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
GDAP2	54834	broad.mit.edu	37	1	118441728	118441728	+	Silent	SNP	C	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr1:118441728C>A	uc001ehf.2	-	7	1046	c.747G>T	c.(745-747)GTG>GTT	p.V249V	GDAP2_uc001ehg.2_Silent_p.V249V	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	249										ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		GTTCAGGTACCACAGGCTCCC	0.438000													61	128					5.39075e-54	6.77299e-54	0.014410	1	0
OR2W3	343171	broad.mit.edu	37	1	248059264	248059264	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr1:248059264A>G	uc001idp.1	+	3	645	c.376A>G	c.(376-378)ATC>GTC	p.I126V	OR2W3_uc010pzb.1_Missense_Mutation_p.I126V	NM_001001957	NP_001001957	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W,	126	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|pancreas(1)	3	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GTGTGTGGCTATCTGCAAGCC	0.607000													20	61					0	0	0.010504	0	0
CELF2	10659	broad.mit.edu	37	10	11363181	11363181	+	Missense_Mutation	SNP	C	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr10:11363181C>G	uc001iki.3	+	11	1179	c.1087C>G	c.(1087-1089)CTG>GTG	p.L363V	CELF2_uc010qbj.1_Missense_Mutation_p.L369V|CELF2_uc001ikk.2_Missense_Mutation_p.L388V|CELF2_uc001ikl.3_Missense_Mutation_p.L376V|CELF2_uc010qbl.1_Missense_Mutation_p.L339V|CELF2_uc010qbm.1_Missense_Mutation_p.L135V|CELF2_uc001iko.3_Missense_Mutation_p.L343V|CELF2_uc001ikp.3_Missense_Mutation_p.L345V|CELF2_uc010qbn.1_Missense_Mutation_p.L351V|CELF2_uc010qbo.1_Missense_Mutation_p.L258V|CELF2_uc010qbp.1_Missense_Mutation_p.L135V	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2	363	Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion.|Ala-rich.				mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						TATGGCGGCTCTGAATGGAGG	0.502000													4	132					0	0	0.009096	0	0
OR51F2	119694	broad.mit.edu	37	11	4843405	4843405	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:4843405A>G	uc010qyn.1	+	1	790	c.790A>G	c.(790-792)ATC>GTC	p.I264V		NM_001004753	NP_001004753	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F,	264	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGCTGTTTCCATCTTCTACCT	0.478000													27	49					0	0	0.021523	0	0
LOC494141	494141	broad.mit.edu	37	11	18231202	18231202	+	RNA	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:18231202G>A	uc009yhh.2	+	2		c.226G>A			LOC494141_uc001mnx.3_RNA|LOC494141_uc009yhi.1_RNA	NR_026541				Homo sapiens cDNA FLJ29025 fis, clone PRS03236.												0						AAAAAAAAAAGAAAAAGTCCT	0.179000													7	21					0	0	0.016723	0	0
CCDC82	79780	broad.mit.edu	37	11	96092275	96092275	+	Missense_Mutation	SNP	A	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:96092275A>T	uc009ywp.2	-	6	1691	c.1448T>A	c.(1447-1449)TTC>TAC	p.F483Y	CCDC82_uc009ywq.2_Missense_Mutation_p.F483Y|CCDC82_uc001pfx.3_Missense_Mutation_p.F483Y|CCDC82_uc009ywr.2_Missense_Mutation_p.F483Y	NM_024725	NP_079001	Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	483							protein binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		GTATAGTTTGAATTTAAAATG	0.343000													31	81					0	0	0.010818	0	0
OR8B4	283162	broad.mit.edu	37	11	124293908	124293908	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:124293908G>A	uc010sak.1	-	1	860	c.860C>T	c.(859-861)TCG>TTG	p.S287L		NM_001005196	NP_001005196	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		ACTGTAGATCGAAGGGTTAAG	0.443000													32	52					0	0	0.012213	0	0
