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	qox	pox_cutoff	pox	oxoGCut	isArtifactMode	t_ref_count	t_alt_count
SP140	11262	broad.mit.edu	37	2	231113619	231113619	+	Silent	SNP	T	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr2:231113619T>A	uc002vql.3	+	8	1027	c.912T>A	c.(910-912)acT>acA	p.T304T	SP140_uc010zma.1_Non-coding_Transcript|SP140_uc002vqk.2_Silent_p.T304T|SP140_uc002vqn.3_Silent_p.T251T|SP140_uc002vqm.3_Silent_p.T278T|SP140_uc010fxl.3_Silent_p.T304T	NM_007237	NP_009168	Q13342	LY10_HUMAN	Homo sapiens SP140 nuclear body protein (SP140), transcript variant 1, mRNA.	304					defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ATCTAAAAACTCCCCAAGTCA	0.423													0	1	0	0	0	27	24
PTCHD3	374308	broad.mit.edu	37	10	27687711	27687711	+	Missense_Mutation	SNP	C	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr10:27687711C>A	uc001itu.2	-	3	1934	c.1816G>T	c.(1816-1818)Gtc>Ttc	p.V606F		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	Homo sapiens patched domain containing 3 (PTCHD3), mRNA.	606					spermatid development	integral to membrane	hedgehog receptor activity			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TATATAAAGACTACAAAATAC	0.378													1.64E-12	1	1.56E-12	0	1	38	19
SUFU	51684	broad.mit.edu	37	10	104353455	104353455	+	Silent	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr10:104353455G>A	uc001kvy.2	+	4	851	c.660G>A	c.(658-660)ctG>ctA	p.L220L	SUFU_uc001kvw.2_Silent_p.L220L|SUFU_uc001kvx.3_Silent_p.L220L|SUFU_uc009xxe.2_5'Flank|SUFU_uc009xxf.2_5'Flank	NM_016169	NP_057253	Q9UMX1	SUFU_HUMAN	Homo sapiens suppressor of fused homolog (Drosophila) (SUFU), transcript variant 1, mRNA.	220					negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		AGGGCATCCTGGAGCTGCTGC	0.612			"""D, F, S"""		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation				0	1	0	0	0	28	3
CTNNAL1	8727	broad.mit.edu	37	9	111706098	111706098	+	Splice_Site	SNP	T	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr9:111706098T>A	uc004bdo.1	-	17	1984	c.1942_splice	c.e17-1	p.L648_splice	CTNNAL1_uc010mts.1_Splice_Site_p.L300_splice|CTNNAL1_uc004bdp.1_Splice_Site_p.L648_splice	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	Homo sapiens catenin (cadherin-associated protein), alpha-like 1 (CTNNAL1), mRNA.	648					Rho protein signal transduction|cell adhesion	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		GTCTTTCAGCTGAAATGTAAT	0.358													0	1	0	0	0	47	14
NCR1	9437	broad.mit.edu	37	19	55423572	55423572	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr19:55423572C>T	uc002qib.2	+	5	757	c.719C>T	c.(718-720)aCg>aTg	p.T240M	NCR1_uc002qic.2_Missense_Mutation_p.T239M|NCR1_uc002qie.2_Intron|NCR1_uc002qid.2_Missense_Mutation_p.T145M|NCR1_uc002qif.2_Intron|NCR1_uc010esj.2_Missense_Mutation_p.T133M	NM_004829	NP_004820	O76036	NCTR1_HUMAN	Homo sapiens natural cytotoxicity triggering receptor 1 (NCR1), transcript variant 1, mRNA.	240					cellular defense response|natural killer cell activation|regulation of natural killer cell mediated cytotoxicity	SWI/SNF complex|integral to plasma membrane	receptor activity|receptor signaling protein activity			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		ACCACAGAGACGGGACTCCAG	0.512													0	1	0	0	0	46	34
