122	broad.mit.edu	37	22	19511188	19511188	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr22:19511188G>T	uc002zpu.2	-	2	1061	c.846C>A	c.(844-846)CCC>CCA	p.P282P	CLDN5_uc010grr.2_Silent_p.P282P	NM_003277	NP_003268	O00501	CLD5_HUMAN	claudin 5	197	Cytoplasmic (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity				0	Colorectal(54;0.0993)					AGTACTTCACGGGGAAGCTGA	0.711													3	5	---	---	---	---	PASS
MYH9	4627	broad.mit.edu	37	22	36681312	36681312	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr22:36681312G>T	uc003apg.2	-	38	5569	c.5338C>A	c.(5338-5340)CGG>AGG	p.R1780R		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1780	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						AGCTGCTGCCGAGCATTCTCG	0.592			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				4	87	---	---	---	---	PASS
SSTR3	6753	broad.mit.edu	37	22	37603528	37603528	+	Silent	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr22:37603528G>T	uc003ara.2	-	2	377	c.315C>A	c.(313-315)GCC>GCA	p.A105A	SSTR3_uc003arb.2_Silent_p.A105A	NM_001051	NP_001042	P32745	SSR3_HUMAN	somatostatin receptor 3	105	Extracellular (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|induction of apoptosis by hormones|negative regulation of cell proliferation	integral to plasma membrane|nonmotile primary cilium	somatostatin receptor activity			lung(1)	1						AGTAGGACAGGGCGTTCTGGG	0.622													8	46	---	---	---	---	PASS
RANGAP1	5905	broad.mit.edu	37	22	41652071	41652071	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr22:41652071C>T	uc003azs.2	-	9	2497	c.1027G>A	c.(1027-1029)GAG>AAG	p.E343K	RANGAP1_uc003azt.2_Missense_Mutation_p.E343K|RANGAP1_uc003azu.2_Missense_Mutation_p.E343K|RANGAP1_uc011aoz.1_Missense_Mutation_p.E288K	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	343	LRR 6.				mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						TCCAGCACCTCCTGAAGCTGT	0.607													9	38	---	---	---	---	PASS
SMC1B	27127	broad.mit.edu	37	22	45795000	45795000	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr22:45795000C>A	uc003bgc.2	-	6	1140	c.1088G>T	c.(1087-1089)CGA>CTA	p.R363L	SMC1B_uc003bgd.2_Missense_Mutation_p.R363L|SMC1B_uc003bge.1_Missense_Mutation_p.R146L	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	363	Potential.				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TTCAATGTCTCGCTTTTTATG	0.353													4	81	---	---	---	---	PASS
EDA2R	60401	broad.mit.edu	37	X	65824983	65824983	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chrX:65824983C>A	uc004dwq.2	-	2	184	c.173G>T	c.(172-174)TGT>TTT	p.C58F	EDA2R_uc004dwr.2_Missense_Mutation_p.C58F|EDA2R_uc004dws.2_Missense_Mutation_p.C58F|EDA2R_uc011mpb.1_RNA|EDA2R_uc011mpc.1_Intron|EDA2R_uc010nkt.1_Missense_Mutation_p.C58F|EDA2R_uc004dwt.1_Missense_Mutation_p.C58F	NM_021783	NP_068555	Q9HAV5	TNR27_HUMAN	X-linked ectodysplasin receptor	58	Extracellular (Potential).|TNFR-Cys 2.				cell differentiation|embryo development|epidermis development|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity	integral to plasma membrane	tumor necrosis factor receptor activity			upper_aerodigestive_tract(1)	1						GCAACTCTGACATCTGTGGTG	0.542													3	9	---	---	---	---	PASS
IL1RAPL2	26280	broad.mit.edu	37	X	104440271	104440271	+	Missense_Mutation	SNP	C	A	A	rs146735893		TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chrX:104440271C>A	uc004elz.1	+	3	953	c.197C>A	c.(196-198)ACG>AAG	p.T66K		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	66	Ig-like C2-type 1.|Extracellular (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						AACTATAGCACGGCCCAGAGC	0.468													9	17	---	---	---	---	PASS
HTR2C	3358	broad.mit.edu	37	X	114141492	114141492	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chrX:114141492G>T	uc004epu.1	+	6	1619	c.891G>T	c.(889-891)AGG>AGT	p.R297S	HTR2C_uc010nqc.1_Missense_Mutation_p.R297S|HTR2C_uc004epv.1_3'UTR	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	297	Cytoplasmic (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)	GACGTCCTAGGGGCACCATGC	0.468													46	50	---	---	---	---	PASS