FAM118B	79607	broad.mit.edu	37	11	126126563	126126563	+	Silent	SNP	C	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:126126563C>G	uc001qdf.2	+	7	981	c.798C>G	c.(796-798)GTC>GTG	p.V266V	FAM118B_uc009zca.2_Silent_p.V270V|FAM118B_uc001qdg.2_Silent_p.V266V	NM_024556	NP_078832	Q9BPY3	F118B_HUMAN	hypothetical protein LOC79607	266											0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		TGGAGGCTGTCAAGCATAAAT	0.448000													41	53					0	0	0.007835	0	0
PRDM10	56980	broad.mit.edu	37	11	129784709	129784709	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr11:129784709G>A	uc001qfm.2	-	18	2975	c.2743C>T	c.(2743-2745)CGA>TGA	p.R915*	PRDM10_uc001qfj.2_Nonsense_Mutation_p.R829*|PRDM10_uc001qfk.2_Nonsense_Mutation_p.R825*|PRDM10_uc001qfl.2_Nonsense_Mutation_p.R829*|PRDM10_uc010sbx.1_Nonsense_Mutation_p.R825*|PRDM10_uc001qfn.2_Nonsense_Mutation_p.R911*|PRDM10_uc009zcs.1_Nonsense_Mutation_p.R98*	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	915	Thr-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TGTGGCGTTCGGTAGTCTGTC	0.552000													11	325					0	0	0.010729	0	0
PYROXD1	79912	broad.mit.edu	37	12	21593340	21593340	+	Silent	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr12:21593340A>G	uc001rew.2	+	2	250	c.123A>G	c.(121-123)GTA>GTG	p.V41V	PYROXD1_uc009ziq.2_5'UTR|PYROXD1_uc009zir.2_Intron	NM_024854	NP_079130	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase	41							oxidoreductase activity			ovary(1)	1						TTCTCTTGGTAACAGCTTCTC	0.289000													9	140					0	0	0.008291	0	0
KRT6C	286887	broad.mit.edu	37	12	52865067	52865067	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr12:52865067A>G	uc001sal.3	-	5	974	c.926T>C	c.(925-927)ATG>ACG	p.M309T		NM_173086	NP_775109	P48668	K2C6C_HUMAN	keratin 6C	309	Coil 1B.|Rod.				cytoskeleton organization	keratin filament	structural molecule activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.0828)		GTGGGTCTGCATCTGGGACAG	0.507000													45	85					0	0	0.014410	0	0
DNAJC14	85406	broad.mit.edu	37	12	56217271	56217271	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr12:56217271G>A	uc001shx.1	-	3	1633	c.1429C>T	c.(1429-1431)CAT>TAT	p.H477Y	DNAJC14_uc001shu.1_Missense_Mutation_p.H477Y|DNAJC14_uc009zob.1_Missense_Mutation_p.H477Y	NM_032364	NP_115740	Q6Y2X3	DJC14_HUMAN	dopamine receptor interacting protein	477	J.				protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4						GCCCGGGGATGATGATTTTTG	0.443000													3	80					0	0	0.009096	0	0
OCA2	4948	broad.mit.edu	37	15	28235791	28235791	+	Silent	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr15:28235791G>A	uc001zbh.3	-	10	1157	c.1047C>T	c.(1045-1047)ATC>ATT	p.I349I	OCA2_uc010ayv.2_Intron	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	349	Cytoplasmic (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		TTCTGTGCACGATCTGGAAAG	0.547000									Oculocutaneous_Albinism				5	167					0	0	0.014758	0	0
THBS1	7057	broad.mit.edu	37	15	39883403	39883403	+	Silent	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr15:39883403A>G	uc001zkh.2	+	15	2444	c.2265A>G	c.(2263-2265)CCA>CCG	p.P755P	THBS1_uc010bbi.2_Silent_p.P227P	NM_003246	NP_003237	P07996	TSP1_HUMAN	thrombospondin 1 precursor	755	TSP type-3 2.				activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding			ovary(3)|central_nervous_system(3)	6		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	Becaplermin(DB00102)	ACAACTGTCCATTCCATTACA	0.448000													60	123					0	0	0.014410	0	0