USP9X	8239	broad.mit.edu	37	X	41073950	41073950	+	Silent	SNP	A	G	G			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrX:41073950A>G	uc004dfb.3	+	33	5952	c.5319A>G	c.(5317-5319)aaA>aaG	p.K1773K	USP9X_uc004dfc.3_Silent_p.K1773K	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	Homo sapiens ubiquitin specific peptidase 9, X-linked (USP9X), transcript variant 3, mRNA.	1773					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						ATTGTGAAAAATGCAATAAAA	0.323													0	1	0	0	0	68	19
EXOC2	55770	broad.mit.edu	37	6	637797	637797	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr6:637797G>A	uc003mtd.3	-	1	156	c.22C>T	c.(22-24)Ccc>Tcc	p.P8S	EXOC2_uc003mte.3_Missense_Mutation_p.P8S|EXOC2_uc011dho.2_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Homo sapiens exocyst complex component 2 (EXOC2), mRNA.	8	IPT/TIG.				exocytosis|protein transport			p.Q6fs*28(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GTCACAAGGGGGGGTTGTCGT	0.473													0	1	0	0	0	51	49
CACNA1G	8913	broad.mit.edu	37	17	48655862	48655862	+	Silent	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr17:48655862C>T	uc002irk.1	+	8	2610	c.2238C>T	c.(2236-2238)ggC>ggT	p.G746G	CACNA1G_uc002iri.1_Silent_p.G746G|CACNA1G_uc002irj.1_Silent_p.G746G|CACNA1G_uc002irl.1_Silent_p.G746G|CACNA1G_uc002irm.1_Silent_p.G746G|CACNA1G_uc002irn.1_Silent_p.G746G|CACNA1G_uc002iro.1_Silent_p.G746G|CACNA1G_uc002irp.1_Silent_p.G746G|CACNA1G_uc002irq.1_Silent_p.G746G|CACNA1G_uc002irr.1_Silent_p.G746G|CACNA1G_uc002irs.1_Silent_p.G746G|CACNA1G_uc002irt.1_Silent_p.G746G|CACNA1G_uc002iru.1_Silent_p.G746G|CACNA1G_uc002irv.1_Silent_p.G746G|CACNA1G_uc002irw.1_Silent_p.G746G|CACNA1G_uc002irx.1_Silent_p.G659G|CACNA1G_uc002iry.1_Silent_p.G659G|CACNA1G_uc002isg.1_Silent_p.G659G|CACNA1G_uc002ish.1_Silent_p.G659G|CACNA1G_uc002isi.1_Silent_p.G659G|CACNA1G_uc002irz.1_Silent_p.G659G|CACNA1G_uc002isa.1_Silent_p.G659G|CACNA1G_uc002isd.1_Silent_p.G659G|CACNA1G_uc002isb.1_Silent_p.G659G|CACNA1G_uc002isc.1_Silent_p.G659G|CACNA1G_uc002ise.1_Silent_p.G659G|CACNA1G_uc002isf.1_Silent_p.G659G	NM_018896	NP_061496	O43497	CAC1G_HUMAN	Homo sapiens calcium channel, voltage-dependent, T type, alpha 1G subunit (CACNA1G), transcript variant 1, mRNA.	746					axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGTACTTTGGCCGGGGAATCA	0.582													0	1	0	0	0	45	3
GPR112	139378	broad.mit.edu	37	X	135430491	135430491	+	Silent	SNP	A	C	C			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chrX:135430491A>C	uc004ezu.1	+	5	4917	c.4626A>C	c.(4624-4626)acA>acC	p.T1542T	GPR112_uc010nsb.1_Silent_p.T1337T|GPR112_uc010nsc.1_Silent_p.T1309T	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	Homo sapiens G protein-coupled receptor 112 (GPR112), mRNA.	1542					neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CTTCTAAAACAATGCATCCAG	0.413													0	1	0	0	0	122	5
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T	rs121913377		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	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	0.368	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				0	1	0	0	0	37	19
SP140	11262	broad.mit.edu	37	2	231113619	231113619	+	Silent	SNP	T	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr2:231113619T>A	uc002vql.3	+	8	1027	c.912T>A	c.(910-912)acT>acA	p.T304T	SP140_uc010zma.1_Non-coding_Transcript|SP140_uc002vqk.2_Silent_p.T304T|SP140_uc002vqn.3_Silent_p.T251T|SP140_uc002vqm.3_Silent_p.T278T|SP140_uc010fxl.3_Silent_p.T304T	NM_007237	NP_009168	Q13342	LY10_HUMAN	Homo sapiens SP140 nuclear body protein (SP140), transcript variant 1, mRNA.	304					defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		ATCTAAAAACTCCCCAAGTCA	0.423													0	1	0	0	0	27	24
