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
MST1P9	11223	broad.mit.edu	37	1	17085609	17085609	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr1:17085609T>C	uc010ock.1	-	9	1112	c.1112A>G	c.(1111-1113)AAG>AGG	p.K371R	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						CTGGACACCCTTGCGGGTCTT	0.731000													5	24					0	0	0.038147	0	0
MAP3K6	9064	broad.mit.edu	37	1	27684232	27684232	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr1:27684232C>G	uc001bny.1	-	22	3300	c.3051G>C	c.(3049-3051)GAG>GAC	p.E1017D	MAP3K6_uc009vsw.1_Missense_Mutation_p.E1009D	NM_004672	NP_004663	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase	1017	Potential.				activation of JUN kinase activity		ATP binding|magnesium ion binding|MAP kinase kinase kinase activity			breast(4)|lung(3)|ovary(1)|central_nervous_system(1)	9		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GGTGCAGATTCTCCGCCAGCG	0.667000											OREG0013282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	15					0	0	0.021553	0	0
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	G	G	rs146714035	by1000genomes	TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr1:145367739A>G	uc001end.3	+	85	10595	c.10560A>G	c.(10558-10560)AAA>AAG	p.K3520K	NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	3445											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.244000													5	77					0	0	0.014758	0	0
CGN	57530	broad.mit.edu	37	1	151508792	151508792	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr1:151508792C>T	uc009wmw.2	+	19	3421	c.3277C>T	c.(3277-3279)CGG>TGG	p.R1093W	CGN_uc010pde.1_Missense_Mutation_p.R87W	NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin	1087	Potential.					myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			TGAAGACGAGCGGCAGCATGT	0.473000													29	35					0	0	0.034045	0	0
PDZRN4	29951	broad.mit.edu	37	12	41582515	41582515	+	5'Flank	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr12:41582515C>T	uc010skn.1	+							NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ACCGCGCCCGCGGCTGCGGCC	0.741000													5	4					0	0	0.029380	0	0
UNG	7374	broad.mit.edu	37	12	109537062	109537062	+	Silent	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr12:109537062C>T	uc001tnz.1	+	3	478	c.408C>T	c.(406-408)ACC>ACT	p.T136T	UNG_uc001toa.1_Silent_p.T127T	NM_080911	NP_550433	P13051	UNG_HUMAN	uracil-DNA glycosylase isoform UNG2	136					base-excision repair|interspecies interaction between organisms	mitochondrion|nucleus	protein binding|uracil DNA N-glycosylase activity			lung(1)|central_nervous_system(1)	2						AAGTCTTCACCTGGACCCAGA	0.358000								BER_DNA_glycosylases	Immune_Deficiency_with_Hyper-IgM				33	42					0	0	0.080422	0	0
Unknown	0	broad.mit.edu	37	16	31973444	31973444	+	RNA	SNP	C	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr16:31973444C>A	uc002ect.2	+	1		c.36C>A								Homo sapiens IGH mRNA for immunoglobulin heavy chain VHDJ region, partial cds, clone:H186.																		GAGGCTTGGTCCAGCCTGGGG	0.577000													4	87					2.56e-06	2.88e-06	0.009096	1	0
CDK5RAP3	80279	broad.mit.edu	37	17	46054123	46054123	+	Missense_Mutation	SNP	G	A	A	rs34460325		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr17:46054123G>A	uc002imr.2	+	9	928	c.844G>A	c.(844-846)GAC>AAC	p.D282N	CDK5RAP3_uc010wlc.1_Missense_Mutation_p.D302N|CDK5RAP3_uc002imq.1_Missense_Mutation_p.D57N|CDK5RAP3_uc002imu.2_Missense_Mutation_p.D126N|CDK5RAP3_uc002ims.2_Missense_Mutation_p.D195N|CDK5RAP3_uc002imv.2_Missense_Mutation_p.D126N|CDK5RAP3_uc002imw.2_Missense_Mutation_p.D126N|CDK5RAP3_uc002imx.2_Missense_Mutation_p.D57N	NM_176096	NP_788276	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	282					brain development|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation		neuronal Cdc2-like kinase binding				0						TGAGGGGACTGACTCTGGCAT	0.502000													24	44					0	0	0.091800	0	0