IGSF6	10261	broad.mit.edu	37	16	21658638	21658638	+	Missense_Mutation	SNP	G	T	T	rs1454374	byFrequency	TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr16:21658638G>T	uc002djg.1	-	2	296	c.243C>A	c.(241-243)GAC>GAA	p.D81E	uc002diq.3_Intron|METTL9_uc002dje.2_Intron|METTL9_uc002djf.2_Intron|IGSF6_uc010vbi.1_Missense_Mutation_p.D81E	NM_005849	NP_005840	O95976	IGSF6_HUMAN	immunoglobulin superfamily, member 6 precursor	81	Extracellular (Potential).|Ig-like C2-type.				cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0				GBM - Glioblastoma multiforme(48;0.066)		TTTTGCACCCGTCCAAGCACA	0.512000													53	68					1.86277e-20	2.28189e-20	0.014410	1	0
TP53	7157	broad.mit.edu	37	17	7577532	7577532	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr17:7577532G>A	uc002gim.2	-	7	943	c.749C>T	c.(748-750)CCC>CTC	p.P250L	TP53_uc002gig.1_Missense_Mutation_p.P250L|TP53_uc002gih.2_Missense_Mutation_p.P250L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.P118L|TP53_uc010cng.1_Missense_Mutation_p.P118L|TP53_uc002gii.1_Missense_Mutation_p.P118L|TP53_uc010cnh.1_Missense_Mutation_p.P250L|TP53_uc010cni.1_Missense_Mutation_p.P250L|TP53_uc002gij.2_Missense_Mutation_p.P250L|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.P157L|TP53_uc002gio.2_Missense_Mutation_p.P118L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	250	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		P -> L (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|P -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|RP -> SS (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|P -> H (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.P250L(37)|p.P250S(12)|p.0?(7)|p.P250P(4)|p.P250F(3)|p.P250N(2)|p.P250A(2)|p.M246_P250delMNRRP(2)|p.P250Q(2)|p.P250_L252delPIL(2)|p.P250H(1)|p.P250_I251insXXXXXX(1)|p.N247_P250delNRRP(1)|p.P250T(1)|p.P250_T253delPILT(1)|p.R249_P250insR(1)|p.R249_I251delRPI(1)|p.R248_P250delRRP(1)|p.P250_I251insXXXXXXX(1)|p.R249_T256delRPILTIIT(1)|p.I251fs*94(1)|p.R249_P250>SS(1)|p.R249_P250delRP(1)|p.P250_I251insX(1)|p.P250fs*14(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GGTGAGGATGGGCCTCCGGTT	0.577000		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			40	15					0	0	0.011902	0	0
CCDC144C	348254	broad.mit.edu	37	17	20241534	20241534	+	RNA	SNP	G	C	C			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr17:20241534G>C	uc010cqy.1	+	4		c.872G>C				NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						GCGAAAATAAGCAGCCACAAG	0.353000													8	14					0	0	0.006214	0	0
SMARCA4	6597	broad.mit.edu	37	19	11132435	11132435	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr19:11132435A>G	uc002mqf.3	+	19	2935	c.2651A>G	c.(2650-2652)CAC>CGC	p.H884R	SMARCA4_uc010dxp.2_Missense_Mutation_p.H884R|SMARCA4_uc010dxo.2_Missense_Mutation_p.H884R|SMARCA4_uc002mqg.1_Missense_Mutation_p.H884R|SMARCA4_uc010dxq.2_Missense_Mutation_p.H884R|SMARCA4_uc010dxr.2_Missense_Mutation_p.H884R|SMARCA4_uc002mqj.3_Missense_Mutation_p.H884R|SMARCA4_uc010dxs.2_Missense_Mutation_p.H884R|SMARCA4_uc010dxt.1_Missense_Mutation_p.H104R|SMARCA4_uc002mqh.3_Missense_Mutation_p.H7R|SMARCA4_uc002mqi.1_Missense_Mutation_p.H87R	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	884	Helicase ATP-binding.|DEGH box.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GACGAAGGTCACCGCATGAAG	0.622000			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				10	21					0	0	0.010729	0	0
