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	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	ref_context	gc_content	COSMIC_n_overlapping_mutations	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_Chromosome	ESP_Position	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	HGNC_AccessionNumbers	HGNC_CCDSIDs	HGNC_Chromosome	HGNC_DateModified	HGNC_DateNameChanged	HGNC_DateSymbolChanged	HGNC_EnsemblGeneID	HGNC_EnsemblIDsuppliedbyEnsembl	HGNC_Genefamilydescription	HGNC_HGNCID	HGNC_LocusGroup	HGNC_LocusType	HGNC_NameSynonyms	HGNC_OMIMIDsuppliedbyNCBI	HGNC_PreviousNames	HGNC_PreviousSymbols	HGNC_PubmedIDs	HGNC_RecordType	HGNC_RefSeqsuppliedbyNCBI	HGNC_Status	HGNC_Synonyms	HGNC_UCSCIDsuppliedbyUCSC	HGNC_UniProtIDsuppliedbyUniProt	HGNC_VEGAIDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	UniProt_alt_uniprot_accessions	annotation_transcript	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	init_n_lod	init_t_lod	isArtifactMode	n_alt_count	n_ref_count	oxoGCut	pox	pox_cutoff	qox	refseq_mrna_id	t_alt_count	t_lod_fstar	t_ref_count	tumor_f
IL18R1	8809	broad.mit.edu	hg19	2	102998134	102998134	+	Missense_Mutation	SNP	T	T	C	rs56076776		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr2:102998134T>C	ENST00000409599.1	+	7	1036	c.680T>C	c.(679-681)gTg>gCg	p.V227A	IL18R1_ENST00000233957.1_Missense_Mutation_p.V227A			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	227	Ig-like C2-type 3.	innate immune response	integral to membrane|plasma membrane	interleukin-1 receptor activity	breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34					CATGTTGCAGTGGAATTAGGT	0.343	0	111.0	103.0	106.0	2	102998134	2203	4300	6503	SO:0001583	missense	U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604	"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5988	protein-coding gene	gene with protein product		604494			8626725, 10191101	Standard	NM_003855	Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.680T>C	2.37:g.102998134T>C	ENSP00000387211:p.Val227Ala	B2R9Y5|Q52LC9	ENST00000409599.1	37	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	T	12.41	1.928888	0.34002	.	.	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957	T;T;T	0.16457	2.34;2.34;2.34	5.03	3.85	0.44370	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.254304	0.27996	N	0.017020	T	0.18087	0.0434	M	0.66506	2.035	0.80722	D	1	B;B	0.33171	0.4;0.4	B;B	0.34873	0.191;0.191	T	0.02505	-1.1149	10	0.30854	T	0.27	.	7.8067	0.29206	0.0:0.1002:0.0:0.8998	.	227;227	B7ZKV7;Q13478	.;IL18R_HUMAN	A	227	ENSP00000386663:V227A;ENSP00000387211:V227A;ENSP00000233957:V227A	ENSP00000233957:V227A	V	+	2	0	IL18R1	102364566	1.000000	0.71417	0.995000	0.50966	0.350000	0.29205	2.040000	0.41203	2.017000	0.59298	0.528000	0.53228	GTG	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2		37.369144	0	-12	30	0	0	1	0	NM_003855	13	37.485592	17	0.433333
C4orf17	84103	broad.mit.edu	hg19	4	100463085	100463085	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr4:100463085C>T	ENST00000326581.4	+	9	1261	c.899C>T	c.(898-900)cCa>cTa	p.P300L		NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	300					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)	CACAAGCCTCCACTACTTATA	0.363	0	32.0	35.0	34.0	4	100463085	2202	4300	6502	SO:0001583	missense	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813		25274	protein-coding gene	gene with protein product					11230166	Standard	NM_032149	Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.899C>T	4.37:g.100463085C>T	ENSP00000322582:p.Pro300Leu	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	ENST00000326581.4	37	CCDS3649.1	.	.	.	.	.	.	.	.	.	.	C	8.105	0.777448	0.16120	.	.	ENSG00000138813	ENST00000326581	T	0.21031	2.03	5.42	3.57	0.40892	.	0.254540	0.28544	N	0.014977	T	0.34279	0.0892	M	0.62723	1.935	0.09310	N	0.999999	D	0.63046	0.992	P	0.60068	0.868	T	0.06463	-1.0825	10	0.54805	T	0.06	-8.5037	7.4637	0.27310	0.1979:0.6184:0.1837:0.0	.	300	Q53FE4	CD017_HUMAN	L	300	ENSP00000322582:P300L	ENSP00000322582:P300L	P	+	2	0	C4orf17	100682108	0.002000	0.14202	0.025000	0.17156	0.009000	0.06853	0.571000	0.23669	1.451000	0.47736	0.650000	0.86243	CCA	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2		45.948313	0	-5	38	0	0	1	0	NM_032149	14	45.977269	16	0.466667
SQSTM1	8878	broad.mit.edu	hg19	5	179251203	179251203	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr5:179251203C>T	ENST00000389805.4	+	4	731	c.553C>T	c.(553-555)Ctc>Ttc	p.L185F	SQSTM1_ENST00000376929.3_Missense_Mutation_p.L101F|SQSTM1_ENST00000402874.3_Missense_Mutation_p.L101F|SQSTM1_ENST00000360718.5_Missense_Mutation_p.L101F|SQSTM1_ENST00000510187.1_Missense_Mutation_p.L185F	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	185	Interaction with GABRR3 (By similarity).|LIM protein-binding (LB).	anti-apoptosis|apoptosis|cell differentiation|endosome transport|induction of apoptosis by extracellular signals|intracellular signal transduction|macroautophagy|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein localization|regulation of I-kappaB kinase/NF-kappaB cascade|ubiquitin-dependent protein catabolic process	cytosol|late endosome|nucleoplasm	protein kinase C binding|receptor tyrosine kinase binding|SH2 domain binding|ubiquitin binding|zinc ion binding	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		CAGCCGCTGGCTCCGGAAGGT	0.667	0	43.0	50.0	48.0	5	179251203	2203	4300	6503	SO:0001583	missense	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011		11280	protein-coding gene	gene with protein product		601530	"""Paget disease of bone 3"", ""oxidative stress induced like"""	PDB3, OSIL	8650207, 8551575	Standard	NM_003900	Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.553C>T	5.37:g.179251203C>T	ENSP00000374455:p.Leu185Phe	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	ENST00000389805.4	37	CCDS34317.1	.	