SELT	51714	broad.mit.edu	37	3	150340184	150340184	+	Frame_Shift_Del	DEL	T	-	-			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr3:150340184delT	uc011bnx.1	+	3	234	c.150delT	c.(148-150)GGTfs	p.G50fs		NM_016275	NP_057359	P62341	SELT_HUMAN	selenoprotein T precursor	50					cell redox homeostasis|selenocysteine incorporation		selenium binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTTCCTGAGGTTATAGGCGGG	0.383													4	2	---	---	---	---	
RASA1	5921	broad.mit.edu	37	5	86679568	86679570	+	In_Frame_Del	DEL	TGA	-	-			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr5:86679568_86679570delTGA	uc003kiw.2	+	21	2847_2849	c.2729_2731delTGA	c.(2728-2733)CTGAAT>CAT	p.910_911LN>H	RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_In_Frame_Del_p.733_734LN>H|RASA1_uc011ctv.1_In_Frame_Del_p.743_744LN>H|RASA1_uc011ctw.1_In_Frame_Del_p.744_745LN>H|RASA1_uc010jaw.2_In_Frame_Del_p.732_733LN>H	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	910_911	Ras-GAP.				cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CCTGCCATCCTGAATCCACGGAT	0.296													16	9	---	---	---	---	
PSORS1C1	170679	broad.mit.edu	37	6	31107683	31107683	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr6:31107683delC	uc003nsl.1	+	6	707	c.433delC	c.(433-435)CCTfs	p.P145fs	PSORS1C1_uc010jsj.1_Frame_Shift_Del_p.P94fs|PSORS1C1_uc003nsn.1_RNA|PSORS1C2_uc003nso.3_5'Flank	NM_014068	NP_054787	Q9UIG5	PS1C1_HUMAN	SEEK1 protein	145										ovary(1)	1						CTCCCATTCTCCTTTTGGTCT	0.448													68	38	---	---	---	---	
DTX3	196403	broad.mit.edu	37	12	58001040	58001040	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:58001040delC	uc001sow.1	+	5	731	c.394delC	c.(394-396)CCCfs	p.P132fs	DTX3_uc001sov.1_Frame_Shift_Del_p.P125fs|DTX3_uc001sox.1_Frame_Shift_Del_p.P125fs|DTX3_uc001soy.1_Frame_Shift_Del_p.P125fs|GEFT_uc009zpy.2_5'Flank	NM_178502	NP_848597	Q8N9I9	DTX3_HUMAN	deltex homolog 3	132	Pro-rich.				Notch signaling pathway	cytoplasm	zinc ion binding			breast(1)|central_nervous_system(1)	2	Melanoma(17;0.122)					CCCACTTCTGCCCCCAGGAGC	0.547													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65938069	65938069	+	RNA	DEL	C	-	-			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr12:65938069delC	uc010ssu.1	-	3		c.674delG								Homo sapiens, clone IMAGE:5172510, mRNA.																		GAAAGACTGGCCTCAACTTCT	0.463													4	2	---	---	---	---	
PHF11	51131	broad.mit.edu	37	13	50102723	50102723	+	Frame_Shift_Del	DEL	A	-	-			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:50102723delA	uc001vdb.2	+	10	1255	c.918delA	c.(916-918)TTAfs	p.L306fs	PHF11_uc001vdc.2_Frame_Shift_Del_p.L267fs|PHF11_uc001vdd.2_RNA	NM_001040443	NP_001035533	Q9UIL8	PHF11_HUMAN	PHD finger protein 11 isoform a	306					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		TTCAGGACTTAAAACAAACCT	0.343													32	23	---	---	---	---	
OXGR1	27199	broad.mit.edu	37	13	97639814	97639815	+	Frame_Shift_Ins	INS	-	T	T			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr13:97639814_97639815insT	uc001vmx.1	-	4	443_444	c.199_200insA	c.(199-201)AGCfs	p.S67fs	OXGR1_uc010afr.1_Frame_Shift_Ins_p.S67fs	NM_080818	NP_543008	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	67	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)|skin(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			GATGGTGCTGCTCTTCCAAGGT	0.470													13	13	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80091962	80091963	+	Frame_Shift_Ins	INS	-	A	A			TCGA-66-2744-01A-01D-0983-08	TCGA-66-2744-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	43be1a37-b18e-4e96-89e6-ed6ee1d8e65a	701bf715-e029-45b5-9c93-4f4a6c8e564d	g.chr17:80091962_80091963insA	uc002kdy.2	-	2	162_163	c.148_149insT	c.(148-150)CATfs	p.H50fs	CCDC57_uc002kdx.1_Intron			Q2TAC2	CCD57_HUMAN	SubName: Full=cDNA FLJ23754 fis, clone HEP17288;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment										ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			AGATGTAAAATGGGGCTGCACC	0.500													4	2	---	---	---	---