C19orf2	8725	broad.mit.edu	37	19	30503230	30503230	+	Missense_Mutation	SNP	G	A	A	rs140683632		TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr19:30503230G>A	uc002nsr.2	+	10	1247	c.1217G>A	c.(1216-1218)CGC>CAC	p.R406H	C19orf2_uc002nsq.2_Missense_Mutation_p.R388H|C19orf2_uc002nss.2_Missense_Mutation_p.R366H|C19orf2_uc002nst.2_Missense_Mutation_p.R330H	NM_003796	NP_003787	O94763	RMP_HUMAN	RPB5-mediating protein isoform a	406					protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)		TATGTCCCTCGCAAATCCATC	0.408000													51	167					0	0	0.014410	0	0
EPS8L1	54869	broad.mit.edu	37	19	55597452	55597452	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr19:55597452G>A	uc002qis.3	+	16	1646	c.1542G>A	c.(1540-1542)TGG>TGA	p.W514*	EPS8L1_uc010ess.1_Nonsense_Mutation_p.W528*|EPS8L1_uc010yfr.1_Nonsense_Mutation_p.W450*|EPS8L1_uc002qiu.2_Nonsense_Mutation_p.W387*|EPS8L1_uc002qiv.2_Nonsense_Mutation_p.W192*|EPS8L1_uc002qiw.2_Nonsense_Mutation_p.W293*	NM_133180	NP_573441	Q8TE68	ES8L1_HUMAN	epidermal growth factor receptor pathway	514	SH3.					cytoplasm					0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		GTCGTAAGTGGTGGAAGGTTC	0.622000													5	85					0	0	0.014758	0	0
SPTBN1	6711	broad.mit.edu	37	2	54880943	54880943	+	Silent	SNP	C	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:54880943C>G	uc002rxu.2	+	27	6024	c.5775C>G	c.(5773-5775)CTC>CTG	p.L1925L	SPTBN1_uc002rxx.2_Silent_p.L1912L|SPTBN1_uc002rxy.2_Silent_p.L70L	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	1925	Spectrin 16.|Interaction with ANK2.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			ACCTCATGCTCTGGATGGAGG	0.577000													14	22					0	0	0.016723	0	0
NEB	4703	broad.mit.edu	37	2	152474871	152474871	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:152474871C>T	uc010fnx.2	-	70	10456	c.10265G>A	c.(10264-10266)CGT>CAT	p.R3422H		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3422	Nebulin 93.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		CGTTTCTGGACGCTGACGGTA	0.443000													54	210					0	0	0.014410	0	0
UBR3	130507	broad.mit.edu	37	2	170917865	170917865	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:170917865A>G	uc010zdi.1	+	35	4931	c.4931A>G	c.(4930-4932)AAA>AGA	p.K1644R	UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_Missense_Mutation_p.K465R|UBR3_uc002uft.3_Missense_Mutation_p.K501R|UBR3_uc010zdj.1_Missense_Mutation_p.K335R|UBR3_uc002ufu.3_Missense_Mutation_p.K150R	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1644					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						TCCATGGAAAAATGCTTACAG	0.363000													109	176					0	0	0.014410	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr2:209113112C>T	uc002vcs.2	-	4	641	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.2_Missense_Mutation_p.R132H|IDH1_uc002vcu.2_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2023)|p.R132C(344)|p.R132?(210)|p.R132G(117)|p.R132S(79)|p.R132L(58)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma 								31	68					0	0	0.012213	0	0
DCLK3	85443	broad.mit.edu	37	3	36779426	36779426	+	Missense_Mutation	SNP	G	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr3:36779426G>T	uc003cgi.2	-	2	1216	c.725C>A	c.(724-726)GCC>GAC	p.A242D		NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	242						cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|breast(1)|skin(1)|ovary(1)|kidney(1)	9						GTCCTTCTTGGCCTTGGCTGC	0.562000													6	139					2.7689e-08	3.23038e-08	0.001984	1	0
