Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
LOC642826	642826	broad.mit.edu	37	10	47207813	47207813	+	RNA	SNP	T	C	C			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr10:47207813T>C	uc001jei.2	-	12		c.1586A>G			uc009xnf.2_Missense_Mutation_p.H132R					Homo sapiens cDNA, FLJ99065.												0						TTTACTTACATGGTTTGTACA	0.294000													8	27	---	---	---	---	0	0	0.004482	0	0
PAOX	196743	broad.mit.edu	37	10	135202535	135202535	+	Silent	SNP	A	G	G			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr10:135202535A>G	uc001lmv.2	+	5	1277	c.1197A>G	c.(1195-1197)GTA>GTG	p.V399V	PAOX_uc001lmw.2_RNA|PAOX_uc001lmx.2_Silent_p.V399V|PAOX_uc001lmy.2_Missense_Mutation_p.Y315C|PAOX_uc001lmz.2_RNA|PAOX_uc001lna.2_RNA|PAOX_uc001lnb.2_RNA|PAOX_uc001lnc.2_RNA	NM_152911	NP_690875	Q6QHF9	PAOX_HUMAN	polyamine oxidase isoform 1	537					polyamine biosynthetic process|xenobiotic metabolic process	peroxisomal matrix	polyamine oxidase activity				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)		ATGAAGAAGTACTTCTGTGTC	0.527000													7	218	---	---	---	---	0	0	0.001984	0	0
B3GAT1	27087	broad.mit.edu	37	11	134252734	134252734	+	Missense_Mutation	SNP	C	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr11:134252734C>T	uc001qhq.2	-	5	1049	c.788G>A	c.(787-789)CGG>CAG	p.R263Q	B3GAT1_uc001qhr.2_Missense_Mutation_p.R263Q|B3GAT1_uc010scv.1_Missense_Mutation_p.R276Q	NM_018644	NP_061114	Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1	263	Lumenal (Potential).				carbohydrate metabolic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|metal ion binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)		CAGAATGAGCCGCAGGTTGAC	0.592000													12	37	---	---	---	---	0	0	0.013537	0	0
CDCA3	83461	broad.mit.edu	37	12	6960070	6960070	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr12:6960070G>A	uc001qrg.2	-	2	175	c.47C>T	c.(46-48)CCG>CTG	p.P16L	CDCA3_uc001qre.2_Missense_Mutation_p.P16L|uc001qrf.1_5'Flank|USP5_uc001qri.3_5'Flank|USP5_uc001qrh.3_5'Flank	NM_031299	NP_112589	Q99618	CDCA3_HUMAN	cell division cycle associated 3	16					cell division|mitosis	cytosol					0						CTTGTTGTGCGGCGGAGGCCG	0.662000													3	37	---	---	---	---	0	0	0.009096	0	0
APAF1	317	broad.mit.edu	37	12	99042229	99042229	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr12:99042229G>A	uc001tfz.2	+	2	669	c.92G>A	c.(91-93)AGT>AAT	p.S31N	APAF1_uc001tfy.2_Missense_Mutation_p.S31N|APAF1_uc001tga.2_Missense_Mutation_p.S31N|APAF1_uc001tgb.2_Missense_Mutation_p.S31N|APAF1_uc001tgc.2_Missense_Mutation_p.S31N	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform	31	CARD.				activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)	CACATGATTAGTGATGGATTT	0.358000													4	136	---	---	---	---	0	0	0.009096	0	0
C15orf52	388115	broad.mit.edu	37	15	40627436	40627436	+	Nonsense_Mutation	SNP	C	A	A			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr15:40627436C>A	uc001zlh.3	-	11	1544	c.1528G>T	c.(1528-1530)GGA>TGA	p.G510*	C15orf52_uc010ucn.1_Nonsense_Mutation_p.G300*	NM_207380	NP_997263	Q6ZUT6	CO052_HUMAN	hypothetical protein LOC388115	510										large_intestine(1)	1		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		TGGCTGCCTCCTCTCGTGGGC	0.682000													6	175	---	---	---	---	3.59834e-05	5.68769e-05	0.001168	1	0