.	.	.	.	.	.	.	.	.	C	9.862	1.196529	0.22037	.	.	ENSG00000161011	ENST00000376929;ENST00000514093;ENST00000422245;ENST00000389805;ENST00000454378;ENST00000402874;ENST00000510187;ENST00000360718	D;T;T;D;D;T;D	0.82433	-1.6;1.91;1.45;-1.61;-1.6;2.44;-1.6	4.79	4.79	0.61399	.	0.200482	0.45867	D	0.000338	T	0.80093	0.4560	L	0.52364	1.645	0.45995	D	0.998802	B;B	0.22276	0.001;0.067	B;B	0.24269	0.004;0.052	T	0.77109	-0.2709	10	0.42905	T	0.14	-33.0609	16.3966	0.83607	0.0:1.0:0.0:0.0	.	185;185	Q13501;E7EMC7	SQSTM_HUMAN;.	F	101;101;101;185;41;101;185;101	ENSP00000366128:L101F;ENSP00000427308:L101F;ENSP00000394534:L101F;ENSP00000374455:L185F;ENSP00000385553:L101F;ENSP00000424477:L185F;ENSP00000353944:L101F	ENSP00000353944:L101F	L	+	1	0	SQSTM1	179183809	1.000000	0.71417	1.000000	0.80357	0.063000	0.16089	1.684000	0.37649	2.367000	0.80283	0.561000	0.74099	CTC	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1		63.470986	0	-6	56	0	0	1	0		21	63.490831	23	0.477273
KIAA1109	84162	broad.mit.edu	hg19	4	123275053	123275053	+	Missense_Mutation	SNP	C	C	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr4:123275053C>G	ENST00000264501.4	+	82	14559	c.14186C>G	c.(14185-14187)gCt>gGt	p.A4729G	KIAA1109_ENST00000388738.3_Missense_Mutation_p.A4729G			Q2LD37	K1109_HUMAN	KIAA1109	4729		regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172					CCATGTGGTGCTTTGGAAAGT	0.383	0	98.0	91.0	93.0	4	123275053	1856	4100	5956	SO:0001583	missense	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688		26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565			16386706	Standard	NM_015312	Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14186C>G	4.37:g.123275053C>G	ENSP00000264501:p.Ala4729Gly	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	4.001660|4.001660	0.74932|0.74932	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707;ENST00000431755|ENST00000306802	T;T;T|.	0.34072|.	2.36;2.36;1.38|.	6.04|6.04	6.04|6.04	0.98038|0.98038	Fragile site-associated protein, C-terminal (1);|.	0.225686|.	0.44688|.	D|.	0.000431|.	T|T	0.74137|0.74137	0.3677|0.3677	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.996;0.999|.	D;D|.	0.83275|.	0.99;0.996|.	T|T	0.68762|0.68762	-0.5323|-0.5323	10|5	0.33141|.	T|.	0.24|.	.|.	20.5891|20.5891	0.99427|0.99427	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4728;4729|.	Q2LD37-4;Q2LD37|.	.;K1109_HUMAN|.	G|V	4729;4729;1398;330|1105	ENSP00000264501:A4729G;ENSP00000373390:A4729G;ENSP00000410874:A1398G|.	ENSP00000264501:A4729G|.	A|L	+|+	2|1	0|0	KIAA1109|KIAA1109	123494503|123494503	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.818000|7.818000	0.86416|0.86416	2.876000|2.876000	0.98609|0.98609	0.650000|0.650000	0.86243|0.86243	GCT|CTT	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1		54.939144	0	-15	44	0	0	1	0	NM_020797	18	55.415304	28	0.391304
FANCA	2175	broad.mit.edu	hg19	16	89882378	89882378	+	Silent	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr16:89882378C>T	ENST00000389301.3	-	2	126	c.96G>A	c.(94-96)agG>agA	p.R32R	FANCA_ENST00000543736.1_Silent_p.R32R|FANCA_ENST00000389302.3_Silent_p.R32R|FANCA_ENST00000563673.1_Silent_p.R32R|FANCA_ENST00000568369.1_Silent_p.R32R|FANCA_ENST00000534992.1_Silent_p.R32R	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	32		DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding	breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)	TATATTTTTCCCTCTTGACCC	0.552	0	112.0	99.0	104.0	16	89882378	2198	4300	6498	SO:0001819	synonymous_variant	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741	"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH	7581462, 9382107	Standard	NM_001286167	Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.96G>A	16.37:g.89882378C>T		A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	ENST00000389301.3	37	CCDS32515.1																																																																																			FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		45.889243	0	3	56	0	0	1	0		16	46.239740	24	0.400000
PTBP2	58155	broad.mit.edu	hg19	1	97278911	97278911	+	Missense_Mutation	SNP	C	C	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr1:97278911C>G	ENST00000609116.1	+	14	1631	c.1549C>G	c.(1549-1551)Ctt>Gtt	p.L517V	PTBP2_ENST00000426398.2_Missense_Mutation_p.L516V|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000370198.1_Missense_Mutation_p.L521V|PTBP2_ENST00000394184.3_Missense_Mutation_p.L533V|PTBP2_ENST00000541987.1_3'UTR|PTBP2_ENST00000370197.1_Missense_Mutation_p.L522V			Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2		RRM 4.			nucleotide binding	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)	TAATTATAACCTTGGAGAAAA	0.363	0	67.0	75.0	72.0	1	97278911	2203	4300	6503	SO:0001583	missense	AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569	"""RNA binding motif (RRM) containing"""	17662	protein-coding gene	gene with protein product		608449			11003644	Standard	XM_005271084	Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.1546C>G	1.37:g.97278911C>G	ENSP00000412788:p.Leu516Val	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	ENST00000426398.2	37	CCDS754.1	.	.	.	.	.	.	.	.	.	.	C	8.228	0.804021	0.16467	.	.	ENSG00000117569	ENST00000236228;ENST00000543738;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184	T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89	5.5	5.5	0.81552	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.151416	0.64402	D	0.000020	T	0.13243	0.0321	M	0.83118	2.625	0.80722	D	1	B;B;B;B;B;B;B	0.16166	0.007;0.001;0.0;0.001;0.016;0.0;0.006	B;B;B;B;B;B;B	0.32211	0.098;0.008;0.0;0.002;0.142;0.037;0.038	T	0.01228	-1.1412	10	0.87932	D	0	-5.3849	14.5806	0.68288	0.1461:0.8539:0.0:0.0	.	525;533;189;521;516;517;522	B4DSU5;B4DSS8;B4DSI2;Q9UKA9-4;Q9UKA9;Q9UKA9-2;Q9UKA9-3	.;.;.;.;PTBP2_HUMAN;.;.	V	517;189;521;522;516;533	ENSP00000236228:L517V;ENSP00000359217:L521V;ENSP00000359216:L522V;ENSP00000412788:L516V;ENSP00000377738:L533V	ENSP00000236228:L517V	L	+	1	0	PTBP2	97051499	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.209000	0.51122	2.734000	0.93682	0.650000	0.86243	CTT	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1		98.253618	0	-30	60	0	0	1	0		33	99.184611	52	0.388235