BCL6	604	broad.mit.edu	37	3	187449545	187449545	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr3:187449545A>G	uc003frp.3	-	4	792	c.335T>C	c.(334-336)CTG>CCG	p.L112P	BCL6_uc011bsf.1_Missense_Mutation_p.L112P|BCL6_uc010hza.2_Missense_Mutation_p.L10P|BCL6_uc003frq.1_Missense_Mutation_p.L112P	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1	112					negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		CTCCATCTGCAGGTACATAGC	0.537000			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								20	51					0	0	0.012319	0	0
WDFY3	23001	broad.mit.edu	37	4	85600267	85600267	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr4:85600267C>T	uc003hpd.2	-	65	10360	c.9952G>A	c.(9952-9954)GCA>ACA	p.A3318T	WDFY3_uc003hpc.2_Missense_Mutation_p.A73T	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	3318						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GCGGCTGTTGCGCGGCAGGAG	0.582000													26	35					0	0	0.021523	0	0
RAPGEF2	9693	broad.mit.edu	37	4	160277114	160277114	+	Silent	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr4:160277114G>A	uc003iqg.3	+	23	4588	c.4278G>A	c.(4276-4278)CCG>CCA	p.P1426P		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	1426					cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GGAAACCGCCGGACTACAACG	0.612000													10	19					0	0	0.008291	0	0
TUBB4Q	56604	broad.mit.edu	37	4	190904306	190904306	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr4:190904306T>C	uc011clg.1	-	4	677	c.674A>G	c.(673-675)AAC>AGC	p.N225S		NM_020040	NP_064424	Q99867	TBB4Q_HUMAN	tubulin, beta polypeptide 4, member Q	226					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;4.1e-31)|Epithelial(3;1.44e-30)|OV - Ovarian serous cystadenocarcinoma(60;2.03e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00839)|READ - Rectum adenocarcinoma(43;0.155)		CACCAGGTGGTTCAGGTCACC	0.537000													3	62					0	0	0.004672	0	0
PRDM9	56979	broad.mit.edu	37	5	23526956	23526956	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr5:23526956C>T	uc003jgo.2	+	11	1941	c.1759C>T	c.(1759-1761)CGG>TGG	p.R587W		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	587	C2H2-type 4.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6						GGAGTGTGGGCGGGGCTTTAG	0.607000										HNSCC(3;0.000094)			34	62					0	0	0.014410	0	0
TNXB	7148	broad.mit.edu	37	6	32039776	32039776	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr6:32039776C>T	uc003nzl.2	-	13	5183	c.4981G>A	c.(4981-4983)GCA>ACA	p.A1661T		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1743					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						CCCGTCTTTGCCTCCACAGAG	0.592000													10	12					0	0	0.013537	0	0
CLVS2	134829	broad.mit.edu	37	6	123332253	123332253	+	Silent	SNP	A	G	G			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr6:123332253A>G	uc003pzi.1	+	3	1382	c.513A>G	c.(511-513)CAA>CAG	p.Q171Q		NM_001010852	NP_001010852	Q5SYC1	CLVS2_HUMAN	retinaldehyde binding protein 1-like 2	171	CRAL-TRIO.				lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						CTTTCAAGCAAGCCTCTAAAC	0.413000													4	86					0	0	0.009096	0	0