PTCHD3	374308	broad.mit.edu	37	10	27687711	27687711	+	Missense_Mutation	SNP	C	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr10:27687711C>A	uc001itu.2	-	3	1934	c.1816G>T	c.(1816-1818)Gtc>Ttc	p.V606F		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	Homo sapiens patched domain containing 3 (PTCHD3), mRNA.	606					spermatid development	integral to membrane	hedgehog receptor activity			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TATATAAAGACTACAAAATAC	0.378													1.56E-12	1	1.56E-12	0	1	38	19
SUFU	51684	broad.mit.edu	37	10	104353455	104353455	+	Silent	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr10:104353455G>A	uc001kvy.2	+	4	851	c.660G>A	c.(658-660)ctG>ctA	p.L220L	SUFU_uc001kvw.2_Silent_p.L220L|SUFU_uc001kvx.3_Silent_p.L220L|SUFU_uc009xxe.2_5'Flank|SUFU_uc009xxf.2_5'Flank	NM_016169	NP_057253	Q9UMX1	SUFU_HUMAN	Homo sapiens suppressor of fused homolog (Drosophila) (SUFU), transcript variant 1, mRNA.	220					negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		AGGGCATCCTGGAGCTGCTGC	0.612			"""D, F, S"""		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation				0	1	0	0	0	28	3
CTNNAL1	8727	broad.mit.edu	37	9	111706098	111706098	+	Splice_Site	SNP	T	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr9:111706098T>A	uc004bdo.1	-	17	1984	c.1942_splice	c.e17-1	p.L648_splice	CTNNAL1_uc010mts.1_Splice_Site_p.L300_splice|CTNNAL1_uc004bdp.1_Splice_Site_p.L648_splice	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	Homo sapiens catenin (cadherin-associated protein), alpha-like 1 (CTNNAL1), mRNA.	648					Rho protein signal transduction|cell adhesion	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		GTCTTTCAGCTGAAATGTAAT	0.358													0	1	0	0	0	47	14
NCR1	9437	broad.mit.edu	37	19	55423572	55423572	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr19:55423572C>T	uc002qib.2	+	5	757	c.719C>T	c.(718-720)aCg>aTg	p.T240M	NCR1_uc002qic.2_Missense_Mutation_p.T239M|NCR1_uc002qie.2_Intron|NCR1_uc002qid.2_Missense_Mutation_p.T145M|NCR1_uc002qif.2_Intron|NCR1_uc010esj.2_Missense_Mutation_p.T133M	NM_004829	NP_004820	O76036	NCTR1_HUMAN	Homo sapiens natural cytotoxicity triggering receptor 1 (NCR1), transcript variant 1, mRNA.	240					cellular defense response|natural killer cell activation|regulation of natural killer cell mediated cytotoxicity	SWI/SNF complex|integral to plasma membrane	receptor activity|receptor signaling protein activity			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		ACCACAGAGACGGGACTCCAG	0.512													0	1	0	0	0	46	34
USP9X	8239	broad.mit.edu	37	X	41073950	41073950	+	Silent	SNP	A	G	G			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chrX:41073950A>G	uc004dfb.3	+	33	5952	c.5319A>G	c.(5317-5319)aaA>aaG	p.K1773K	USP9X_uc004dfc.3_Silent_p.K1773K	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	Homo sapiens ubiquitin specific peptidase 9, X-linked (USP9X), transcript variant 3, mRNA.	1773					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						ATTGTGAAAAATGCAATAAAA	0.323													0	1	0	0	0	68	19
EXOC2	55770	broad.mit.edu	37	6	637797	637797	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr6:637797G>A	uc003mtd.3	-	1	156	c.22C>T	c.(22-24)Ccc>Tcc	p.P8S	EXOC2_uc003mte.3_Missense_Mutation_p.P8S|EXOC2_uc011dho.2_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Homo sapiens exocyst complex component 2 (EXOC2), mRNA.	8	IPT/TIG.				exocytosis|protein transport			p.Q6fs*28(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GTCACAAGGGGGGGTTGTCGT	0.473													0	1	0	0	0	51	49