ATP1B4	23439	broad.mit.edu	hg19	X	119513467	119513467	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chrX:119513467T>C	ENST00000218008.3	+	8	1109	c.1052T>C	c.(1051-1053)tTt>tCt	p.F351S	ATP1B4_ENST00000361319.3_Missense_Mutation_p.F347S|ATP1B4_ENST00000539306.1_Missense_Mutation_p.F308S	NM_001142447.2	NP_001135919.1	Q9UN42	AT1B4_HUMAN	ATPase, Na+/K+ transporting, beta 4 polypeptide	351		ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	33					AGGGTAATCTTTACCCTGAAC	0.438	0	109.0	90.0	97.0	X	119513467	2203	4300	6503	SO:0001583	missense	AF158383	CCDS14598.1, CCDS48158.1	Xq24	2012-10-22	2010-04-20		ENSG00000101892	ENSG00000101892	"""ATPases / P-type"""	808	protein-coding gene	gene with protein product	"""Na,K-ATPase beta m-subunit"""		"""ATPase, (Na+)/K+ transporting, beta 4 polypeptide"""		10456317, 17592128	Standard	NM_012069	Approved		uc004esr.3	Q9UN42	OTTHUMG00000022299	ENST00000218008.3:c.1052T>C	X.37:g.119513467T>C	ENSP00000218008:p.Phe351Ser	Q17RR0|Q9UN41	ENST00000218008.3	37	CCDS48158.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022110	0.75275	.	.	ENSG00000101892	ENST00000218008;ENST00000361319;ENST00000539306	T;T;T	0.35973	1.28;1.28;1.28	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.65585	0.2705	M	0.88640	2.97	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.73088	-0.4093	10	0.87932	D	0	-18.2946	13.4601	0.61223	0.0:0.0:0.0:1.0	.	308;316;351;347	B7ZKW0;B7ZKV9;Q9UN42;Q9UN42-2	.;.;AT1B4_HUMAN;.	S	351;347;308	ENSP00000218008:F351S;ENSP00000355346:F347S;ENSP00000443334:F308S	ENSP00000218008:F351S	F	+	2	0	ATP1B4	119397495	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.215000	0.77966	1.773000	0.52216	0.486000	0.48141	TTT	ATP1B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058095.1		127.628209	0	-41	66	0	0	1	0	NM_001142447	36	134.019498	4	0.900000
GNAQ	2776	broad.mit.edu	hg19	9	80537255	80537255	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr9:80537255C>A	ENST00000286548.4	-	2	365	c.143G>T	c.(142-144)gGa>gTa	p.G48V		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	48		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					GCCACTCTCTCCTGTCCCTGA	0.448	0	164.0	154.0	157.0	9	80537255	2203	4300	6503	SO:0001583	missense		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.143G>T	9.37:g.80537255C>A	ENSP00000286548:p.Gly48Val	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.769355	0.90020	.	.	ENSG00000156052	ENST00000286548;ENST00000411677	T;D	0.90133	-1.16;-2.62	5.87	5.87	0.94306	G protein alpha subunit, helical insertion (1);	0.000000	0.85682	D	0.000000	D	0.97714	0.9250	H	0.98883	4.36	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98541	1.0632	10	0.72032	D	0.01	.	20.2192	0.98319	0.0:1.0:0.0:0.0	.	48	P50148	GNAQ_HUMAN	V	48;19	ENSP00000286548:G48V;ENSP00000391501:G19V	ENSP00000286548:G48V	G	-	2	0	GNAQ	79727075	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.818000	0.86416	2.780000	0.95670	0.655000	0.94253	GGA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		72.354486	1	-47	81	0	2.14196e-07	1	2.20889e-07	NM_002072	25	73.613242	45	0.357143
ST18	9705	broad.mit.edu	hg19	8	53030985	53030985	+	Silent	SNP	T	T	C			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr8:53030985T>C	ENST00000276480.7	-	24	3455	c.2772A>G	c.(2770-2772)gaA>gaG	p.E924E		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)	924			nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)			GCCTAATTTCTTCATCACTCT	0.308	0	142.0	137.0	139.0	8	53030985	2202	4297	6499	SO:0001819	synonymous_variant	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488	"""Zinc fingers, C2HC-type containing"""	18695	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 3"""		"""zinc finger protein 387"", ""suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"""	ZNF387	15489893	Standard	NM_014682	Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2772A>G	8.37:g.53030985T>C		Q17RY1	ENST00000276480.7	37	CCDS6149.1																																																																																			ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1		-12.337843	0	-23	70	0	0	1	0		3	6.745674	79	0.036585
COL9A2	1298	broad.mit.edu	hg19	1	40771434	40771434	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr1:40771434G>A	ENST00000372748.3	-	21	1156	c.1060C>T	c.(1060-1062)Ccg>Tcg	p.P354S		NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	354	Triple-helical region 3 (COL3).	axon guidance|skeletal system development	collagen type IX		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)		TGCGGGCCCGGCTCACCCTGC	0.602	0	40.0	42.0	41.0	1	40771434	2203	4300	6503	SO:0001583	missense	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089	"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2218	protein-coding gene	gene with protein product		120260		EDM2	8454052, 8528240, 1429648	Standard	NM_001852	Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.1060C>T	1.37:g.40771434G>A	ENSP00000361834:p.Pro354Ser	B2RMP9	ENST00000372748.3	37	CCDS450.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.866352	0.32977	.	.	ENSG00000049089	ENST00000372748	D	0.92965	-3.14	5.82	5.82	0.92795	.	0.106109	0.64402	D	0.000003	D	0.94241	0.8151	L	0.60067	1.865	0.53688	D	0.999973	D	0.61080	0.989	P	0.60117	0.869	D	0.92703	0.6176	10	0.33141	T	0.24	.	17.5892	0.87991	0.0:0.0:1.0:0.0	.	354	Q14055	CO9A2_HUMAN	S	354	ENSP00000361834:P354S	ENSP00000361834:P354S	P	-	1	0	COL9A2	40544021	0.996000	0.38824	0.998000	0.56505	0.283000	0.27025	2.259000	0.43259	2.767000	0.95098	0.655000	0.94253	CCG	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3		0.198722	0	-35	36	0	0	1	0	NM_001852	3	6.549482	33	0.083333