FBN1	2200	broad.mit.edu	37	15	48704920	48704920	+	Missense_Mutation	SNP	C	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr15:48704920C>T	uc001zwx.1	-	65	8400	c.8072G>A	c.(8071-8073)GGC>GAC	p.G2691D	FBN1_uc010beo.1_RNA	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	2691					heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TCGGCCCATGCCCATTCCAGA	0.502000													4	184	---	---	---	---	0	0	0.009096	0	0
TRPM4	54795	broad.mit.edu	37	19	49684617	49684617	+	Missense_Mutation	SNP	T	C	C			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr19:49684617T>C	uc002pmw.2	+	10	1234	c.1162T>C	c.(1162-1164)TCG>CCG	p.S388P	TRPM4_uc010emu.2_Missense_Mutation_p.S388P|TRPM4_uc010yak.1_5'UTR|TRPM4_uc002pmx.2_Missense_Mutation_p.S214P|TRPM4_uc010emv.2_Missense_Mutation_p.S273P|TRPM4_uc010yal.1_Intron|TRPM4_uc002pmy.2_5'Flank	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,	388	Cytoplasmic (Potential).				dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		CTGTGGGAGCTCGGAGGCCTC	0.557000													3	99	---	---	---	---	0	0	0.004672	0	0
RANBP2	5903	broad.mit.edu	37	2	109365442	109365442	+	Missense_Mutation	SNP	C	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr2:109365442C>T	uc002tem.3	+	9	1256	c.1130C>T	c.(1129-1131)GCC>GTC	p.A377V		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	377					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						GAAACTTTTGCCAACAAAAGC	0.348000													5	290	---	---	---	---	0	0	0.001168	0	0
TRMT6	51605	broad.mit.edu	37	20	5923212	5923212	+	Silent	SNP	C	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr20:5923212C>T	uc002wmh.1	-	7	1010	c.888G>A	c.(886-888)CAG>CAA	p.Q296Q	TRMT6_uc010zra.1_Silent_p.Q126Q|TRMT6_uc010gbn.1_Silent_p.Q126Q|TRMT6_uc010gbo.1_RNA	NM_015939	NP_057023	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6	296					regulation of translational initiation|tRNA processing	nucleus	protein binding|translation initiation factor activity			pancreas(1)	1						GTTCAGAAGCCTGTTTTTCCT	0.443000													15	50	---	---	---	---	0	0	0.003163	0	0
FRG1B	284802	broad.mit.edu	37	20	29628251	29628251	+	Missense_Mutation	SNP	A	G	G			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr20:29628251A>G	uc010ztl.1	+	3	195	c.163A>G	c.(163-165)AAT>GAT	p.N55D	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.N7D					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GTTGGCCTCAAATAGCTGCTT	0.358000													8	102	---	---	---	---	0	0	0.010729	0	0
CBFA2T2	9139	broad.mit.edu	37	20	32199070	32199070	+	Missense_Mutation	SNP	C	G	G			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr20:32199070C>G	uc002wzg.1	+	4	913	c.376C>G	c.(376-378)CTG>GTG	p.L126V	CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Missense_Mutation_p.L117V|CBFA2T2_uc002wzf.1_RNA|CBFA2T2_uc002wzh.1_Missense_Mutation_p.L97V|CBFA2T2_uc002wzi.1_RNA|CBFA2T2_uc002wzj.1_RNA	NM_005093	NP_005084	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit	126	TAFH.					nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2						TCTTACCACTCTGCAACAGTT	0.507000													29	112	---	---	---	---	0	0	0.008361	0	0
