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
KRTAP5-2	440021	broad.mit.edu	37	11	1619378	1619378	+	Missense_Mutation	SNP	G	G	A	rs138454470	byFrequency	TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr11:1619378G>A	ENST00000412090.1	-	1	146	c.103C>T	c.(103-105)Cgt>Tgt	p.R35C	KRTAP5-AS1_ENST00000424148.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	35						keratin filament				large_intestine(1)|lung(2)|skin(1)	4		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CAGCCCCCACGGCCGGAGCCA	0.687000													5	72					0	0	0.021553	0	0
CTD-2139B15.2	0	broad.mit.edu	37	5	17354234	17354234	+	RNA	SNP	C	C	T	rs2652638	by1000genomes	TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr5:17354234C>T	ENST00000511821.1	+	0	101				FTH1P10_ENST00000401830.3_RNA																							CACACTCCATCGCATTCAGCC	0.468000													6	128					0	0	0.038147	0	0
FOXP2	93986	broad.mit.edu	37	7	114269973	114269973	+	Silent	SNP	A	A	G	rs149757187		TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr7:114269973A>G	ENST00000393500.3	+	11	1105	c.285A>G	c.(283-285)caA>caG	p.Q95Q	FOXP2_ENST00000360232.4_Silent_p.Q170Q|FOXP2_ENST00000403559.4_Silent_p.Q187Q|FOXP2_ENST00000378237.3_Silent_p.Q170Q|FOXP2_ENST00000393498.2_Silent_p.Q150Q|FOXP2_ENST00000393491.3_Silent_p.Q78Q|FOXP2_ENST00000390668.3_Silent_p.Q194Q|FOXP2_ENST00000350908.4_Silent_p.Q170Q|FOXP2_ENST00000393494.2_Silent_p.Q170Q|FOXP2_ENST00000393489.3_Silent_p.Q78Q|FOXP2_ENST00000408937.3_Silent_p.Q195Q|AC020606.1_ENST00000580664.1_RNA			O15409	FOXP2_HUMAN	forkhead box P2	170	Gln-rich.				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	p.Q195Q(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						agcagcagcaacaacaacaac	0.502000													3	48					0	0	0.004672	0	0
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418000													5	49					0	0	0.014758	0	0
NCOR1	9611	broad.mit.edu	37	17	15973810	15973810	+	Silent	SNP	T	T	A			TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr17:15973810T>A	ENST00000268712.3	-	31	4439	c.4182A>T	c.(4180-4182)tcA>tcT	p.S1394S	NCOR1_ENST00000395851.1_Silent_p.S1410S|NCOR1_ENST00000395857.3_5'UTR	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1394	Interaction with ETO.				cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CAGATTGACCTGAGTTGTTGT	0.428000													21	62					0	0	0.069288	0	0
TPTE2P6	0	broad.mit.edu	37	13	25168501	25168501	+	RNA	SNP	G	G	A	rs4770716	by1000genomes	TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr13:25168501G>A	ENST00000453498.1	+	0	1173																											TTTTCTCTTCGGTGAGTAATC	0.388000													3	31					0	0	0.009096	0	0
LL22NC03-80A10.6	0	broad.mit.edu	37	22	22663087	22663087	+	RNA	SNP	A	A	G	rs1054158		TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr22:22663087A>G	ENST00000426066.1	+	0	526					NR_027293.1																						GCTGCCACATAAGTTGTCCTT	0.303000													3	26					0	0	0.004672	0	0
PLXNA1	5361	broad.mit.edu	37	3	126707544	126707544	+	Silent	SNP	T	T	G			TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr3:126707544T>G	ENST00000251772.4	+	1	108	c.39T>G	c.(37-39)ggT>ggG	p.G13G	PLXNA1_ENST00000393409.2_Silent_p.G36G			Q9UIW2	PLXA1_HUMAN	plexin A1	36					axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity	p.G13G(4)		breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CAGGCGGGGGTTCACAGCCCC	0.682000													6	14					0	0	0.105934	0	0
GRM2	2912	broad.mit.edu	37	3	51746681	51746681	+	Missense_Mutation	SNP	G	G	T			TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr3:51746681G>T	ENST00000395052.3	+	3	877	c.643G>T	c.(643-645)Gac>Tac	p.D215Y	GRM2_ENST00000475478.1_Intron|GRM2_ENST00000442933.2_Missense_Mutation_p.D215Y	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	215					synaptic transmission	integral to plasma membrane				breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)	GTCTGAGGGCGACTATGGCGA	0.602000													24	62					6.36457e-07	7.2738e-07	0.091800	1	0
UBAP2	55833	broad.mit.edu	37	9	33948652	33948652	+	Translation_Start_Site	SNP	T	T	C	rs307654	by1000genomes	TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr9:33948652T>C	ENST00000379225.1	-	0	312				UBAP2_ENST00000360802.1_Intron|UBAP2_ENST00000379238.1_Intron|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000449054.1_Intron|UBAP2_ENST00000539807.1_Intron			Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		CTTTAAAACATATCAAGTATT	0.303000													3	40					0	0	0.004672	0	0
LSP1	4046	broad.mit.edu	37	11	1907970	1907970	+	Silent	SNP	C	C	T			TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr11:1907970C>T	ENST00000406638.2	+	8	1842	c.540C>T	c.(538-540)ggC>ggT	p.G180G	LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000405957.2_Silent_p.G180G|LSP1_ENST00000381775.1_Silent_p.G370G|LSP1_ENST00000311604.3_Silent_p.G242G	NM_001013254.1|NM_001013255.1	NP_001013272.1|NP_001013273.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	242					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		AGACCGCTGGCCGGACCCCCA	0.602000													8	84					0	0	0.038147	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	v-raf murine sarcoma viral oncogene homolog B	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(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(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	0.020292	0	0
AKR7L	246181	broad.mit.edu	37	1	19594919	19594921	+	RNA	DEL	AAG	AAG	-	rs138196141		TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr1:19594919_19594921delAAG	ENST00000420396.2	-	0	637				AKR7L_ENST00000429712.1_RNA					aldo-keto reductase family 7-like											breast(1)|endometrium(2)|ovary(1)|prostate(1)|urinary_tract(1)	6						aaaaaaaaaaaaGACCAGTGGGA	0.419													4	9	---	---	---	---					
AC074391.1	0	broad.mit.edu	37	2	65738863	65738863	+	RNA	DEL	G	G	-			TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr2:65738863delG	ENST00000377977.3	+	0	862																											TTTTTTTTTTGTCCAGGAGGC	0.303													3	5	---	---	---	---					
HLA-F-AS1	0	broad.mit.edu	37	6	29709414	29709414	+	RNA	DEL	A	A	-			TCGA-ET-A3DT-01A-11D-A19J-08	TCGA-ET-A3DT-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71d4fa4b-f805-4b31-957e-defc6913a3c5	79039652-38f5-4155-8ee4-bf4312bde77d	g.chr6:29709414delA	ENST00000458236.1	-	0	349																											tagtttccccatttcatagat	0.458													2	4	---	---	---	---