REC8	9985	ucsc.edu	hg19	14	24648841	24648841	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7																										TCCTGCATTGCCCGTGGTGCC	0.622	0	69.0	80.0	76.0	14	24648841	2128	4234	6362	SO:0001583	missense	AF006264	CCDS41932.1	14q11.2-q12	2013-08-06	2013-08-06	2007-04-03		ENSG00000100918		16879	protein-coding gene	gene with protein product		608193	"""REC8-like 1 (yeast)"", ""REC8 homolog (yeast)"""	REC8L1	10207075, 15935783, 12759374	Standard	NM_005132	Approved	Rec8p, kleisin-alpha	uc001wms.3	O95072		ENST00000311457.3:c.1357C>T	14.37:g.24648841C>T	ENSP00000308699:p.Pro453Ser	A8K576|D3DS62|Q658V5|Q6IA92|Q8WUV8|Q9BTF2|Q9NVQ9	ENST00000311457.3	37	CCDS41932.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.501840	0.64298	.	.	ENSG00000100918	ENST00000311457;ENST00000447460	T	0.24151	1.87	5.53	5.53	0.82687	.	0.277767	0.35525	N	0.003145	T	0.34687	0.0906	L	0.34521	1.04	0.34748	D	0.731463	D;D	0.67145	0.996;0.994	P;P	0.61477	0.889;0.777	T	0.35699	-0.9778	10	0.35671	T	0.21	-7.605	12.7355	0.57220	0.0:0.835:0.165:0.0	.	437;454	O95072-2;O95072	.;REC8_HUMAN	S	453;436	ENSP00000308699:P453S	ENSP00000308699:P453S	P	+	1	0	REC8	23718681	1.000000	0.71417	0.977000	0.42913	0.621000	0.37620	2.601000	0.46249	2.627000	0.88993	0.456000	0.33151	CCC	REC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415889.3				-26	60					NM_005132	4		35	
NOD2	64127	broad.mit.edu	hg19	16	50757249	50757249	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr16:50757249G>A	ENST00000300589.2	+	9	2941	c.2836G>A	c.(2836-2838)Gcc>Acc	p.A946T		NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	946		activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding	cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)			GGGTGCCCAAGCCTTGGCACT	0.507	0	150.0	117.0	128.0	16	50757249	2198	4300	6498	SO:0001583	missense	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207	"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15	7809109, 8587604	Standard	XM_005256084	Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2836G>A	16.37:g.50757249G>A	ENSP00000300589:p.Ala946Thr	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	ENST00000300589.2	37	CCDS10746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.035405|4.035405	0.75617|0.75617	.|.	.|.	ENSG00000167207|ENSG00000167207	ENST00000526417;ENST00000300589;ENST00000431240|ENST00000534057	T|.	0.55413|.	0.52|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.078127|.	0.51477|.	D|.	0.000094|.	T|T	0.79125|0.79125	0.4393|0.4393	M|M	0.84773|0.84773	2.715|2.715	0.47065|0.47065	D|D	0.999301|0.999301	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.997;0.999|.	T|T	0.80710|0.80710	-0.1261|-0.1261	10|5	0.40728|.	T|.	0.16|.	.|.	15.4739|15.4739	0.75461|0.75461	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	919;946|.	Q9HC29-2;Q9HC29|.	.;NOD2_HUMAN|.	T|N	919;946;86|157	ENSP00000300589:A946T|.	ENSP00000300589:A946T|.	A|S	+|+	1|2	0|0	NOD2|NOD2	49314750|49314750	0.999000|0.999000	0.42202|0.42202	0.951000|0.951000	0.38953|0.38953	0.334000|0.334000	0.28698|0.28698	3.732000|3.732000	0.55021|0.55021	2.732000|2.732000	0.93576|0.93576	0.655000|0.655000	0.94253|0.94253	GCC|AGC	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2		29.942697	0	-13	22	0	0	1	0	NM_022162	10	30.341515	17	0.370370
BRCA2	675	broad.mit.edu	hg19	13	32945119	32945119	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr13:32945119A>T	ENST00000544455.1	+	20	8741	c.8514A>T	c.(8512-8514)ttA>ttT	p.L2838F	BRCA2_ENST00000380152.3_Missense_Mutation_p.L2838F	NM_000059.3	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	2838		cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding	NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)	CATCTGGATTATACATATTTC	0.373	0	84.0	82.0	82.0	13	32945119	2203	4300	6503	SO:0001583	missense	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618	"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD	8091231, 7581463, 15057823	Standard	NM_000059	Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8514A>T	13.37:g.32945119A>T	ENSP00000369497:p.Leu2838Phe	O00183|O15008|Q13879|Q5TBJ7	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.573775	0.28092	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.59364	0.27;0.27	5.1	-0.309	0.12769	Nucleic acid-binding, OB-fold-like (1);Tower (1);	0.828622	0.10977	N	0.613109	T	0.46464	0.1394	L	0.47716	1.5	0.25184	N	0.990187	B	0.25390	0.125	B	0.29598	0.104	T	0.37220	-0.9715	10	0.23891	T	0.37	.	7.4138	0.27032	0.2368:0.341:0.4222:0.0	.	2838	P51587	BRCA2_HUMAN	F	2838	ENSP00000369497:L2838F;ENSP00000439902:L2838F	ENSP00000369497:L2838F	L	+	3	2	BRCA2	31843119	0.000000	0.05858	0.985000	0.45067	0.996000	0.88848	-1.057000	0.03486	-0.071000	0.12886	0.397000	0.26171	TTA	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2		47.689012	0	-18	43	0	0	1	0	NM_000059	16	48.408471	28	0.363636
