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
SH3PXD2A	9644	broad.mit.edu	37	10	105365619	105365619	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:105365619G>A	uc001kxj.1	-	13	1420	c.1280C>T	c.(1279-1281)ACC>ATC	p.T427I	SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_Missense_Mutation_p.T262I|SH3PXD2A_uc010qqt.1_Missense_Mutation_p.T304I|SH3PXD2A_uc009xxn.1_Missense_Mutation_p.T262I|SH3PXD2A_uc010qqu.1_Missense_Mutation_p.T370I	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1	455	SH3 3.				cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		TTCGGCAATGGTGTAGTACTC	0.537000											OREG0020500	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	32	38	---	---	---	---	0	0	0.144211	0	0
SORCS3	22986	broad.mit.edu	37	10	106974207	106974207	+	Missense_Mutation	SNP	C	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:106974207C>T	uc001kyi.1	+	18	2610	c.2383C>T	c.(2383-2385)CGG>TGG	p.R795W	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	795	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TAGGTATCGGCGGATTGTGTC	0.483000													8	15	---	---	---	---	0	0	0.058154	0	0
TACC2	10579	broad.mit.edu	37	10	123970987	123970987	+	Silent	SNP	T	C	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:123970987T>C	uc001lfv.2	+	9	7407	c.7047T>C	c.(7045-7047)CCT>CCC	p.P2349P	TACC2_uc001lfw.2_Silent_p.P495P|TACC2_uc009xzx.2_Silent_p.P2304P|TACC2_uc010qtv.1_Silent_p.P2353P|TACC2_uc001lfx.2_Silent_p.P53P|TACC2_uc001lfy.2_Silent_p.P53P|TACC2_uc001lfz.2_Silent_p.P427P|TACC2_uc001lga.2_Silent_p.P427P|TACC2_uc009xzy.2_Silent_p.P427P|TACC2_uc001lgb.2_Silent_p.P384P|TACC2_uc010qtw.1_Silent_p.P444P	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	2349	SPAZ.					microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				ATTTTAACCCTTTTTCTTCCA	0.468000													4	219	---	---	---	---	0	0	0.009096	0	0
JAKMIP3	282973	broad.mit.edu	37	10	133930583	133930583	+	Silent	SNP	C	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:133930583C>T	uc001lkx.3	+	2	138	c.138C>T	c.(136-138)GTC>GTT	p.V46V		NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TCTTTCAGGTCAGCAAAGTGG	0.572000													9	32	---	---	---	---	0	0	0.069234	0	0
MALAT1	378938	broad.mit.edu	37	11	65268525	65268525	+	RNA	SNP	A	C	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr11:65268525A>C	uc010roh.1	+	1		c.3293A>C			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						TGAATTTGATAGCCAAATTGA	0.348000													25	51	---	---	---	---	0	0	0.091800	0	0
CTSW	1521	broad.mit.edu	37	11	65651008	65651008	+	Silent	SNP	T	C	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr11:65651008T>C	uc001ogc.1	+	10	1092	c.1050T>C	c.(1048-1050)AAT>AAC	p.N350N	CTSW_uc001ogb.1_3'UTR	NM_001335	NP_001326	P56202	CATW_HUMAN	cathepsin W preproprotein	350					immune response|proteolysis		cysteine-type endopeptidase activity			central_nervous_system(1)	1				READ - Rectum adenocarcinoma(159;0.168)		GAGGGAGCAATACCTGTGGCA	0.622000													47	77	---	---	---	---	0	0	0.139131	0	0
DCPS	28960	broad.mit.edu	37	11	126201357	126201357	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr11:126201357G>A	uc001qdp.2	+	3	763	c.434G>A	c.(433-435)CGC>CAC	p.R145H		NM_014026	NP_054745	Q96C86	DCPS_HUMAN	mRNA decapping enzyme	145				R->A: Increases decapping activity to 180% of wild-type.	deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	exoribonuclease activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		AAGTACCTGCGCCAGGACCTC	0.557000													4	96	---	---	---	---	0	0	0.009096	0	0
C13orf23	80209	broad.mit.edu	37	13	39587564	39587564	+	Missense_Mutation	SNP	T	C	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr13:39587564T>C	uc001uwy.2	-	11	2698	c.1825A>G	c.(1825-1827)ACT>GCT	p.T609A	C13orf23_uc001uwz.2_Missense_Mutation_p.T587A	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	609	Ser-rich.									ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)		GTGGGCTCAGTTTTGATCATA	0.532000													18	106	---	---	---	---	0	0	0.043863	0	0