NCK1	4690	broad.mit.edu	37	3	136647064	136647064	+	Missense_Mutation	SNP	C	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr3:136647064C>T	uc003erh.2	+	2	328	c.221C>T	c.(220-222)ACC>ATC	p.T74I	NCK1_uc011bme.1_5'Flank	NM_006153	NP_006144	P16333	NCK1_HUMAN	NCK adaptor protein 1	74					axon guidance|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of translation|signal complex assembly|T cell activation|T cell receptor signaling pathway	cytosol|endoplasmic reticulum|nucleus	cytoskeletal adaptor activity|receptor binding|receptor signaling complex scaffold activity			pancreas(1)	1						CTAAAGGATACCTTAGGTAAG	0.333000													11	23	---	---	---	---	0	0	0.008291	0	0
TPRG1	285386	broad.mit.edu	37	3	189028237	189028237	+	Missense_Mutation	SNP	G	A	A			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr3:189028237G>A	uc003frv.1	+	10	1769	c.542G>A	c.(541-543)CGC>CAC	p.R181H	TPRG1_uc003frw.1_Missense_Mutation_p.R181H	NM_198485	NP_940887	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	181											0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		CTTCTGTCCCGCTGGAACCCA	0.473000													4	60	---	---	---	---	0	0	0.009096	0	0
SDHAP2	727956	broad.mit.edu	37	3	195400820	195400820	+	Missense_Mutation	SNP	A	G	G	rs111433895		TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr3:195400820A>G	uc003fuw.2	+	9	1310	c.116A>G	c.(115-117)CAG>CGG	p.Q39R	SDHAP2_uc011btb.1_Silent_p.S186S|SDHAP2_uc011btc.1_RNA|SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						TTGTCTGGTCAGGCATGTGCC	0.567000													3	32	---	---	---	---	0	0	0.009096	0	0
PRDM8	56978	broad.mit.edu	37	4	81124216	81124216	+	Missense_Mutation	SNP	C	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr4:81124216C>T	uc010ijo.2	+	8	2439	c.1600C>T	c.(1600-1602)CCC>TCC	p.P534S	PRDM8_uc003hmb.3_Missense_Mutation_p.P534S|PRDM8_uc003hmc.3_Missense_Mutation_p.P534S	NM_020226	NP_064611	Q9NQV8	PRDM8_HUMAN	PR domain containing 8	534					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						CGGCGTGGGCCCCACCAGACT	0.731000													6	6	---	---	---	---	0	0	0.003080	0	0
GPRIN3	285513	broad.mit.edu	37	4	90170054	90170054	+	Missense_Mutation	SNP	G	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr4:90170054G>T	uc003hsm.1	-	2	1727	c.1208C>A	c.(1207-1209)GCT>GAT	p.A403D		NM_198281	NP_938022	Q6ZVF9	GRIN3_HUMAN	G protein-regulated inducer of neurite outgrowth	403										ovary(3)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CCGTTGGAAAGCTGTAGACTC	0.532000													7	127	---	---	---	---	0.00198382	0.00294567	0.001984	1	0
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr5:99715528C>T	uc011cuw.1	-	4		c.382G>A				NR_027503				Homo sapiens glucuronidase, beta pseudogene (LOC100133050), non-coding RNA.												0						AGCGGACAGTCGAAGCCCTTC	0.607000													5	13	---	---	---	---	0	0	0.000602	0	0
PCDHA10	56139	broad.mit.edu	37	5	140237799	140237799	+	Silent	SNP	G	A	A			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr5:140237799G>A	uc003lhx.2	+	1	2166	c.2166G>A	c.(2164-2166)TCG>TCA	p.S722S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc011dad.1_Silent_p.S722S	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	722	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGGTGCTCGGCGGCGCCCA	0.662000													15	27	---	---	---	---	0	0	0.002450	0	0