STYXL1	51657	broad.mit.edu	hg19	7	75625885	75625885	+	Silent	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr7:75625885G>A	ENST00000248600.1	-	9	1185	c.843C>T	c.(841-843)aaC>aaT	p.N281N	STYXL1_ENST00000431581.1_Silent_p.N281N|STYXL1_ENST00000340062.5_Silent_p.N185N|STYXL1_ENST00000359697.3_Silent_p.N281N|STYXL1_ENST00000360591.3_3'UTR	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	281	Tyrosine-protein phosphatase.	intracellular signal transduction|protein dephosphorylation	intracellular	protein binding|protein tyrosine/serine/threonine phosphatase activity	endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10					GACACATGTTGTTTTTGCACT	0.478	0	164.0	133.0	143.0	7	75625885	2203	4300	6503	SO:0001819	synonymous_variant	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	18165	protein-coding gene	gene with protein product			"""dual specificity phosphatase 24 (putative)"""	DUSP24	9757831	Standard	NM_016086	Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.843C>T	7.37:g.75625885G>A		Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	ENST00000248600.1	37	CCDS5580.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.502381	0.44455	.	.	ENSG00000127952	ENST00000404050;ENST00000454618	.	.	.	4.96	-0.315	0.12746	.	1.082260	0.07045	N	0.830932	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.8894	1.5846	0.02641	0.2395:0.2577:0.3712:0.1316	.	.	.	.	X	244;199	.	ENSP00000385904:Q244X	Q	-	1	0	STYXL1	75463821	0.796000	0.28864	0.296000	0.24974	0.946000	0.59487	0.947000	0.29082	-0.130000	0.11599	0.561000	0.74099	CAA	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1		95.827466	0	-33	57	0	0	1	0	NM_016086	31	95.860772	28	0.525424
C1orf86	199990	broad.mit.edu	hg19	1	2125233	2125233	+	Translation_Start_Site	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr1:2125233G>A	ENST00000400919.3	-	0	306				C1orf86_ENST00000378545.3_Silent_p.H208H|C1orf86_ENST00000378546.4_Silent_p.H105H|C1orf86_ENST00000487186.1_5'UTR	NM_001282671.1	NP_001269600.1	Q6NZ36	CA086_HUMAN	chromosome 1 open reading frame 86						central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	CTCCTGCCCCGTGAAGCAGCC	0.697	0	19.0	26.0	24.0	1	2125233	2194	4292	6486			AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585		26428	protein-coding gene	gene with protein product		615183			14702039	Standard	NM_182533	Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000400919.3:c.-763C>T	1.37:g.2125233G>A		A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	ENST00000400919.3	37		.	.	.	.	.	.	.	.	.	.	G	8.403	0.842324	0.16963	.	.	ENSG00000162585	ENST00000378543;ENST00000420515	T	0.46451	0.87	3.47	-6.65	0.01795	.	.	.	.	.	T	0.25158	0.0611	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31251	-0.9950	8	0.87932	D	0	-0.0172	4.798	0.13282	0.5643:0.0:0.1606:0.2751	.	101	Q6ZRT9	.	M	60;105	ENSP00000367804:T60M	ENSP00000367804:T60M	T	-	2	0	C1orf86	2115093	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-4.202000	0.00275	-1.480000	0.01865	-0.521000	0.04368	ACG	C1orf86-202	KNOWN	basic	protein_coding	protein_coding			35.962752	0	-21	29	0	0	1	0	NM_182533	13	37.181361	28	0.317073
FAM71F1	84691	broad.mit.edu	hg19	7	128363345	128363345	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr7:128363345C>T	ENST00000315184.5	+	4	835	c.782C>T	c.(781-783)gCc>gTc	p.A261V	FAM71F1_ENST00000485070.1_Missense_Mutation_p.A162V|FAM71F1_ENST00000469348.1_3'UTR	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	261					NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18					CAGATTTTTGCCGACTTACAC	0.502	1	118.0	116.0	117.0	7	128363345	2203	4300	6503	SO:0001583	missense	AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248		30704	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member A"""	FAM137A	12477932	Standard	XM_005250645	Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000485070.1:c.485C>T	7.37:g.128363345C>T	ENSP00000418192:p.Ala162Val	Q8IY75|Q8NA48	ENST00000485070.1	37		.	.	.	.	.	.	.	.	.	.	C	15.05	2.717581	0.48622	.	.	ENSG00000135248	ENST00000485070;ENST00000315184;ENST00000466842	T;T;T	0.24151	1.87;3.23;1.92	5.2	3.36	0.38483	.	0.643829	0.14692	N	0.304119	T	0.17365	0.0417	L	0.33485	1.01	0.26152	N	0.980124	B;B;B;B;B	0.18310	0.011;0.01;0.003;0.002;0.027	B;B;B;B;B	0.15052	0.012;0.006;0.004;0.002;0.006	T	0.17992	-1.0351	10	0.30854	T	0.27	-2.5683	6.5261	0.22303	0.1782:0.7313:0.0:0.0905	.	153;261;261;261;162	B4DY15;F8WC62;Q96KD3-2;Q96KD3;Q8NA48	.;.;.;F71F1_HUMAN;.	V	162;261;117	ENSP00000418192:A162V;ENSP00000326652:A261V;ENSP00000417930:A117V	ENSP00000326652:A261V	A	+	2	0	FAM71F1	128150581	0.133000	0.22466	0.998000	0.56505	0.995000	0.86356	0.071000	0.14594	0.862000	0.35528	0.555000	0.69702	GCC	FAM71F1-001	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000350543.1		-10.770608	0	-28	68	0	0	1	0	NM_032599	4	8.088225	82	0.046512
HOXA4	3201	broad.mit.edu	hg19	7	27168859	27168859	+	Silent	SNP	A	A	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr7:27168859A>T	ENST00000360046.5	-	2	1013	c.948T>A	c.(946-948)gtT>gtA	p.V316V	HOXA4_ENST00000428284.2_Silent_p.V316V|HOXA-AS2_ENST00000521159.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA3_ENST00000521401.1_Intron	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	316			nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12					tggaggagggaacgggtgtgg	0.572	0	87.0	97.0	94.0	7	27168859	2203	4300	6503	SO:0001819	synonymous_variant		CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576	"""Homeoboxes / ANTP class : HOXL subclass"""	5105	protein-coding gene	gene with protein product		142953	"""homeo box A4"""	HOX1D, HOX1	1973146, 1358459	Standard	NM_002141	Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.948T>A	7.37:g.27168859A>T		A4D180|O43366	ENST00000360046.5	37	CCDS5405.1	.	.	.	.	.	.	.	.	.	.	A	3.350	-0.132749	0.06711	.	.	ENSG00000197576	ENST00000511914	.	.	.	5.42	1.4	0.22301	.	.	.	.	.	T	0.43809	0.1264	.	.	.	0.36697	D	0.87992	.	.	.	.	.	.	T	0.40739	-0.9547	4	.	.	.	.	3.2044	0.06661	0.4841:0.0:0.334:0.1819	.	.	.	.	T	136	.	.	S	-	1	0	HOXA4	27135384	0.999000	0.42202	0.976000	0.42696	0.813000	0.45954	1.349000	0.33998	0.464000	0.27142	0.529000	0.55759	TCC	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4		19.889726	0	-10	39	0	0	1	0		8	20.747266	18	0.307692