LIMD2	80774	broad.mit.edu	37	17	61776286	61776286	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr17:61776286G>A	uc002jbj.3	-	4	275	c.97C>T	c.(97-99)CGG>TGG	p.R33W	LIMD2_uc002jbk.3_Missense_Mutation_p.A34V|LIMD2_uc002jbl.3_Missense_Mutation_p.R33W	NM_030576	NP_085053	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	33							zinc ion binding				0						ACCTGGGCCCGCAGGCTGAAG	0.662000													4	99					0	0	0.009096	0	0
LRFN1	57622	broad.mit.edu	37	19	39805231	39805231	+	Missense_Mutation	SNP	A	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr19:39805231A>C	uc002okw.2	-	1	746	c.746T>G	c.(745-747)TTC>TGC	p.F249C		NM_020862	NP_065913	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III	249	Extracellular (Potential).					cell junction|integral to membrane|postsynaptic density|postsynaptic membrane				ovary(2)	2	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GTTGCCGCCGAAGCTGACGGT	0.692000													10	22					0	0	0.093190	0	0
ZNF404	342908	broad.mit.edu	37	19	44378036	44378036	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr19:44378036C>T	uc002oxs.3	-	2	330	c.321G>A	c.(319-321)ATG>ATA	p.M107I		NM_001033719	NP_001028891	Q494X3	ZN404_HUMAN	zinc finger protein 404	110					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				TTTTGAATATCATTTGACTAA	0.328000													23	186					0	0	0.048971	0	0
SNTG2	54221	broad.mit.edu	37	2	1271203	1271203	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr2:1271203G>A	uc002qwq.2	+	14	1272	c.1144G>A	c.(1144-1146)GAG>AAG	p.E382K	SNTG2_uc010ewi.2_Missense_Mutation_p.E255K	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	382	PH.				central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		TTTTGACTTTGAGGACCAGAG	0.522000													5	16					0	0	0.014758	0	0
HPCAL1	3241	broad.mit.edu	37	2	10566867	10566867	+	Missense_Mutation	SNP	G	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr2:10566867G>C	uc002raj.2	+	5	876	c.502G>C	c.(502-504)GAA>CAA	p.E168Q	HPCAL1_uc002rak.2_Missense_Mutation_p.E168Q|HPCAL1_uc002ral.2_Missense_Mutation_p.E168Q|HPCAL1_uc010exe.2_RNA|HPCAL1_uc010exf.2_Missense_Mutation_p.E168Q	NM_002149	NP_002140	P37235	HPCL1_HUMAN	hippocalcin-like 1	168	EF-hand 4.|3 (Potential).						calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)		GTCCTTGGAAGAATTCATCAG	0.582000													77	111					0	0	0.048971	0	0
FLJ40330	645784	broad.mit.edu	37	2	89084134	89084134	+	RNA	SNP	A	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr2:89084134A>G	uc010fhf.2	+	5		c.490A>G			FLJ40330_uc010fhg.2_RNA|FLJ40330_uc010fhh.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						AGAAACAACCAGCTGAGAAGG	0.299000													3	40					0	0	0.009096	0	0
GLI2	2736	broad.mit.edu	37	2	121744182	121744182	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr2:121744182C>T	uc010flp.2	+	12	2315	c.2285C>T	c.(2284-2286)CCG>CTG	p.P762L	GLI2_uc002tmq.1_Missense_Mutation_p.P434L|GLI2_uc002tmr.1_Missense_Mutation_p.P417L|GLI2_uc002tmt.3_Missense_Mutation_p.P434L|GLI2_uc002tmu.3_Missense_Mutation_p.P417L|GLI2_uc002tmw.1_Missense_Mutation_p.P745L	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	762					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				CCTCCCCTCCCGGGAAGTGGT	0.597000													32	33					0	0	0.050027	0	0
CEP250	11190	broad.mit.edu	37	20	34054842	34054842	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr20:34054842C>T	uc002xcm.2	+	9	1215	c.544C>T	c.(544-546)CGG>TGG	p.R182W	CEP250_uc010zve.1_5'UTR|CEP250_uc010gfe.1_RNA|CEP250_uc010zvd.1_RNA|CEP250_uc002xco.2_5'UTR	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	182					centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CAGTCTATGGCGGGAGGTTGT	0.532000													30	46					0	0	0.059317	0	0
ZNF334	55713	broad.mit.edu	37	20	45130587	45130587	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr20:45130587T>C	uc002xsc.2	-	5	1575	c.1391A>G	c.(1390-1392)AAT>AGT	p.N464S	ZNF334_uc002xsa.2_Missense_Mutation_p.N487S|ZNF334_uc002xsb.2_Missense_Mutation_p.N426S|ZNF334_uc002xsd.2_Missense_Mutation_p.N426S|ZNF334_uc010ghl.2_Missense_Mutation_p.N463S	NM_018102	NP_060572	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334 isoform a	464	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)				CCCACATTCATTACATTCATA	0.363000													66	68					0	0	0.048971	0	0
