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
OTX1	5013	broad.mit.edu	37	2	63283329	63283329	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A2P1-01A-11D-A202-08	TCGA-EM-A2P1-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6655200-75a5-4c42-8360-5b6d42f24775	019e120c-aefd-4aa7-a80f-6aa6fea09969	g.chr2:63283329G>A	uc021vim.1	+	4	1219	c.943G>A	c.(943-945)Gac>Aac	p.D315N	OTX1_uc002scd.3_Missense_Mutation_p.D315N|OTX1_uc010ypt.2_Missense_Mutation_p.D249N	NM_001199770	NP_001186699	P32242	OTX1_HUMAN	Homo sapiens orthodenticle homeobox 1 (OTX1), transcript variant 2, mRNA.	315						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.D315E(1)|p.A314A(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					CAACTCTGCCGACTGCTTGGA	0.607													0	4.58E-01	0	0	0	70	15
PRRC2A	7916	broad.mit.edu	37	6	31599848	31599848	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A2P1-01A-11D-A202-08	TCGA-EM-A2P1-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6655200-75a5-4c42-8360-5b6d42f24775	019e120c-aefd-4aa7-a80f-6aa6fea09969	g.chr6:31599848C>T	uc003nvb.4	+	15	3647	c.3398C>T	c.(3397-3399)aCc>aTc	p.T1133I	PRRC2A_uc011dnv.1_Intron|PRRC2A_uc003nvc.4_Missense_Mutation_p.T1133I	NM_080686	NP_542417	P48634	PRC2A_HUMAN	Homo sapiens proline-rich coiled-coil 2A (PRRC2A), transcript variant 1, mRNA.	1133	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GGAACACTCACCCAGGTCCCT	0.672													0	3.35E-01	0	0	0	104	8
GRAMD4	23151	broad.mit.edu	37	22	47059056	47059056	+	Silent	SNP	C	T	T	rs145387351		TCGA-EM-A2P1-01A-11D-A202-08	TCGA-EM-A2P1-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6655200-75a5-4c42-8360-5b6d42f24775	019e120c-aefd-4aa7-a80f-6aa6fea09969	g.chr22:47059056C>T	uc003bhx.3	+	4	635	c.586C>T	c.(586-588)Ctg>Ttg	p.L196L	GRAMD4_uc010had.3_Silent_p.L135L	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	Homo sapiens GRAM domain containing 4 (GRAMD4), mRNA.	196					apoptosis	integral to membrane|mitochondrial membrane				breast(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	12		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		AGAGGAACCCCTGAGCGCCCG	0.657													0	6.25E-01	0	0	0	102	23
XRN1	54464	broad.mit.edu	37	3	142037638	142037638	+	Silent	SNP	T	C	C			TCGA-EM-A2P1-01A-11D-A202-08	TCGA-EM-A2P1-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6655200-75a5-4c42-8360-5b6d42f24775	019e120c-aefd-4aa7-a80f-6aa6fea09969	g.chr3:142037638T>C	uc003eus.3	-	37	4576	c.4509A>G	c.(4507-4509)caA>caG	p.Q1503Q	XRN1_uc010huu.3_Silent_p.Q970Q|XRN1_uc003eut.3_Silent_p.Q1503Q|XRN1_uc003euu.3_Silent_p.Q1504Q	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	Homo sapiens 5'-3' exoribonuclease 1 (XRN1), transcript variant 1, mRNA.	1503					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	Golgi apparatus|cytosol|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|RNA binding|protein binding			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TTACCAACTGTTGTAAAGCAA	0.363													0	1.85E-01	0	0	0	52	5
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T	rs121913377		TCGA-EM-A2P1-01A-11D-A202-08	TCGA-EM-A2P1-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6655200-75a5-4c42-8360-5b6d42f24775	019e120c-aefd-4aa7-a80f-6aa6fea09969	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	3.35E-01	0	0	0	54	9
FCGRT	2217	broad.mit.edu	37	19	50017183	50017183	+	Missense_Mutation	SNP	C	G	G			TCGA-EM-A2P1-01A-11D-A202-08	TCGA-EM-A2P1-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6655200-75a5-4c42-8360-5b6d42f24775	019e120c-aefd-4aa7-a80f-6aa6fea09969	g.chr19:50017183C>G	uc002pog.2	+	1	340	c.118C>G	c.(118-120)Cct>Gct	p.P40A	FCGRT_uc002poe.2_Missense_Mutation_p.P40A|FCGRT_uc002pof.2_5'UTR|FCGRT_uc010yax.2_Missense_Mutation_p.P40A|FCGRT_uc002poh.2_5'Flank	NM_004107	NP_004098	P55899	FCGRN_HUMAN	Homo sapiens Fc fragment of IgG, receptor, transporter, alpha (FCGRT), transcript variant 2, mRNA.	40	Alpha-1.				antigen processing and presentation|female pregnancy|immune response	MHC class I protein complex|integral to membrane	IgG binding|receptor activity			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		GGTGTCCTCGCCTGCCCCGGG	0.657													0	8.70E-01	0	0	0	212	49
CSMD2	114784	broad.mit.edu	37	1	34128590	34128590	+	Silent	SNP	C	T	T	rs115110975	byFrequency	TCGA-EM-A2P1-01A-11D-A202-08	TCGA-EM-A2P1-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6655200-75a5-4c42-8360-5b6d42f24775	019e120c-aefd-4aa7-a80f-6aa6fea09969	g.chr1:34128590C>T	uc001bxm.1	-	25	4332	c.4155G>A	c.(4153-4155)ccG>ccA	p.P1385P	CSMD2_uc001bxn.1_Silent_p.P1345P|CSMD2_uc001bxo.1_Silent_p.P258P	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	Homo sapiens CUB and Sushi multiple domains 2 (CSMD2), mRNA.	1345	Sushi 8.					integral to membrane|plasma membrane	protein binding	p.A1346S(1)|p.P1345P(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGGGCAGGGCCGGGCCACTCA	0.572													0	2.49E-01	0	0	0	102	7
