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
NPAS2	4862	broad.mit.edu	37	2	101598737	101598737	+	Silent	SNP	A	A	G			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr2:101598737A>G	uc010yvt.1	+	15	1724	c.1722A>G	c.(1720-1722)ctA>ctG	p.L574L	NPAS2_uc002tap.1_Silent_p.L509L|NPAS2_uc010fit.1_Silent_p.L87L	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	Homo sapiens neuronal PAS domain protein 2 (NPAS2), mRNA.	509					central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	p.A573A(1)		cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AAGACCAGCTAGAGCAGCGGA	0.527000													4	55					0	0	1	0	0
EXPH5	23086	broad.mit.edu	37	11	108384325	108384325	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr11:108384325C>T	uc001pkk.3	-	5	2020	c.1909G>A	c.(1909-1911)Gac>Aac	p.D637N	EXPH5_uc010rvz.2_Missense_Mutation_p.D481N|EXPH5_uc010rvy.2_Missense_Mutation_p.D449N	NM_015065	NP_055880	Q149M6	Q149M6_HUMAN	Homo sapiens exophilin 5 (EXPH5), mRNA.	637					intracellular protein transport		Rab GTPase binding			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TTCCTTCTGTCATCAGAAATC	0.408000													10	91					0	0	1	0	0
CDH12	1010	broad.mit.edu	37	5	22078769	22078769	+	Missense_Mutation	SNP	C	C	G			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr5:22078769C>G	uc010iuc.2	-	1	475	c.17G>C	c.(16-18)tGt>tCt	p.C6S	CDH12_uc011cno.1_Missense_Mutation_p.C6S|CDH12_uc003jgk.2_Missense_Mutation_p.C6S	NM_004061	NP_004052	P55289	CAD12_HUMAN	Homo sapiens cadherin 12, type 2 (N-cadherin 2) (CDH12), mRNA.	6					adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						CAGGGATAAACAGTTCCTTGT	0.448000										HNSCC(59;0.17)			29	55					0	0	1	0	0
LPL	4023	broad.mit.edu	37	8	19811648	19811648	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr8:19811648C>T	uc003wzk.4	+	4	929	c.559C>T	c.(559-561)Cct>Tct	p.P187S		NM_000237	NP_000228	P06858	LIPL_HUMAN	Homo sapiens lipoprotein lipase (LPL), mRNA.	187					fatty acid biosynthetic process|lipoprotein metabolic process|phospholipid metabolic process|positive regulation of cholesterol storage|positive regulation of sequestering of triglyceride|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	anchored to membrane|chylomicron|plasma membrane|very-low-density lipoprotein particle	heparin binding|lipoprotein lipase activity|phospholipase activity|receptor binding|triglyceride lipase activity			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	Clofibrate(DB00636)|Gemfibrozil(DB01241)|Orlistat(DB01083)	TCCAGCTGGACCTAACTTTGA	0.453000													27	50					0	0	1	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	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				14	40					0	0	1	0	0
MAST2	23139	broad.mit.edu	37	1	46501483	46501483	+	Silent	SNP	C	C	T			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr1:46501483C>T	uc001cov.3	+	28	5425	c.5142C>T	c.(5140-5142)gcC>gcT	p.A1714A	MAST2_uc001cow.3_Silent_p.A1713A|MAST2_uc001cpa.3_Non-coding_Transcript	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	Homo sapiens microtubule associated serine/threonine kinase 2 (MAST2), mRNA.	1714					regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCAGACTGGCCCATCCATCTT	0.577000													4	85					0	0	1	0	0
CEACAM5	1048	broad.mit.edu	37	19	42213808	42213808	+	Missense_Mutation	SNP	G	G	C			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr19:42213808G>C	uc002orl.3	+	1	395	c.274G>C	c.(274-276)Ggg>Cgg	p.G92R	CEACAM5_uc010ehz.1_Missense_Mutation_p.G92R|CEACAM5_uc002orj.1_Missense_Mutation_p.G92R	NM_004363	NP_004354	P06731	CEAM5_HUMAN	Homo sapiens carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), mRNA.	92	Ig-like 1.					anchored to membrane|basolateral plasma membrane|integral to plasma membrane				breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		AGCTACCCCAGGGCCCGCATA	0.473000													6	223					0	0	1	0	0
RGS21	431704	broad.mit.edu	37	1	192321267	192321267	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr1:192321267C>T	uc001gsh.3	+	3	353	c.179C>T	c.(178-180)aCg>aTg	p.T60M		NM_001039152	NP_001034241	Q2M5E4	RGS21_HUMAN	Homo sapiens regulator of G-protein signaling 21 (RGS21), mRNA.	60	RGS.				negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						TTTAAGAAAACGAAAAATGCA	0.348000													3	16					0	0	1	0	0
SLC25A3	5250	broad.mit.edu	37	12	98991696	98991696	+	Silent	SNP	T	T	G			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr12:98991696T>G	uc001tfo.3	+	3	465	c.345T>G	c.(343-345)ggT>ggG	p.G115G	SLC25A3_uc001tfm.3_Silent_p.G114G|SLC25A3_uc001tfn.3_Silent_p.G114G|SLC25A3_uc001tfp.3_Silent_p.G114G|SLC25A3_uc001tfq.3_5'UTR|SLC25A3_uc001tfr.3_Silent_p.G115G|SLC25A3_uc001tfs.3_Silent_p.G71G|SNORA53_uc001tfu.1_5'Flank	NM_005888	NP_005879	Q00325	MPCP_HUMAN	Homo sapiens solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 (SLC25A3), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	115					generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity			breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		AAGAGGATGGTGTTCGTGGTT	0.393000													27	51					0	0	1	0	0
LIFR	3977	broad.mit.edu	37	5	38511959	38511959	+	Silent	SNP	G	G	A			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr5:38511959G>A	uc010ive.1	-	5	1001	c.669C>T	c.(667-669)taC>taT	p.Y223Y	LIFR_uc003jli.2_Silent_p.Y223Y	NM_001127671	NP_002301	P42702	LIFR_HUMAN	Homo sapiens leukemia inhibitory factor receptor alpha (LIFR), transcript variant 1, mRNA.	223					positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GATTGTCAATGTAGCATCTAA	0.393000			T	PLAG1	salivary adenoma								12	29					0	0	1	0	0
MUC16	94025	broad.mit.edu	37	19	8962361	8962361	+	Frame_Shift_Del	DEL	C	C	-			TCGA-ET-A3BS-01A-11D-A202-08	TCGA-ET-A3BS-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f353a576-14db-4817-9ac8-64d6328adab8	6d88ce09-4e88-4449-a114-ad99a7f5f873	g.chr19:8962361delC	uc002mkp.3	-	81	43542	c.43338delG	c.(43336-43338)gggfs	p.G14446fs	MUC16_uc010dwi.3_Non-coding_Transcript|MUC16_uc010dwj.3_Frame_Shift_Del_p.G1246fs|MUC16_uc021uog.1_Non-coding_Transcript	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	Homo sapiens mucin 16, cell surface associated (MUC16), mRNA.	13920	SEA 16.			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TACCAGAATTCCCAGTTAAGG	0.478													2	4	---	---	---	---