MAPKBP1	23005	broad.mit.edu	hg19	15	42117611	42117611	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr15:42117611C>T	ENST00000457542.2	+	31	4790	c.4504C>T	c.(4504-4506)Cgg>Tgg	p.R1502W	RP11-23P13.4_ENST00000510176.1_RNA|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.R1225W|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R1385W|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.R1341W|MAPKBP1_ENST00000456763.2_Missense_Mutation_p.R1508W	NM_014994.2	NP_055809.2	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	1508					breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)	AGCCGTGGAACGGCGTATGGA	0.587	0	30.0	29.0	30.0	15	42117611	2203	4300	6503	SO:0001583	missense	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802	"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""		9628581, 10471813	Standard	NM_014994	Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000457542.2:c.4504C>T	15.37:g.42117611C>T	ENSP00000397570:p.Arg1502Trp	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	ENST00000457542.2	37	CCDS32201.1	.	.	.	.	.	.	.	.	.	.	.	17.86	3.492570	0.64074	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T;T	0.63096	0.28;0.31;-0.02;0.33;0.14	4.64	3.68	0.42216	.	0.281258	0.30800	N	0.008860	T	0.75079	0.3801	M	0.67397	2.05	0.30984	N	0.72215	D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.986;1.0;1.0	P;P;P;P;D;D	0.87578	0.781;0.855;0.763;0.636;0.969;0.998	T	0.75619	-0.3255	10	0.87932	D	0	-5.3019	12.1831	0.54223	0.3021:0.6979:0.0:0.0	.	1341;1383;1341;1225;1508;1502	F8WC21;O60336-3;B4DYK7;O60336-2;O60336;O60336-6	.;.;.;.;MABP1_HUMAN;.	W	1502;1385;1341;1508;1225	ENSP00000397570:R1502W;ENSP00000221214:R1385W;ENSP00000260357:R1341W;ENSP00000393099:R1508W;ENSP00000426154:R1225W	ENSP00000221214:R1385W	R	+	1	2	MAPKBP1	39904903	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	1.579000	0.36536	2.409000	0.81822	0.655000	0.94253	CGG	MAPKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359744.1		82.918470	0	-9	10	0	0	1	0	NM_014994	24	86.360584	4	0.857143
NCAM1	4684	broad.mit.edu	hg19	11	113102955	113102955	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr11:113102955C>T	ENST00000316851.7	+	10	1274	c.1274C>T	c.(1273-1275)aCc>aTc	p.T425I	NCAM1_ENST00000533760.1_Missense_Mutation_p.T307I|NCAM1_ENST00000401611.2_Missense_Mutation_p.T434I|NCAM1_ENST00000397957.4_3'UTR	NM_001242607.1|NM_181351.4	NP_001229536.1|NP_851996.2	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	435	Ig-like C2-type 5.	axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane		breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)	GTGAACATCACCTGCGAGGTA	0.512	0	65.0	66.0	65.0	11	113102955	1978	4173	6151	SO:0001583	missense		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294	"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930				Standard	NM_000615	Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.920C>T	11.37:g.113102955C>T	ENSP00000473281:p.Thr307Ile	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	C	24.4	4.531194	0.85706	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.69040	-0.37;-0.37	5.51	5.51	0.81932	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.060472	0.64402	U	0.000004	D	0.83547	0.5278	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;D;D;D	0.76575	0.984;0.97;0.982;0.988	D	0.85038	0.0921	9	0.87932	D	0	-29.2533	19.7829	0.96424	0.0:1.0:0.0:0.0	.	435;425;435;425	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	I	307;434;425	ENSP00000384055:T434I;ENSP00000318472:T425I	ENSP00000318472:T425I	T	+	2	0	NCAM1	112608165	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.991000	0.63883	2.758000	0.94735	0.460000	0.39030	ACC	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2		32.519216	0	-23	23	0	0	1	0	NM_000615	11	32.800490	17	0.392857
DMXL1	1657	broad.mit.edu	hg19	5	118469695	118469695	+	Silent	SNP	C	C	T	rs141146454		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr5:118469695C>T	ENST00000311085.8	+	12	2156	c.2076C>T	c.(2074-2076)gaC>gaT	p.D692D	DMXL1_ENST00000539542.1_Silent_p.D692D	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	692					breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)	GCACTGTTGACGTGGCATTTC	0.428	0	122.0	119.0	120.0	5	118469695	2202	4300	6502	SO:0001819	synonymous_variant	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869	"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671			10708522	Standard	NM_005509	Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2076C>T	5.37:g.118469695C>T			ENST00000311085.8	37	CCDS4125.1																																																																																			DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1		143.937543	0	-10	114	0	0	1	0	NM_005509	46	144.238930	58	0.442308
GNAQ	2776	broad.mit.edu	hg19	9	80537256	80537256	+	Nonsense_Mutation	SNP	C	C	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr9:80537256C>A	ENST00000286548.4	-	2	364	c.142G>T	c.(142-144)Gga>Tga	p.G48*		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	48		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					CCACTCTCTCCTGTCCCTGAA	0.448	0	162.0	152.0	156.0	9	80537256	2203	4300	6503	SO:0001587	stop_gained		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.142G>T	9.37:g.80537256C>A	ENSP00000286548:p.Gly48*	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	C	39	7.540765	0.98348	.	.	ENSG00000156052	ENST00000286548;ENST00000411677	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.2192	0.98319	0.0:1.0:0.0:0.0	.	.	.	.	X	48;19	.	ENSP00000286548:G48X	G	-	1	0	GNAQ	79727076	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	7.818000	0.86416	2.780000	0.95670	0.655000	0.94253	GGA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		70.378349	1	-47	79	0	1.74197e-06	1	1.74197e-06	NM_002072	24	71.789050	45	0.347826