RAI1	10743	broad.mit.edu	37	17	17696275	17696275	+	Nonsense_Mutation	SNP	C	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr17:17696275C>T	uc002grm.2	+	3	482	c.13C>T	c.(13-15)CGA>TGA	p.R5*	RAI1_uc002grn.1_Nonsense_Mutation_p.R5*	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	5						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)		GCAGTCTTTTCGAGAAAGGTG	0.388000													17	10	---	---	---	---	0	0	0.043863	0	0
MIR632	693217	broad.mit.edu	37	17	30677219	30677219	+	RNA	SNP	C	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr17:30677219C>A	hsa-mir-632|MI0003647	+			c.92C>A			ZNF207_uc002hhj.3_5'UTR|ZNF207_uc002hhh.3_5'UTR|ZNF207_uc002hhi.3_5'UTR|ZNF207_uc010csz.2_5'UTR|ZNF207_uc002hhk.1_5'UTR																	0						TGGTGGTAGCCGTTGGGTTGG	0.567000													43	76	---	---	---	---	1.8453e-21	2.53728e-21	0.117977	1	0
HDAC5	10014	broad.mit.edu	37	17	42170141	42170141	+	Silent	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr17:42170141G>A	uc002ifd.1	-	7	886	c.675C>T	c.(673-675)TCC>TCT	p.S225S	HDAC5_uc002ife.1_Silent_p.S225S|HDAC5_uc002iff.1_Silent_p.S226S|HDAC5_uc010czp.1_Silent_p.S225S|HDAC5_uc002ifh.2_Silent_p.S225S	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1	225					B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TCTGGGGAGGGGAACTCTGGT	0.642000													11	20	---	---	---	---	0	0	0.080935	0	0
MIB1	57534	broad.mit.edu	37	18	19378075	19378075	+	Missense_Mutation	SNP	A	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr18:19378075A>T	uc002ktq.2	+	8	1123	c.1123A>T	c.(1123-1125)ATT>TTT	p.I375F	MIB1_uc002ktp.2_Missense_Mutation_p.I14F	NM_020774	NP_065825	Q86YT6	MIB1_HUMAN	mindbomb homolog 1	375					Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)			AGTACAACAGATTTATTCAGA	0.378000													10	33	---	---	---	---	0	0	0.058154	0	0
RHOQ	23433	broad.mit.edu	37	2	46803383	46803383	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr2:46803383G>A	uc002rva.2	+	3	678	c.359G>A	c.(358-360)GGA>GAA	p.G120E	uc002rvb.2_Intron	NM_012249	NP_036381	P17081	RHOQ_HUMAN	ras-like protein TC10 precursor	120					cortical actin cytoskeleton organization|insulin receptor signaling pathway|negative regulation of establishment of protein localization in plasma membrane|positive regulation of filopodium assembly|positive regulation of glucose import|positive regulation of transcription from RNA polymerase II promoter|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	actin filament|cytosol|plasma membrane	GBD domain binding|GTP binding|GTPase activity|profilin binding			skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			TTATTAATAGGAACTCAGGTA	0.418000													12	18	---	---	---	---	0	0	0.080935	0	0
RGPD4	285190	broad.mit.edu	37	2	108477236	108477236	+	Missense_Mutation	SNP	T	G	G			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr2:108477236T>G	uc010ywk.1	+	13	1855	c.1773T>G	c.(1771-1773)AAT>AAG	p.N591K	RGPD4_uc002tdu.2_5'UTR|RGPD4_uc010ywl.1_RNA	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	591	TPR 2.				intracellular transport		binding			skin(2)	2						GTGGTCTTAATTCTTTTTATG	0.323000													38	65	---	---	---	---	0	0	0.104719	0	0
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	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													3	7	---	---	---	---	0	0	0.115264	0	0
HLA-DMB	3109	broad.mit.edu	37	6	32906598	32906598	+	Missense_Mutation	SNP	C	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:32906598C>T	uc003ocl.1	-	2	433	c.200G>A	c.(199-201)GGG>GAG	p.G67E	HLA-DMB_uc003ocj.1_Missense_Mutation_p.G67E|HLA-DMB_uc003ock.1_5'Flank|HLA-DMB_uc010jud.1_5'Flank|HLA-DMB_uc010jue.1_5'Flank|HLA-DMB_uc010juf.1_5'Flank|HLA-DMB_uc011dql.1_Missense_Mutation_p.G67E	NM_002118	NP_002109	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM	67	Beta-1.|Lumenal (Potential).				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						ATTCAGCACCCCAAATTCGCA	0.517000													23	25	---	---	---	---	0	0	0.069288	0	0