TBC1D7	51256	broad.mit.edu	37	6	13307947	13307947	+	Nonsense_Mutation	SNP	C	A	A			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr6:13307947C>A	uc003naj.2	-	6	641	c.550G>T	c.(550-552)GAA>TAA	p.E184*	TBC1D7_uc011dis.1_Intron|TBC1D7_uc003nan.2_Nonsense_Mutation_p.E184*|TBC1D7_uc003nal.2_Nonsense_Mutation_p.E184*|TBC1D7_uc003nam.2_Nonsense_Mutation_p.E184*|TBC1D7_uc003nao.2_Nonsense_Mutation_p.E157*|TBC1D7_uc010jpd.2_Nonsense_Mutation_p.E138*|TBC1D7_uc003nap.2_Nonsense_Mutation_p.E157*	NM_016495	NP_057579	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7 isoform a	184	Rab-GAP TBC.				positive regulation of protein ubiquitination	cytoplasmic membrane-bounded vesicle	protein binding|Rab GTPase activator activity			ovary(1)	1	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			CTGCCATCTTCCAGATTCAAG	0.423000													15	54	---	---	---	---	1.15088e-07	1.87977e-07	0.004007	1	0
TIAM2	26230	broad.mit.edu	37	6	155569232	155569232	+	Missense_Mutation	SNP	A	G	G			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr6:155569232A>G	uc003qqb.2	+	22	5024	c.3751A>G	c.(3751-3753)AGA>GGA	p.R1251G	TIAM2_uc003qqe.2_Missense_Mutation_p.R1251G|TIAM2_uc010kjj.2_Missense_Mutation_p.R784G|TIAM2_uc003qqf.2_Missense_Mutation_p.R627G|TIAM2_uc011efl.1_Missense_Mutation_p.R587G|TIAM2_uc003qqg.2_Missense_Mutation_p.R563G|TIAM2_uc003qqh.2_Missense_Mutation_p.R176G	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1251	DH.				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GCCGGTTCAGAGAGTGCTCAA	0.607000											OREG0017745	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	65	---	---	---	---	0	0	0.004672	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				23	54	---	---	---	---	0	0	0.002780	0	0
GPM6B	2824	broad.mit.edu	37	X	13798077	13798077	+	Missense_Mutation	SNP	G	C	C			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chrX:13798077G>C	uc004cvz.2	-	4	728	c.437C>G	c.(436-438)GCC>GGC	p.A146G	GPM6B_uc004cvx.2_Missense_Mutation_p.A127G|GPM6B_uc011min.1_Missense_Mutation_p.A60G|GPM6B_uc004cwa.2_Missense_Mutation_p.A127G|GPM6B_uc004cvw.2_Missense_Mutation_p.A186G|GPM6B_uc011mim.1_Missense_Mutation_p.A160G|GPM6B_uc004cvy.2_Missense_Mutation_p.A186G	NM_005278	NP_005269	Q13491	GPM6B_HUMAN	glycoprotein M6B isoform 3	146	Helical; (Potential).				cell differentiation|nervous system development	integral to membrane					0						ACCCAGCCAGGCCACTCCAAG	0.493000													9	92	---	---	---	---	0	0	0.006214	0	0
Unknown	0	broad.mit.edu	37	1	700532	700532	+	RNA	DEL	T	-	-			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr1:700532delT	uc001abo.2	-	7		c.1022delA								Homo sapiens cDNA clone IMAGE:4129277, partial cds.																		aaaaaaaaaaTTCCTTTGGGA	0.214													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	10	66736386	66736387	+	IGR	DEL	TT	-	-	rs34610191		TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr10:66736386_66736387delTT								ANXA2P3 (149752 upstream) : CTNNA3 (943338 downstream)																							tgaaggaaggtttaaactcaga	0.000													3	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	13	19532389	19532389	+	IGR	DEL	T	-	-			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr13:19532389delT								LOC284232 (86280 upstream) : LOC348021 (50010 downstream)																							TTTGGGAGCCTTTTTTTTTTG	0.542													2	4	---	---	---	---					
NF1P1	440225	broad.mit.edu	37	15	22146377	22146378	+	5'Flank	DEL	GT	-	-			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr15:22146377_22146378delGT	uc010tzs.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0						tTGAgtgtgggtgtgtgtgtgt	0.233													3	3	---	---	---	---					