COL18A1	80781	broad.mit.edu	37	21	46888159	46888159	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr21:46888159G>A	uc011afs.1	+	2	1376	c.1355G>A	c.(1354-1356)CGC>CAC	p.R452H	COL18A1_uc002zhg.2_Missense_Mutation_p.R37H|COL18A1_uc002zhi.2_Missense_Mutation_p.R217H	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	452					cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TTTGCAGAGCGCATCAGCGAG	0.667000													3	37					0	0	0.009096	0	0
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587000													3	25					0	0	0.004672	0	0
SGSM1	129049	broad.mit.edu	37	22	25320198	25320198	+	Missense_Mutation	SNP	G	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr22:25320198G>A	uc003abg.2	+	26	3561	c.3404G>A	c.(3403-3405)CGG>CAG	p.R1135Q	SGSM1_uc003abh.2_Missense_Mutation_p.R1074Q|SGSM1_uc010guu.1_Missense_Mutation_p.R1080Q|SGSM1_uc003abj.2_Missense_Mutation_p.R1019Q|SGSM1_uc003abi.1_Missense_Mutation_p.R1055Q	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	1135						Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5						AAGCTGGCGCGGGACCTCGTG	0.562000													10	24					0	0	0.080935	0	0
ROBO1	6091	broad.mit.edu	37	3	78987932	78987932	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr3:78987932C>G	uc003dqe.2	-	4	526	c.318G>C	c.(316-318)GAG>GAC	p.E106D	ROBO1_uc003dqb.2_Missense_Mutation_p.E67D|ROBO1_uc003dqc.2_Missense_Mutation_p.E67D|ROBO1_uc003dqd.2_Missense_Mutation_p.E67D	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	106	Extracellular (Potential).|Ig-like C2-type 1.				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TCTCCACTCTCTCTCCCCCTT	0.478000													36	2					0	0	0.074837	0	0
MRPL3	11222	broad.mit.edu	37	3	131220486	131220486	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr3:131220486C>G	uc003eoh.2	-	2	330	c.166G>C	c.(166-168)GAA>CAA	p.E56Q	MRPL3_uc011blo.1_5'UTR|MRPL3_uc011blp.1_Missense_Mutation_p.E83Q	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	56					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						GGGACATTTTCTTCAGAAAGA	0.378000													110	135					0	0	0.048971	0	0
WDR49	151790	broad.mit.edu	37	3	167196719	167196719	+	Missense_Mutation	SNP	C	A	A			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr3:167196719C>A	uc003fev.1	-	15	2347	c.2041G>T	c.(2041-2043)GCC>TCC	p.A681S	WDR49_uc003feu.1_Missense_Mutation_p.A506S|WDR49_uc011bpd.1_Missense_Mutation_p.A646S|WDR49_uc003few.1_3'UTR	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	681										large_intestine(1)|ovary(1)|skin(1)	3						AATTGCTTGGCTTTTCGTTCA	0.313000													15	12					1.3612e-06	1.56394e-06	0.024245	1	0
WDR17	116966	broad.mit.edu	37	4	177046324	177046324	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr4:177046324C>T	uc003iuj.2	+	6	836	c.680C>T	c.(679-681)ACG>ATG	p.T227M	WDR17_uc003iuk.2_Missense_Mutation_p.T203M|WDR17_uc003ium.3_Missense_Mutation_p.T203M|WDR17_uc003iul.1_Intron	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1	227	WD 4.									ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GATCCAGTTACGGCCTTGGAA	0.363000													41	2					0	0	0.092188	0	0
HSD17B4	3295	broad.mit.edu	37	5	118814681	118814681	+	Missense_Mutation	SNP	C	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr5:118814681C>G	uc003ksj.2	+	8	710	c.587C>G	c.(586-588)GCG>GGG	p.A196G	HSD17B4_uc011cwg.1_Missense_Mutation_p.A172G|HSD17B4_uc011cwh.1_Missense_Mutation_p.A178G|HSD17B4_uc011cwi.1_Missense_Mutation_p.A221G|HSD17B4_uc003ksk.3_Missense_Mutation_p.A49G|HSD17B4_uc011cwj.1_Missense_Mutation_p.A49G|HSD17B4_uc010jcn.1_5'UTR	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	196	NAD.|(3R)-hydroxyacyl-CoA dehydrogenase.				bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)	GCTCCTAATGCGGGATCACGG	0.408000													5	76					0	0	0.029380	0	0