COL19A1	1310	broad.mit.edu	37	6	70866046	70866046	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:70866046G>A	uc003pfc.1	+	32	2224	c.2107G>A	c.(2107-2109)GTC>ATC	p.V703I	COL19A1_uc010kam.1_Missense_Mutation_p.V599I	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	703	Triple-helical region 4 (COL4).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						CCAAGCCAGTGTCCCAGGGCT	0.463000													9	7	---	---	---	---	0	0	0.047766	0	0
MTO1	25821	broad.mit.edu	37	6	74171794	74171794	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:74171794G>A	uc003pgy.3	+	1	341	c.217G>A	c.(217-219)GGT>AGT	p.G73S	MTO1_uc010kav.2_Missense_Mutation_p.G73S|MTO1_uc003pgz.3_Missense_Mutation_p.G73S|MTO1_uc003pha.3_5'UTR|MTO1_uc003phb.3_Intron|MTO1_uc003phc.1_5'Flank	NM_133645	NP_598400	Q9Y2Z2	MTO1_HUMAN	mitochondrial translation optimization 1 homolog	73					tRNA processing	mitochondrion	flavin adenine dinucleotide binding			ovary(3)|skin(2)|pancreas(1)	6						GGACACGATCGGTGAGGAGCG	0.657000													3	48	---	---	---	---	0	0	0.115264	0	0
PPIL6	285755	broad.mit.edu	37	6	109757309	109757309	+	Missense_Mutation	SNP	T	C	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:109757309T>C	uc003ptg.3	-	2	283	c.229A>G	c.(229-231)AGG>GGG	p.R77G	PPIL6_uc010kdo.2_Intron|PPIL6_uc010kdp.2_Missense_Mutation_p.R77G	NM_173672	NP_775943	Q8IXY8	PPIL6_HUMAN	peptidylprolyl isomerase-like 6 isoform 1	77					protein folding		peptidyl-prolyl cis-trans isomerase activity				0		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)		TCCTTTACCCTTTTTTTCTCC	0.338000													3	97	---	---	---	---	0	0	0.115264	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	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				11	11	---	---	---	---	0	0	0.080935	0	0
COL5A1	1289	broad.mit.edu	37	9	137690287	137690287	+	Missense_Mutation	SNP	C	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr9:137690287C>T	uc004cfe.2	+	37	3314	c.2932C>T	c.(2932-2934)CCT>TCT	p.P978S		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	978	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCAGGACACCCTGGACAGAG	0.577000													6	65	---	---	---	---	0	0	0.029380	0	0
PPEF1	5475	broad.mit.edu	37	X	18842187	18842187	+	Missense_Mutation	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:18842187G>A	uc004cyq.2	+	17	2129	c.1648G>A	c.(1648-1650)GAA>AAA	p.E550K	PPEF1_uc004cyp.2_Missense_Mutation_p.E522K|PPEF1_uc004cyr.2_Missense_Mutation_p.E488K|PPEF1_uc004cys.2_Missense_Mutation_p.E550K|PPEF1_uc011mja.1_Missense_Mutation_p.E485K|PPEF1_uc011mjb.1_Missense_Mutation_p.E494K	NM_006240	NP_006231	O14829	PPE1_HUMAN	protein phosphatase with EF hand calcium-binding	550					detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)					TATCCGCATTGAAAAACCTGT	0.418000													13	27	---	---	---	---	0	0	0.093190	0	0
USP9X	8239	broad.mit.edu	37	X	40988337	40988337	+	Nonsense_Mutation	SNP	G	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:40988337G>T	uc004dfb.2	+	3	814	c.181G>T	c.(181-183)GAA>TAA	p.E61*	USP9X_uc004dfc.2_Nonsense_Mutation_p.E61*	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	61					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						ACCACAGCTTGAAGATGAGGA	0.458000													14	15	---	---	---	---	1.52009e-12	1.96718e-12	0.132662	1	0
CENPI	2491	broad.mit.edu	37	X	100383791	100383791	+	Silent	SNP	G	A	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:100383791G>A	uc004egx.2	+	11	1431	c.1161G>A	c.(1159-1161)AGG>AGA	p.R387R	CENPI_uc011mrg.1_Silent_p.R387R|CENPI_uc004egy.2_Silent_p.R387R	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I	387					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1						TCTTGCTGAGGTTTTATTACT	0.413000													25	43	---	---	---	---	0	0	0.091800	0	0