PLEKHA8	84725	broad.mit.edu	37	7	30092391	30092391	+	Silent	SNP	C	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr7:30092391C>T	uc003tam.1	+	7	796	c.705C>T	c.(703-705)ATC>ATT	p.I235I	PLEKHA8_uc003tao.2_Silent_p.I119I|PLEKHA8_uc003tap.1_Silent_p.I235I|PLEKHA8_uc003tan.2_Silent_p.I235I	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A	235					protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4						AGGAAGAAATCCTAATGAAAA	0.308000													21	106					0	0	0.010504	0	0
ZMIZ2	83637	broad.mit.edu	37	7	44805131	44805131	+	Missense_Mutation	SNP	C	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr7:44805131C>A	uc003tlr.2	+	16	2318	c.2195C>A	c.(2194-2196)CCC>CAC	p.P732H	ZMIZ2_uc003tlq.2_Missense_Mutation_p.P674H|ZMIZ2_uc003tls.2_Missense_Mutation_p.P706H|ZMIZ2_uc003tlt.2_Missense_Mutation_p.P355H|ZMIZ2_uc010kyj.2_Missense_Mutation_p.P254H|ZMIZ2_uc003tlu.2_5'Flank	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	732	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding			ovary(2)|large_intestine(2)|breast(1)	5						CCCTTTGCCCCCCTGCAGCCC	0.687000													28	11					6.38683e-12	7.63304e-12	0.008361	1	0
ABCB4	5244	broad.mit.edu	37	7	87046828	87046828	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr7:87046828T>C	uc003uiv.1	-	21	2558	c.2482A>G	c.(2482-2484)ACA>GCA	p.T828A	ABCB4_uc003uiw.1_Missense_Mutation_p.T828A|ABCB4_uc003uix.1_Missense_Mutation_p.T828A	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	828	ABC transmembrane type-1 2.|Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					CTGGTTCCTGTGGCCTGGGAG	0.428000													18	43					0	0	0.008871	0	0
CSMD3	114788	broad.mit.edu	37	8	113304784	113304784	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr8:113304784G>A	uc003ynu.2	-	55	8929	c.8770C>T	c.(8770-8772)CCT>TCT	p.P2924S	CSMD3_uc003yns.2_Missense_Mutation_p.P2126S|CSMD3_uc003ynt.2_Missense_Mutation_p.P2884S|CSMD3_uc011lhx.1_Missense_Mutation_p.P2755S	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2924	Extracellular (Potential).|Sushi 19.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ATAGGTGGAGGATGGCTCCAC	0.403000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			57	235					0	0	0.014410	0	0
FLJ43860	389690	broad.mit.edu	37	8	142488812	142488812	+	Silent	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr8:142488812G>A	uc003ywi.2	-	10	1230	c.1149C>T	c.(1147-1149)TAC>TAT	p.Y383Y	FLJ43860_uc011ljs.1_RNA|FLJ43860_uc010meu.1_RNA	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690	383							binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			CCACCTGGCCGTATGCCAGGA	0.642000													13	11					0	0	0.013537	0	0
DENND4C	55667	broad.mit.edu	37	9	19346705	19346705	+	Missense_Mutation	SNP	G	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr9:19346705G>T	uc003znq.2	+	18	3116	c.3083G>T	c.(3082-3084)GGC>GTC	p.G1028V	DENND4C_uc011lnc.1_Missense_Mutation_p.G358V|DENND4C_uc011lnd.1_Missense_Mutation_p.G316V|DENND4C_uc003znr.2_Missense_Mutation_p.G316V|DENND4C_uc003zns.2_Missense_Mutation_p.G210V|DENND4C_uc003znt.2_Missense_Mutation_p.G210V	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1028						integral to membrane				ovary(1)|skin(1)	2						AGAGAGTCTGGCATGACTACT	0.398000													4	84					0.000602214	0.000686244	0.014758	1	0
Unknown	0	broad.mit.edu	37	9	84676088	84676088	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr9:84676088C>T	uc010mpu.1	-	3	340	c.337G>A	c.(337-339)GAT>AAT	p.D113N		NM_001164339	NP_001157811			hypothetical protein LOC404770																		GAGGCCAGATCCTGAGGATGC	0.572000													11	268					0	0	0.010729	0	0
