Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
AK300387	0	broad.mit.edu	37	16	32192662	32192662	+	RNA	SNP	G	G	A			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr16:32192662G>A	uc010vfv.1	-	4		c.684C>T								Homo sapiens cDNA FLJ60890 complete cds, moderately similar to HECT domain and RCC1-like domain-containing protein 2.																		TGGCCTTTTGGTGCCTGGCGT	0.547000													5	28					0	0	1	0	0
BCKDK	10295	broad.mit.edu	37	16	31122082	31122082	+	Splice_Site	SNP	G	G	T			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr16:31122082G>T	uc002eaw.4	+	8	1032	c.716_splice	c.e8+1	p.R239_splice	BCKDK_uc002eav.4_Splice_Site_p.R239_splice|BCKDK_uc010cai.3_Splice_Site_p.R239_splice	NM_005881	NP_005872	O14874	BCKD_HUMAN	Homo sapiens branched chain ketoacid dehydrogenase kinase (BCKDK), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	239	Histidine kinase.				branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation	mitochondrial alpha-ketoglutarate dehydrogenase complex	ATP binding|[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|protein binding|protein serine/threonine kinase activity|two-component sensor activity			breast(1)|stomach(1)	2						GACTTTGCCAGGTGAGGCAAG	0.577000													40	57					0	0	1	0	0
HMCN1	83872	broad.mit.edu	37	1	186052052	186052052	+	Missense_Mutation	SNP	C	C	A			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr1:186052052C>A	uc001grq.1	+	56	9072	c.8843C>A	c.(8842-8844)aCa>aAa	p.T2948K	MIR548F1_uc021pgf.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	Homo sapiens hemicentin 1 (HMCN1), mRNA.	2948	Ig-like C2-type 27.				response to stimulus|visual perception	basement membrane	calcium ion binding			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCTGAGAACACAGCTGGGAGT	0.353000													9	20					0	0	1	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr7:140453136A>T	uc003vwc.4	-	14	1860	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	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(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_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				25	45					0	0	1	0	0
SETD5	55209	broad.mit.edu	37	3	9482327	9482327	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr3:9482327C>T	uc003brt.3	+	7	1190	c.755C>T	c.(754-756)aCt>aTt	p.T252I	SETD5_uc003brs.1_Missense_Mutation_p.T233I|SETD5_uc003bru.3_Missense_Mutation_p.T154I|SETD5_uc003brv.3_Missense_Mutation_p.T141I|SETD5_uc010hck.3_5'Flank|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.3_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	Homo sapiens SET domain containing 5 (SETD5), mRNA.	252								p.I252I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		ATTTTAGACACTATTAATAAG	0.393000													5	13					0	0	1	0	0
SSX1	6756	broad.mit.edu	37	X	48118021	48118021	+	Missense_Mutation	SNP	T	T	A			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chrX:48118021T>A	uc004djb.1	+	3	326	c.235T>A	c.(235-237)Ttc>Atc	p.F79I		NM_005635	NP_005626	Q16384	SSX1_HUMAN	Homo sapiens synovial sarcoma, X breakpoint 1 (SSX1), mRNA.	79	KRAB-related.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription corepressor activity		SS18/SSX1(1169)|SS18L1/SSX1(2)	endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9						GGCCACAGACTTCCAGGGGAA	0.453000			T	SS18	synovial sarcoma								62	94					0	0	1	0	0
LRRC33	375387	broad.mit.edu	37	3	196387348	196387348	+	Silent	SNP	G	G	C			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr3:196387348G>C	uc003fwv.3	+	2	938	c.834G>C	c.(832-834)ctG>ctC	p.L278L		NM_198565	NP_940967	Q86YC3	LRC33_HUMAN	Homo sapiens leucine rich repeat containing 33 (LRRC33), mRNA.	278						integral to membrane				NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(17)|ovary(3)|prostate(3)	40	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.9e-23)|all cancers(36;1.76e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		GGACCCTCCTGCTGCGCGACA	0.627000													34	92					0	0	1	0	0
GPC6	10082	broad.mit.edu	37	13	94482634	94482634	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr13:94482634A>C	uc001vlt.3	+	2	1179	c.547A>C	c.(547-549)Agt>Cgt	p.S183R	GPC6_uc010tig.1_Missense_Mutation_p.S183R|GPC6_uc001vlu.1_Missense_Mutation_p.S113R	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	Homo sapiens glypican 6 (GPC6), mRNA.	183						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GTATCACTTCAGTGAAGACTA	0.493000													6	45					0	0	1	0	0
LCE1C	353133	broad.mit.edu	37	1	152777911	152777911	+	Missense_Mutation	SNP	T	T	A			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr1:152777911T>A	uc001fap.1	-	1	95	c.44A>T	c.(43-45)aAg>aTg	p.K15M	LCE1C_uc021ozi.1_Missense_Mutation_p.K15M	NM_178351	NP_848128	Q5T751	LCE1C_HUMAN	Homo sapiens late cornified envelope 1C (LCE1C), mRNA.	15	Pro-rich.				keratinization					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gggggtgcacttgggagggGG	0.607000													9	20					0	0	1	0	0
ARCN1	372	broad.mit.edu	37	11	118455289	118455289	+	Missense_Mutation	SNP	A	A	G			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr11:118455289A>G	uc009zag.3	+	5	1073	c.871A>G	c.(871-873)Atg>Gtg	p.M291V	ARCN1_uc001ptq.3_Missense_Mutation_p.M250V|ARCN1_uc010ryg.2_Missense_Mutation_p.M162V	NM_001142281	NP_001135753	P48444	COPD_HUMAN	Homo sapiens archain 1 (ARCN1), transcript variant 2, mRNA.	250	MHD.				COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|clathrin adaptor complex|cytosol				endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		TGAAACCATCATGTCCTCTAG	0.413000													25	40					0	0	1	0	0
NELL2	4753	broad.mit.edu	37	12	45269298	45269298	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EL-A4K0-01A-11D-A257-08	TCGA-EL-A4K0-11A-11D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220d117b-cc76-4c53-8f51-5eee3409a703	939a3085-5656-44fb-a757-67e40ab49b32	g.chr12:45269298delA	uc001rof.3	-	0	147	c.44delT	c.(43-45)ctgfs	p.L15fs	NELL2_uc001rog.2_Intron|NELL2_uc001roh.2_Intron|NELL2_uc009zkd.2_Frame_Shift_Del_p.L15fs|NELL2_uc010skz.1_Intron|NELL2_uc010sla.1_Intron|NELL2_uc001roi.1_Intron|NELL2_uc010slb.1_Frame_Shift_Del_p.L15fs|NELL2_uc001roj.2_Intron	NM_001145109	NP_001138581	Q99435	NELL2_HUMAN	Homo sapiens NEL-like 2 (chicken) (NELL2), transcript variant 4, mRNA.	0					cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		ACCTGAGATCAGCAGCCAAGC	0.557													6	13	---	---	---	---