IL32	9235	broad.mit.edu	37	16	3119304	3119305	+	Frame_Shift_Ins	INS	-	G	G	rs2981599		TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr16:3119304_3119305insG	uc002cto.2	+	6	864_865	c.653_654insG	c.(652-654)GACfs	p.D218fs	IL32_uc002ctk.2_Frame_Shift_Ins_p.D115fs|IL32_uc010uwp.1_Frame_Shift_Ins_p.D152fs|IL32_uc010btb.2_Frame_Shift_Ins_p.D162fs|IL32_uc002ctl.2_Frame_Shift_Ins_p.D172fs|IL32_uc002ctm.2_Frame_Shift_Ins_p.D172fs|IL32_uc002ctn.2_Frame_Shift_Ins_p.D172fs|IL32_uc002cts.3_Frame_Shift_Ins_p.D172fs|IL32_uc002ctp.2_Frame_Shift_Ins_p.D152fs|IL32_uc002ctq.2_Frame_Shift_Ins_p.D218fs|IL32_uc002ctr.2_Frame_Shift_Ins_p.D152fs|IL32_uc002ctt.2_Frame_Shift_Ins_p.D172fs|IL32_uc010uwr.1_Frame_Shift_Ins_p.D132fs|IL32_uc002ctu.2_Frame_Shift_Ins_p.D163fs	NM_004221	NP_004212	P24001	IL32_HUMAN	interleukin 32 isoform B	218					cell adhesion|defense response|immune response	extracellular space	cytokine activity			pancreas(1)	1						CCACGGGGGGACAAGGAGGAGC	0.574													14	247	---	---	---	---					
PBRM1	55193	broad.mit.edu	37	3	52713876	52713877	+	5'Flank	INS	-	T	T			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr3:52713876_52713877insT	uc003des.2	-						PBRM1_uc003dex.2_5'Flank|PBRM1_uc003deq.2_5'Flank|PBRM1_uc003der.2_5'Flank|PBRM1_uc003det.2_5'Flank|PBRM1_uc003deu.2_5'Flank|PBRM1_uc003dev.2_5'Flank|PBRM1_uc003dew.2_5'Flank|PBRM1_uc010hmk.1_5'Flank|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_5'Flank|PBRM1_uc003dfb.1_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CTAGCTATAAGTTTTTTTTTTT	0.361			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								2	4	---	---	---	---					
MIR567	693152	broad.mit.edu	37	3	111831724	111831724	+	RNA	DEL	A	-	-			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr3:111831724delA	hsa-mir-567|MI0003573	+			c.77delA			C3orf52_uc003dyq.3_Intron|C3orf52_uc011bhs.1_Intron|C3orf52_uc011bht.1_Intron|C3orf52_uc003dyr.1_Intron																	0						ATGCAAAACTAAAAAAAAAAA	0.323													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	180165983	180165984	+	IGR	INS	-	C	C	rs2054696	by1000genomes	TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr5:180165983_180165984insC								FLT4 (89359 upstream) : OR2Y1 (139 downstream)																							tgttccccccgccaccaaaaaa	0.188													3	6	---	---	---	---					
AMPH	273	broad.mit.edu	37	7	38671031	38671033	+	5'Flank	DEL	GGA	-	-			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr7:38671031_38671033delGGA	uc003tgu.2	-						AMPH_uc003tgv.2_5'Flank	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						aggaggagcgggaggaggaggag	0.296													2	4	---	---	---	---					
RELN	5649	broad.mit.edu	37	7	103629803	103629804	+	Translation_Start_Site	INS	-	GCCGCC	GCCGCC			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chr7:103629803_103629804insGCCGCC	uc003vca.2	-	1					RELN_uc010liz.2_Translation_Start_Site	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CTGCGCTCCATgccgccgccgc	0.569													3	5	---	---	---	---					
VENTXP1	139538	broad.mit.edu	37	X	26575831	26575831	+	5'Flank	DEL	C	-	-			TCGA-DJ-A2PT-01A-11D-A18F-08	TCGA-DJ-A2PT-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	23e2a898-3fc0-4fc6-9ac8-36a2508d60f4	1a164574-d0ea-4e7d-b658-7dfd876c02e9	g.chrX:26575831delC	uc004dbs.2	+							NR_001559				Homo sapiens tumor antigen NA88-A pseudogene, complete sequence.												0						CCGGCAGCAGCCCTCCAGGTT	0.677													7	2	---	---	---	---					