FAM123B	139285	broad.mit.edu	37	X	63411385	63411385	+	Silent	SNP	G	A	A			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chrX:63411385G>A	uc004dvo.2	-	2	2055	c.1782C>T	c.(1780-1782)CAC>CAT	p.H594H		NM_152424	NP_689637	Q5JTC6	F123B_HUMAN	family with sequence similarity 123B	594					Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane		p.0?(40)		kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1)	112						CCTCCCTGGCGTGGGCCTCCC	0.612000													3	38					0	0	0.004672	0	0
RGAG1	57529	broad.mit.edu	37	X	109694416	109694416	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chrX:109694416T>C	uc004eor.1	+	3	817	c.571T>C	c.(571-573)TCC>CCC	p.S191P	RGAG1_uc011msr.1_Missense_Mutation_p.S191P	NM_020769	NP_065820	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	191										lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4						TGAGGCAATGTCCACACCATT	0.483000													67	48					0	0	0.014410	0	0
SLTM	79811	broad.mit.edu	37	15	59182564	59182565	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr15:59182564_59182565delCT	uc002afp.2	-	15	2082_2083	c.1994_1995delAG	c.(1993-1995)GAGfs	p.E665fs	SLTM_uc002afn.2_Frame_Shift_Del_p.E207fs|SLTM_uc002afo.2_Frame_Shift_Del_p.E647fs|SLTM_uc002afq.2_Frame_Shift_Del_p.E234fs|SLTM_uc010bgd.2_Frame_Shift_Del_p.E234fs	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	665	Arg/Glu-rich.|Potential.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						TTTCTAGGCGCTCTCTCTCTCT	0.475													8	236	---	---	---	---					
CCDC64B	146439	broad.mit.edu	37	16	3078744	3078744	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr16:3078744delC	uc002ctf.3	-	7	1240	c.1195delG	c.(1195-1197)GCCfs	p.A399fs	CCDC64B_uc002cte.3_Frame_Shift_Del_p.A192fs	NM_001103175	NP_001096645	A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	399	Potential.										0						CTGTGCAGGGCCTCCCCAGGG	0.667													2	4	---	---	---	---					
TK2	7084	broad.mit.edu	37	16	66551051	66551053	+	In_Frame_Del	DEL	CTT	-	-			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr16:66551051_66551053delCTT	uc002eos.2	-	8	955_957	c.730_732delAAG	c.(730-732)AAGdel	p.K244del	TK2_uc010vip.1_In_Frame_Del_p.K105del|TK2_uc002eor.2_In_Frame_Del_p.K171del|TK2_uc010cdq.2_Intron|TK2_uc010cdr.2_In_Frame_Del_p.K153del|TK2_uc010viq.1_In_Frame_Del_p.K226del|TK2_uc010vir.1_In_Frame_Del_p.K219del	NM_004614	NP_004605	O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial	202					pyrimidine base metabolic process|pyrimidine nucleoside salvage	mitochondrial matrix	ATP binding|phosphotransferase activity, alcohol group as acceptor|thymidine kinase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)		GCGGAATGACCTTCTCCTCTTCC	0.512											OREG0032067	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	10	485	---	---	---	---					
KRT20	54474	broad.mit.edu	37	17	39034595	39034596	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-CS-5393-01A-01D-1468-08	TCGA-CS-5393-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	ddc229a3-8c45-4736-9cff-6495193c3c55	53327aaf-fa9c-44ed-8c21-1c557f76186e	g.chr17:39034595_39034596delAG	uc002hvl.2	-	6	982_983	c.940_941delCT	c.(940-942)CTAfs	p.L314fs		NM_019010	NP_061883	P35900	K1C20_HUMAN	keratin 20	314	Rod.|Coil 2.				apoptosis|intermediate filament organization	Golgi apparatus|intermediate filament	protein binding|structural constituent of cytoskeleton			large_intestine(1)|kidney(1)|skin(1)	3		Breast(137;0.000301)|Ovarian(249;0.15)				GGTCTCCTCTAGAGTGTGCTCC	0.460													30	86	---	---	---	---					
