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
CCBP2	1238	broad.mit.edu	37	3	42906480	42906480	+	Silent	SNP	G	G	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr3:42906480G>T	uc003cme.3	+	2	664	c.486G>T	c.(484-486)ctG>ctT	p.L162L	CCBP2_uc003cmf.3_Silent_p.L162L|CCBP2_uc003cmg.3_Intron|CCBP2_uc021wwm.1_Silent_p.L162L	NM_001296	NP_001287	O00590	CCBP2_HUMAN	Homo sapiens chemokine binding protein 2 (CCBP2), mRNA.	162					chemotaxis|immune response|multicellular organismal development	integral to plasma membrane	C-X-C chemokine receptor activity			NS(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(10)|skin(2)|urinary_tract(1)	26				KIRC - Kidney renal clear cell carcinoma(284;0.241)		CCAAGAGCCTGCTCCTTGCTA	0.537000													30	73					0	0	1	0	0
CLTCL1	8218	broad.mit.edu	37	22	19222058	19222058	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr22:19222058C>T	uc021wle.1	-	6	1216	c.1141G>A	c.(1141-1143)Gcc>Acc	p.A381T	CLTCL1_uc021wld.1_Missense_Mutation_p.A381T|CLTCL1_uc021wlc.1_Missense_Mutation_p.A381T|CLTCL1_uc021wlf.1_Missense_Mutation_p.A381T|CLTCL1_uc011agw.1_Missense_Mutation_p.A381T	NM_007098	NP_009029	P53675	CLH2_HUMAN	Homo sapiens clathrin, heavy chain-like 1 (CLTCL1), transcript variant 1, mRNA.	381	Globular terminal domain.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GCAACTTTGGCGGCTTCAGCA	0.453000			T	?	ALCL								3	31					0	0	1	0	0
GPR179	440435	broad.mit.edu	37	17	36486995	36486995	+	Silent	SNP	G	G	A			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr17:36486995G>A	uc002hpz.3	-	10	2478	c.2457C>T	c.(2455-2457)agC>agT	p.S819S		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	Homo sapiens G protein-coupled receptor 179 (GPR179), mRNA.	819						integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GGTTGTGGGCGCTGGCTGACC	0.652000													5	5					0	0	1	0	0
TDO2	6999	broad.mit.edu	37	4	156825198	156825198	+	Missense_Mutation	SNP	G	G	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr4:156825198G>T	uc003ipf.1	+	1	128	c.64G>T	c.(64-66)Ggc>Tgc	p.G22C		NM_005651	NP_005642	P48775	T23O_HUMAN	Homo sapiens tryptophan 2,3-dioxygenase (TDO2), mRNA.	22					tryptophan catabolic process to kynurenine	cytosol	tryptophan 2,3-dioxygenase activity			breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)	L-Tryptophan(DB00150)	CCCCGTAGAAGGCAGCGAAGA	0.388000													20	36					0	0	1	0	0
GJD2	57369	broad.mit.edu	37	15	35045227	35045227	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr15:35045227G>A	uc001zis.1	-	1	418	c.418C>T	c.(418-420)Cga>Tga	p.R140*	AK092087_uc001zit.1_5'Flank	NM_020660	NP_065711	Q9UKL4	CXD2_HUMAN	Homo sapiens gap junction protein, delta 2, 36kDa (GJD2), mRNA.	140					synaptic transmission	connexon complex|integral to membrane	gap junction channel activity			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTATCTTCTCGTTTGCCCCCA	0.532000													40	132					0	0	1	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	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				26	43					0	0	1	0	0
CDH9	1007	broad.mit.edu	37	5	26903745	26903745	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr5:26903745C>T	uc010iug.3	-	5	1169	c.1000G>A	c.(1000-1002)Gtt>Att	p.V334I	CDH9_uc003jgs.1_Splice_Site_p.Q333_splice	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	Homo sapiens cadherin 9, type 2 (T1-cadherin) (CDH9), mRNA.	0	Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TGAAAAGAAACCTGTTTGACA	0.383000													7	183					0	0	1	0	0
ATR	545	broad.mit.edu	37	3	142266707	142266707	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr3:142266707G>A	uc003eux.4	-	15	3339	c.3217C>T	c.(3217-3219)Caa>Taa	p.Q1073*		NM_001184	NP_001175	Q13535	ATR_HUMAN	Homo sapiens ataxia telangiectasia and Rad3 related (ATR), mRNA.	1073					DNA damage checkpoint|DNA repair|DNA replication|cell cycle|cellular response to UV|cellular response to gamma radiation|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TGCAATCCTTGGAAATCTTGT	0.348000								Other conserved DNA damage response genes					16	32					0	0	1	0	0
CEP164	22897	broad.mit.edu	37	11	117280645	117280645	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr11:117280645G>A	uc001prc.3	+	29	4207	c.4060G>A	c.(4060-4062)Gac>Aac	p.D1354N	CEP164_uc001prb.3_Missense_Mutation_p.D1349N|CEP164_uc001prf.3_Non-coding_Transcript|CEP164_uc009yzp.1_Non-coding_Transcript|CEP164_uc001prg.1_Missense_Mutation_p.D779N	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	Homo sapiens centrosomal protein 164kDa (CEP164), mRNA.	1354					DNA repair|G2/M transition of mitotic cell cycle|cell division|mitosis	centriole|cytosol|nucleus				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		AACGGTGGACGACTTCCTGTT	0.587000													25	61					0	0	1	0	0
CD74	972	broad.mit.edu	37	5	149784320	149784321	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr5:149784320_149784321delCT	uc003lsc.3	-	5	734_735	c.547_548delAG	c.(547-549)agcfs	p.S183fs	CD74_uc003lsd.3_Frame_Shift_Del_p.S183fs|CD74_uc003lse.3_Intron	NM_001025159	NP_001020330	P04233	HG2A_HUMAN	Homo sapiens CD74 molecule, major histocompatibility complex, class II invariant chain (CD74), transcript variant 1, mRNA.	183					antigen processing and presentation of endogenous antigen|cell proliferation|immunoglobulin mediated immune response|intracellular protein transport|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of apoptosis|negative regulation of peptide secretion|positive regulation of B cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of chemokine (C-X-C motif) ligand 2 production|positive regulation of cytokine-mediated signaling pathway|positive regulation of fibroblast proliferation|positive regulation of macrophage cytokine production|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|prostaglandin biosynthetic process|protein complex assembly|regulation of macrophage activation	Golgi apparatus|endoplasmic reticulum membrane|integral to membrane|lysosome|receptor complex	MHC class II protein binding|beta-amyloid binding|cytokine receptor activity|identical protein binding			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTGCATCCAGCTCTCAAAGACC	0.559			T	ROS1	NSCLC								2	4	---	---	---	---					
CPD	1362	broad.mit.edu	37	17	28706683	28706683	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DJ-A4V2-01A-11D-A257-08	TCGA-DJ-A4V2-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c5ac429-f523-4c6c-b4d6-0de91d50a945	47627937-0a98-41cf-ac54-096a2900b4ae	g.chr17:28706683delC	uc002hfb.2	+	0	742	c.685delC	c.(685-687)cccfs	p.P229fs	CPD_uc010wbo.2_5'Flank|CPD_uc010wbp.2_5'Flank	NM_001304	NP_001295	O75976	CBPD_HUMAN	Homo sapiens carboxypeptidase D (CPD), transcript variant 1, mRNA.	229	Carboxypeptidase-like 1.				proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(13)|skin(5)|stomach(1)|urinary_tract(1)	36						CACCGGCGAACCCCCCGCCCT	0.701													3	5	---	---	---	---