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_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
NOD2	64127	broad.mit.edu	37	16	50757249	50757249	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.507000													10	17					0	0	1	0	0
COL9A2	1298	broad.mit.edu	37	1	40771434	40771434	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.602000													3	33					0	0	1	0	0
IL18R1	8809	broad.mit.edu	37	2	102998134	102998134	+	Missense_Mutation	SNP	T	T	C	rs56076776		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.343000													13	17					0	0	1	0	0
STYXL1	51657	broad.mit.edu	37	7	75625885	75625885	+	Silent	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.478000													31	28					0	0	1	0	0
KIAA1109	84162	broad.mit.edu	37	4	123275053	123275053	+	Missense_Mutation	SNP	C	C	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.383000													18	28					0	0	1	0	0
NCAM1	4684	broad.mit.edu	37	11	113102955	113102955	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.512000													11	17					0	0	1	0	0
MAPKBP1	23005	broad.mit.edu	37	15	42117611	42117611	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.587000													24	4					0	0	1	0	0
FAM71F1	84691	broad.mit.edu	37	7	128363345	128363345	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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								p.A261V(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						CAGATTTTTGCCGACTTACAC	0.502000													4	82					0	0	1	0	0
PTBP2	58155	broad.mit.edu	37	1	97278911	97278911	+	Missense_Mutation	SNP	C	C	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.363000													33	52					0	0	1	0	0
HOXA4	3201	broad.mit.edu	37	7	27168859	27168859	+	Silent	SNP	A	A	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.572000													8	18					0	0	1	0	0
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr22:29091841G>A	ENST00000544772.1	-	12	1889	c.453C>T	c.(451-453)tcC>tcT	p.S151S	CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000382580.2_Silent_p.S415S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN	checkpoint kinase 2	372	FHA.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413000			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					5	57					0	0	1	0	0
TYRO3	7301	broad.mit.edu	37	15	41863798	41863798	+	Missense_Mutation	SNP	A	A	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.502000													46	30					0	0	1	0	0
C1orf94	84970	broad.mit.edu	37	1	34663232	34663232	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.547000													23	17					0	0	1	0	0
SQSTM1	8878	broad.mit.edu	37	5	179251203	179251203	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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		SQSTM1/ALK(2)	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	0.667000													21	23					0	0	1	0	0
BRCA2	675	broad.mit.edu	37	13	32945119	32945119	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.373000			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			16	28					0	0	1	0	0
BZW2	28969	broad.mit.edu	37	7	16722416	16722416	+	Silent	SNP	A	A	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.289000													6	34					0	0	1	0	0
HEPN1	641654	broad.mit.edu	37	11	124789907	124789907	+	Silent	SNP	A	A	G			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.547000													18	33					0	0	1	0	0
GNAQ	2776	broad.mit.edu	37	9	80537256	80537256	+	Nonsense_Mutation	SNP	C	C	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.448000			Mis		uveal melanoma								24	45					1.74197e-06	1.74197e-06	1	1	0
FANCA	2175	broad.mit.edu	37	16	89882378	89882378	+	Silent	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.552000			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				16	24					0	0	1	0	0
C4orf17	84103	broad.mit.edu	37	4	100463085	100463085	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.363000													14	16					0	0	1	0	0
SLC6A10P	0	broad.mit.edu	37	16	32890639	32890639	+	RNA	SNP	T	T	C	rs79284655		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr16:32890639T>C	ENST00000330048.5	-	0	3159					NR_003083.2																						ACCAGCGGCTTGTAGTACACA	0.627000													4	11					0	0	1	0	0
GNAQ	2776	broad.mit.edu	37	9	80537255	80537255	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.448000			Mis		uveal melanoma								25	45					2.14196e-07	2.20889e-07	1	1	0
ATP1B4	23439	broad.mit.edu	37	X	119513467	119513467	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.438000													36	4					0	0	1	0	0
DMXL1	1657	broad.mit.edu	37	5	118469695	118469695	+	Silent	SNP	C	C	T	rs141146454		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.428000													46	58					0	0	1	0	0
ST18	9705	broad.mit.edu	37	8	53030985	53030985	+	Silent	SNP	T	T	C			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.308000													3	79					0	0	1	0	0
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr22:29091840T>C	ENST00000544772.1	-	12	1890	c.454A>G	c.(454-456)Aag>Gag	p.K152E	CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN	checkpoint kinase 2	373	FHA.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418000			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					5	57					0	0	1	0	0
SULF2	55959	broad.mit.edu	37	20	46295178	46295178	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.627000													27	41					0	0	1	0	0
FOXF2	2295	broad.mit.edu	37	6	1391338	1391338	+	Missense_Mutation	SNP	C	C	T			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.677000													10	9					0	0	1	0	0
RP11-798G7.5	0	broad.mit.edu	37	17	43587576	43587576	+	RNA	SNP	A	A	G	rs145439557	by1000genomes	TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr17:43587576A>G	ENST00000253803.2	+	0	267				LRRC37A4P_ENST00000579913.1_RNA																							tctgaaaagaaaagaaaaaaa	0.428000													3	42					0	0	1	0	0
C1orf86	199990	broad.mit.edu	37	1	2125233	2125233	+	Translation_Start_Site	SNP	G	G	A			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	0.697000													13	28					0	0	1	0	0
RP11-798G7.5	0	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs149697015	by1000genomes	TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr17:43587569G>C	ENST00000253803.2	+	0	267				LRRC37A4P_ENST00000579913.1_RNA																							aactccgtctgaaaagaaaag	0.443000													3	30					0	0	1	0	0
BAP1	8314	broad.mit.edu	37	3	52437427	52437448	+	Splice_Site	DEL	CCCACCTGTCAGCGCCAGGGGA	CCCACCTGTCAGCGCCAGGGGA	-			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	p.P572fs*69(1)		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			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""							4	3	---	---	---	---					
AC226119.5	0	broad.mit.edu	37	4	3951121	3951122	+	RNA	INS	-	-	TGTC	rs35568143		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr4:3951121_3951122insTGTC	ENST00000281228.8	-	0	344				FAM86EP_ENST00000313946.8_RNA																							cgttttcACTTTGTGCAGGAAG	0.515													3	5	---	---	---	---					
SP8	221833	broad.mit.edu	37	7	20824941	20824943	+	In_Frame_Del	DEL	GCC	GCC	-			TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c8d94ef-ded9-432d-bcd8-20beaf8e8ef6	8534bc2e-1fb6-4f5c-9b95-59691cece7c7	g.chr7:20824941_20824943delGCC	ENST00000361443.4	-	3	676_678	c.439_441delGGC	c.(439-441)ggcdel	p.G147del	SP8_ENST00000418710.2_In_Frame_Del_p.G165del	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	147					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.G165delG(1)|p.G147delG(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						GCGCGGAGGAgccgccgccgccg	0.729													6	1	---	---	---	---					
BRCA2	675	broad.mit.edu	37	13	32945125	32945135	+	Frame_Shift_Del	DEL	ATTTCGCAATG	ATTTCGCAATG	-	rs80359105		TCGA-VD-A8KI-01A-11D-A39W-08	TCGA-VD-A8KI-10A-01D-A39Z-08								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	p.F2841I(2)|p.R2842C(1)		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			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			17	36	---	---	---	---					