TRA2A	29896	broad.mit.edu	37	7	23552514	23552514	+	Missense_Mutation	SNP	T	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr7:23552514T>C	uc003swi.2	-	4	738	c.524A>G	c.(523-525)GAG>GGG	p.E175G	TRA2A_uc011jzb.1_RNA|TRA2A_uc011jzc.1_Missense_Mutation_p.E74G|TRA2A_uc011jzd.1_Missense_Mutation_p.E74G|TRA2A_uc010kuo.1_RNA	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha	175	RRM.				nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						CAAATTTACCTCCTTTGAGTC	0.333000													42	21					0	0	0.042209	0	0
C7orf25	79020	broad.mit.edu	37	7	42949705	42949705	+	Silent	SNP	T	C	C			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr7:42949705T>C	uc003thw.2	-	2	1259	c.795A>G	c.(793-795)GGA>GGG	p.G265G	C7orf25_uc010kxq.2_Silent_p.G265G|C7orf25_uc003thx.3_Silent_p.G323G|C7orf25_uc010kxr.2_Silent_p.G323G	NM_024054	NP_076959	Q9BPX7	CG025_HUMAN	hypothetical protein LOC79020 b	265										skin(1)	1						AGTGGCAGCCTCCATAGCTGA	0.428000													3	173					0	0	0.004672	0	0
ZFHX4	79776	broad.mit.edu	37	8	77766275	77766275	+	Missense_Mutation	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr8:77766275C>T	uc003yav.2	+	10	7370	c.6983C>T	c.(6982-6984)GCT>GTT	p.A2328V	ZFHX4_uc003yau.1_Missense_Mutation_p.A2373V|ZFHX4_uc003yaw.1_Missense_Mutation_p.A2328V	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2328						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACGGATGCAGCTAAAAACGCT	0.512000										HNSCC(33;0.089)			49	56					0	0	0.048971	0	0
ATRX	546	broad.mit.edu	37	X	76814318	76814318	+	Splice_Site	SNP	C	T	T			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chrX:76814318C>T	uc004ecp.3	-	29	6559	c.6327_splice	c.e29-1	p.R2109_splice	ATRX_uc004ecq.3_Splice_Site_p.R2071_splice|ATRX_uc004eco.3_Splice_Site_p.R1894_splice	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TAATCGTCCTCTGAAAATGAA	0.274000			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						22	11					0	0	0.069288	0	0
TAF7L	54457	broad.mit.edu	37	X	100538563	100538563	+	Missense_Mutation	SNP	G	A	A	rs145455495		TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chrX:100538563G>A	uc004ehb.2	-	4	424	c.412C>T	c.(412-414)CGC>TGC	p.R138C	TAF7L_uc004eha.2_Missense_Mutation_p.R52C|TAF7L_uc004ehc.1_Missense_Mutation_p.R52C	NM_024885	NP_079161	Q5H9L4	TAF7L_HUMAN	TATA box binding protein-associated factor, RNA	138					cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription initiation from RNA polymerase II promoter	cytoplasm|transcription factor TFIID complex	binding			breast(1)	1						ACTGCATGGCGCCCATCAGCT	0.398000													115	128					0	0	0.048971	0	0
Unknown	0	broad.mit.edu	37	15	56038833	56038833	+	IGR	DEL	G	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr15:56038833delG								PRTG (3656 upstream) : NEDD4 (80298 downstream)																							aaaaaaaaaagaaGCTCCTGG	0.279													3	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	16	32176904	32176904	+	IGR	DEL	G	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr16:32176904delG								HERC2P4 (13030 upstream) : TP53TG3B (507937 downstream)																							AAAAAAAAAAGAAATCAAAGC	0.284													2	4	---	---	---	---					
LOC651250	651250	broad.mit.edu	37	17	66122028	66122029	+	RNA	DEL	AA	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr17:66122028_66122029delAA	uc002jgq.2	+	6		c.1151_1152delAA			LOC651250_uc002kit.2_RNA|LOC651250_uc002jgo.1_Intron	NR_027418				Homo sapiens cDNA FLJ33831 fis, clone CTONG2003937.												0						TTCGTGAGCTaaaaaaaaaaaa	0.267													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	64602903	64602905	+	IGR	DEL	CAC	-	-			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr2:64602903_64602905delCAC								PELI1 (231298 upstream) : HSPC159 (78422 downstream)																							ccaccaccatcaccaccatcacc	0.000													4	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	29769921	29769922	+	IGR	INS	-	G	G			TCGA-C5-A0TN-01A-21D-A14W-08	TCGA-C5-A0TN-10B-01D-A14W-08									Somatic	Phase_I	Capture				Illumina GAIIx	1a006bbb-6b95-4d82-8d1f-1b416a803c06	7a14d340-4758-457c-8fb0-6239640621b8	g.chr6:29769921_29769922insG								HCG4 (9071 upstream) : HLA-G (24834 downstream)																							TAGGATCTCATGCCCTGCCTCC	0.510													6	4	---	---	---	---					