F8	2157	broad.mit.edu	37	X	154157148	154157148	+	Silent	SNP	G	A	A	rs147629393		TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:154157148G>A	uc004fmt.2	-	14	5088	c.4917C>T	c.(4915-4917)CCC>CCT	p.P1639P		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	1639	B.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTTCTATTTCGGGCTTATTTT	0.423000													25	77	---	---	---	---	0	0	0.091800	0	0
MMS19	64210	broad.mit.edu	37	10	99220481	99220481	+	Frame_Shift_Del	DEL	G	-	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:99220481delG	uc001kns.3	-	25	2665	c.2440delC	c.(2440-2442)CATfs	p.H814fs	MMS19_uc001knq.2_Frame_Shift_Del_p.H77fs|MMS19_uc009xvs.2_Frame_Shift_Del_p.H399fs|MMS19_uc009xvt.2_Frame_Shift_Del_p.H558fs|MMS19_uc001knr.2_Frame_Shift_Del_p.H655fs|MMS19_uc010qox.1_Frame_Shift_Del_p.H792fs|MMS19_uc001knt.2_Frame_Shift_Del_p.H814fs|MMS19_uc001knu.1_RNA	NM_022362	NP_071757	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog	814					chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		CTGAGAGGATGGTATCTGAGC	0.488								Direct_reversal_of_damage|NER					2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	14	74865395	74865396	+	IGR	DEL	CA	-	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr14:74865395_74865396delCA								C14orf115 (38685 upstream) : TMEM90A (7200 downstream)																							cacgtgcgtgcacacacacaca	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	76490463	76490463	+	5'Flank	DEL	C	-	-	rs34910684		TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr17:76490463delC	uc002jvt.1	+											Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		TTGCCTGAAGCCCCCCCAGCC	0.627													3	6	---	---	---	---					
KCNK12	56660	broad.mit.edu	37	2	47797390	47797392	+	In_Frame_Del	DEL	GCA	-	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr2:47797390_47797392delGCA	uc002rwb.2	-	1	79_81	c.79_81delTGC	c.(79-81)TGCdel	p.C27del	MSH2_uc002rvz.2_Intron	NM_022055	NP_071338	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	27	Cytoplasmic (Potential).|Poly-Cys.					integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(1)	1		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCGAAcggcggcagcagcagcag	0.384													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	187126500	187126501	+	IGR	DEL	TG	-	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr2:187126500_187126501delTG								None (None upstream) : ZC3H15 (224384 downstream)																							TGCAGATCGTtgtgtgtgtgtg	0.381													2	4	---	---	---	---					
SNX18	112574	broad.mit.edu	37	5	53814143	53814143	+	Frame_Shift_Del	DEL	C	-	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr5:53814143delC	uc003jpj.3	+	1	551	c.361delC	c.(361-363)CCGfs	p.P121fs	SNX18_uc011cqg.1_Frame_Shift_Del_p.P121fs|SNX18_uc003jpi.3_Frame_Shift_Del_p.P121fs	NM_052870	NP_443102	Q96RF0	SNX18_HUMAN	sorting nexin 18 isoform b	121					cell communication|endocytosis|positive regulation of GTPase activity|protein transport	endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane	phosphatidylinositol binding|protein binding				0		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CACCTTCCAGCCGCCCGGCGC	0.746													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	130525844	130525845	+	IGR	INS	-	T	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr7:130525844_130525845insT								KLF14 (106984 upstream) : MIR29A (35661 downstream)																							CAGttctttgcttttttttttt	0.168													2	4	---	---	---	---					
FAM120C	54954	broad.mit.edu	37	X	54209302	54209303	+	In_Frame_Ins	INS	-	GGCGGC	GGCGGC			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08									Somatic	Phase_I	Capture				Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:54209302_54209303insGGCGGC	uc004dsz.3	-	1	412_413	c.329_330insGCCGCC	c.(328-330)CCC>CCGCCGCCC	p.110_110P>PPP	FAM120C_uc011moh.1_In_Frame_Ins_p.110_110P>PPP|FAM120C_uc004dta.2_In_Frame_Ins_p.110_110P>PPP	NM_017848	NP_060318	Q9NX05	F120C_HUMAN	hypothetical protein LOC54954	110										ovary(1)|central_nervous_system(1)	2						GCAGCTGAGGGGGCGGCGGCGG	0.748													4	9	---	---	---	---					