SULF2	55959	broad.mit.edu	hg19	20	46295178	46295178	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr20:46295178A>T	ENST00000359930.4	-	12	2482	c.1631T>A	c.(1630-1632)gTg>gAg	p.V544E	SULF2_ENST00000361612.4_Missense_Mutation_p.V544E|SULF2_ENST00000484875.1_Missense_Mutation_p.V544E|SULF2_ENST00000467815.1_Missense_Mutation_p.V544E	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	544		bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding	breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54					CCTGCCGTCCACCTCGATGGC	0.627	0	91.0	84.0	87.0	20	46295178	2203	4300	6503	SO:0001583	missense	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562		20392	protein-coding gene	gene with protein product		610013			12368295	Standard	NM_018837	Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1631T>A	20.37:g.46295178A>T	ENSP00000353007:p.Val544Glu	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	ENST00000359930.4	37	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	A	6.367	0.435806	0.12104	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815	D;D;D;D	0.99014	-5.33;-5.33;-5.33;-5.33	4.6	2.29	0.28610	Extracellular sulfatase, C-terminal (1);Alkaline-phosphatase-like, core domain (1);	1.329430	0.04621	N	0.401912	D	0.96929	0.8997	N	0.22421	0.69	0.32422	N	0.54928	B;B	0.28470	0.178;0.213	B;B	0.33339	0.048;0.162	D	0.93975	0.7253	10	0.41790	T	0.15	-3.2586	8.4626	0.32936	0.8315:0.0:0.1685:0.0	.	544;544	Q8IWU5-2;Q8IWU5	.;SULF2_HUMAN	E	544	ENSP00000353007:V544E;ENSP00000418290:V544E;ENSP00000354662:V544E;ENSP00000418442:V544E	ENSP00000353007:V544E	V	-	2	0	SULF2	45728585	0.358000	0.24947	0.271000	0.24616	0.036000	0.12997	1.856000	0.39389	0.272000	0.22027	-0.400000	0.06385	GTG	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1		81.316729	0	-43	60	0	0	1	0	NM_018837	27	81.945189	41	0.397059
FOXF2	2295	broad.mit.edu	hg19	6	1391338	1391338	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr6:1391338C>T	ENST00000259806.1	+	1	1270	c.1156C>T	c.(1156-1158)Cgc>Tgc	p.R386C		NM_001452.1	NP_001443.1	Q12947	FOXF2_HUMAN	forkhead box F2	386		epithelial to mesenchymal transition|genitalia development|palate development|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding	large_intestine(2)|lung(5)|prostate(1)	8	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)	CCAGAACGCTCGCGAGGACCT	0.677	0	18.0	17.0	17.0	6	1391338	2166	4236	6402	SO:0001583	missense	U13220	CCDS4472.1	6p25.3	2008-04-10			ENSG00000137273	ENSG00000137273	"""Forkhead boxes"""	3810	protein-coding gene	gene with protein product		603250		FKHL6	9799607, 7957066	Standard	NM_001452	Approved	FREAC2	uc003mtm.3	Q12947	OTTHUMG00000016243	ENST00000259806.1:c.1156C>T	6.37:g.1391338C>T	ENSP00000259806:p.Arg386Cys	Q5TGJ1|Q9UQ85	ENST00000259806.1	37	CCDS4472.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222901	0.58668	.	.	ENSG00000137273	ENST00000259806	D	0.93189	-3.18	4.58	4.58	0.56647	.	0.177694	0.34268	N	0.004119	D	0.93903	0.8049	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	P	0.57846	0.828	D	0.94263	0.7504	10	0.62326	D	0.03	.	16.1463	0.81575	0.0:1.0:0.0:0.0	.	386	Q12947	FOXF2_HUMAN	C	386	ENSP00000259806:R386C	ENSP00000259806:R386C	R	+	1	0	FOXF2	1336337	0.995000	0.38212	0.984000	0.44739	0.907000	0.53573	0.598000	0.24074	2.375000	0.81037	0.561000	0.74099	CGC	FOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043558.1		30.248096	0	-4	20	0	0	1	0		10	30.259389	9	0.526316
TYRO3	7301	broad.mit.edu	hg19	15	41863798	41863798	+	Missense_Mutation	SNP	A	A	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr15:41863798A>G	ENST00000263798.3	+	14	1890	c.1666A>G	c.(1666-1668)Atc>Gtc	p.I556V	TYRO3_ENST00000559066.1_Missense_Mutation_p.I511V	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	556	Protein kinase.		integral to plasma membrane	ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)	CCTAGCTGACATCATTGCCTC	0.502	0	110.0	97.0	101.0	15	41863798	2203	4300	6503	SO:0001583	missense	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE	7851890	Standard	NM_006293	Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1666A>G	15.37:g.41863798A>G	ENSP00000263798:p.Ile556Val	O14953|Q86VR3	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.542258	0.65198	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	D	0.82344	-1.6	6.16	6.16	0.99307	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43260	D	0.000581	T	0.81842	0.4908	N	0.25485	0.75	0.80722	D	1	P	0.46578	0.88	P	0.52031	0.688	T	0.79787	-0.1656	10	0.27082	T	0.32	-20.8649	16.8061	0.85666	1.0:0.0:0.0:0.0	.	556	Q06418	TYRO3_HUMAN	V	488;556	ENSP00000263798:I556V	ENSP00000263798:I556V	I	+	1	0	TYRO3	39651090	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.962000	0.93254	2.367000	0.80283	0.528000	0.53228	ATC	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		146.962298	0	-5	65	0	0	1	0		46	147.698694	30	0.605263
BZW2	28969	broad.mit.edu	hg19	7	16722416	16722416	+	Silent	SNP	A	A	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr7:16722416A>G	ENST00000433922.2	+	5	529	c.351A>G	c.(349-351)aaA>aaG	p.K117K	BZW2_ENST00000258761.3_Silent_p.K117K|BZW2_ENST00000432311.1_3'UTR|BZW2_ENST00000405202.1_Silent_p.K41K|BZW2_ENST00000452975.2_Silent_p.K117K	NM_001159767.1	NP_001153239.1	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	117		cell differentiation|nervous system development|RNA metabolic process		protein binding	cervix(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	15	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)	TCTTCAATAAACTCATCAGGA	0.289	0	46.0	49.0	48.0	7	16722416	2200	4296	6496	SO:0001819	synonymous_variant	AF083246	CCDS5362.1	7p21.3	2008-07-18			ENSG00000136261	ENSG00000136261		18808	protein-coding gene	gene with protein product					11042152	Standard	NM_001159767	Approved	HSPC028, MST017, MSTP017	uc003stj.2	Q9Y6E2	OTTHUMG00000130755	ENST00000433922.2:c.351A>G	7.37:g.16722416A>G		A4D123|Q3B779|Q96JW5|Q9H3F7	ENST00000433922.2	37	CCDS5362.1																																																																																			BZW2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253256.2		11.725608	0	-1	42	0	0	1	0	NM_014038	6	16.421173	34	0.150000