CACNA1G	8913	broad.mit.edu	37	17	48655862	48655862	+	Silent	SNP	C	T	T			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr17:48655862C>T	uc002irk.1	+	8	2610	c.2238C>T	c.(2236-2238)ggC>ggT	p.G746G	CACNA1G_uc002iri.1_Silent_p.G746G|CACNA1G_uc002irj.1_Silent_p.G746G|CACNA1G_uc002irl.1_Silent_p.G746G|CACNA1G_uc002irm.1_Silent_p.G746G|CACNA1G_uc002irn.1_Silent_p.G746G|CACNA1G_uc002iro.1_Silent_p.G746G|CACNA1G_uc002irp.1_Silent_p.G746G|CACNA1G_uc002irq.1_Silent_p.G746G|CACNA1G_uc002irr.1_Silent_p.G746G|CACNA1G_uc002irs.1_Silent_p.G746G|CACNA1G_uc002irt.1_Silent_p.G746G|CACNA1G_uc002iru.1_Silent_p.G746G|CACNA1G_uc002irv.1_Silent_p.G746G|CACNA1G_uc002irw.1_Silent_p.G746G|CACNA1G_uc002irx.1_Silent_p.G659G|CACNA1G_uc002iry.1_Silent_p.G659G|CACNA1G_uc002isg.1_Silent_p.G659G|CACNA1G_uc002ish.1_Silent_p.G659G|CACNA1G_uc002isi.1_Silent_p.G659G|CACNA1G_uc002irz.1_Silent_p.G659G|CACNA1G_uc002isa.1_Silent_p.G659G|CACNA1G_uc002isd.1_Silent_p.G659G|CACNA1G_uc002isb.1_Silent_p.G659G|CACNA1G_uc002isc.1_Silent_p.G659G|CACNA1G_uc002ise.1_Silent_p.G659G|CACNA1G_uc002isf.1_Silent_p.G659G	NM_018896	NP_061496	O43497	CAC1G_HUMAN	Homo sapiens calcium channel, voltage-dependent, T type, alpha 1G subunit (CACNA1G), transcript variant 1, mRNA.	746					axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGTACTTTGGCCGGGGAATCA	0.582													0	1	0	0	0	45	3
GPR112	139378	broad.mit.edu	37	X	135430491	135430491	+	Silent	SNP	A	C	C			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chrX:135430491A>C	uc004ezu.1	+	5	4917	c.4626A>C	c.(4624-4626)acA>acC	p.T1542T	GPR112_uc010nsb.1_Silent_p.T1337T|GPR112_uc010nsc.1_Silent_p.T1309T	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	Homo sapiens G protein-coupled receptor 112 (GPR112), mRNA.	1542					neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CTTCTAAAACAATGCATCCAG	0.413													0	1	0	0	0	122	5
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T	rs121913377		TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	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	0.368	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				0	1	0	0	0	37	19
SVOPL	136306	broad.mit.edu	37	7	138305790	138305790	+	Splice_Site	DEL	C	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	2d6382de-9762-4d76-9d4b-7c5ac5575ef9	g.chr7:138305790delC	uc011kqh.2	-	13	1353	c.1353_splice	c.e13+1	p.Q451_splice	SVOPL_uc003vue.3_Splice_Site_p.Q299_splice	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	Homo sapiens SVOP-like (SVOPL), transcript variant 1, mRNA.	451						integral to membrane	transmembrane transporter activity			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						CTTGGCTGTACCTGGGATATA	0.567																		15	8
SVOPL	136306	broad.mit.edu	37	7	138305790	138305790	+	Splice_Site	DEL	C	-	-			TCGA-EM-A1CV-01A-11D-A13W-08	TCGA-EM-A1CV-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e0ccf372-5e5d-4f3a-8673-280ce712d84f	415c9e9c-96db-43f7-8e67-cc1d6bf5fef2	g.chr7:138305790delC	uc011kqh.2	-	13	1353	c.1353_splice	c.e13+1	p.Q451_splice	SVOPL_uc003vue.3_Splice_Site_p.Q299_splice	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	Homo sapiens SVOP-like (SVOPL), transcript variant 1, mRNA.	451						integral to membrane	transmembrane transporter activity			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						CTTGGCTGTACCTGGGATATA	0.567																		15	8