C1orf94	84970	broad.mit.edu	hg19	1	34663232	34663232	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr1:34663232T>C	ENST00000488417.1	+	2	847	c.727T>C	c.(727-729)Ttc>Ctc	p.F243L	C1orf94_ENST00000373374.3_Missense_Mutation_p.F53L	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	53				protein binding	central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)			TCTGTCCCAGTTCCCACTGAA	0.547	0	84.0	75.0	78.0	1	34663232	2203	4300	6503	SO:0001583	missense	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698		28250	protein-coding gene	gene with protein product					12477932	Standard	NM_001134734	Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.727T>C	1.37:g.34663232T>C	ENSP00000435634:p.Phe243Leu	B3KVT1|D3DPR3|E9PJ76|Q96IC8	ENST00000488417.1	37	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.961276	0.34565	.	.	ENSG00000142698	ENST00000373374;ENST00000488417	T;T	0.23348	1.91;1.91	4.98	3.84	0.44239	.	0.100155	0.44483	D	0.000451	T	0.16471	0.0396	N	0.24115	0.695	0.34708	D	0.727476	B	0.11235	0.004	B	0.14578	0.011	T	0.09729	-1.0661	10	0.49607	T	0.09	-19.8309	8.0269	0.30442	0.181:0.0:0.0:0.819	.	243	Q6P1W5	CA094_HUMAN	L	53;243	ENSP00000362472:F53L;ENSP00000435634:F243L	ENSP00000362472:F53L	F	+	1	0	C1orf94	34435819	1.000000	0.71417	0.983000	0.44433	0.752000	0.42762	3.176000	0.50863	0.722000	0.32252	0.460000	0.39030	TTC	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2		77.830932	0	-6	46	0	0	1	0	NM_032884	23	78.027222	17	0.575000
HEPN1	641654	broad.mit.edu	hg19	11	124789907	124789907	+	Silent	SNP	A	A	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr11:124789907A>G	ENST00000408930.5	+	1	762	c.261A>G	c.(259-261)ttA>ttG	p.L87L	HEPACAM_ENST00000298251.4_3'UTR	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN	hepatocellular carcinoma, down-regulated 1	87			cytoplasm		large_intestine(1)|lung(1)|stomach(1)	3	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)	TTTTGATGTTAGTGTGATTAG	0.547	0	59.0	61.0	61.0	11	124789907	1945	4142	6087	SO:0001819	synonymous_variant	BC148521	CCDS41729.1	11q24	2013-07-02	2011-02-11		ENSG00000221932	ENSG00000221932		34400	protein-coding gene	gene with protein product	"""cancer susceptibility gene HEPN1"""	611641	"""HEPACAM opposite strand 1"""		12971969, 23548416	Standard	NM_001037558	Approved		uc001qbj.1	Q6WQI6	OTTHUMG00000165939	ENST00000408930.5:c.261A>G	11.37:g.124789907A>G			ENST00000408930.5	37	CCDS41729.1																																																																																			HEPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387129.1		54.436160	0	-25	58	0	0	1	0	NM_001037558	18	55.408161	33	0.352941
BRCA2	675	broad.mit.edu	hg19	13	32945125	32945135	+	Frame_Shift_Del	DEL	ATTTCGCAATG	ATTTCGCAATG	-	rs80359105		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr13:32945125_32945135delATTTCGCAATG	ENST00000544455.1	+	20	8747_8757	c.8520_8530delATTTCGCAATG	c.(8518-8532)atatttcgcaatgaafs	p.FRNE2841fs	BRCA2_ENST00000380152.3_Frame_Shift_Del_p.FRNE2841fs	NM_000059.3	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	2841		cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding	NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)	GATTATACATATTTCGCAATGAAAGAGAGGA	0.355	3									SO:0001589	frameshift_variant	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618	"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD	8091231, 7581463, 15057823	Standard	NM_000059	Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8520_8530delATTTCGCAATG	13.37:g.32945125_32945135delATTTCGCAATG	ENSP00000369497:p.Phe2841fs	O00183|O15008|Q13879|Q5TBJ7	ENST00000380152.3	37	CCDS9344.1																																																																																			BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	.	.		-8	47					NM_000059	17		36	0.32
BAP1	8314	broad.mit.edu	hg19	3	52437427	52437448	+	Splice_Site	DEL	CCCACCTGTCAGCGCCAGGGGA	CCCACCTGTCAGCGCCAGGGGA	-			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr3:52437427_52437448delCCCACCTGTCAGCGCCAGGGGA	ENST00000460680.1	-	13	2184_2201	c.1713_1730delTCCCCTGGCGCTGACAGGTGGG	c.(1711-1731)agtcccctggcgctgacaggt>agt	p.PLALTG572fs	BAP1_ENST00000296288.5_Splice_Site_p.PLALTG554fs	NM_004656.2	NP_004647.1	Q92560	BAP1_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	572		monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	CAGTCCAAGGCCCACCTGTCAGCGCCAGGGGACTCAGCACCC	0.595	1									SO:0001630	splice_region_variant	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1729+1TCCCCTGGCGCTGACAGGTGGG>-	3.37:g.52437427_52437448delCCCACCTGTCAGCGCCAGGGGA		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1	37	CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	.	.		-3	39						4		3	0.57
BAP1	8314	broad.mit.edu	hg19	3	52437426	52437448	+	Splice_Site	DEL	GCCCACCTGTCAGCGCCAGGGGA	GCCCACCTGTCAGCGCCAGGGGA	-			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr3:52437426_52437448delGCCCACCTGTCAGCGCCAGGGGA	ENST00000460680.1	-	13	2184_2201	c.1713_1730delTCCCCTGGCGCTGACAGGTGGGC	c.(1711-1731)agtcccctggcgctgacaggt>agt	p.PLALTG572fs	BAP1_ENST00000296288.5_Splice_Site_p.PLALTG554fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0		anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	CCAGTCCAAGGCCCACCTGTCAGCGCCAGGGGACTCAGCACCC	0.596	1									SO:0001630	splice_region_variant	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1729+1TCCCCTGGCGCTGACAGGTGGGC>-	3:g.52437426_52437448delGCCCACCTGTCAGCGCCAGGGGA		B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1		CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	1.469000e+01	2.597000e+01		0	40						6		1	8.570000e-01