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	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
PITPNM1	9600	broad.mit.edu	36	11	67022304	67022304	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0240-01	TCGA-06-0240-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67022304G>C	uc001olx.1	-	c.1550C>G	c.(1549-1551)GCC>GGC	p.A517G	PITPNM1_uc001olw.1_5'UTR|PITPNM1_uc001oly.1_Missense_Mutation_p.A517G|PITPNM1_uc001olz.1_Missense_Mutation_p.A517G	NM_004910	NP_004901	O00562	PITM1_HUMAN	phosphatidylinositol transfer protein,	517					brain development|lipid metabolic process|phototransduction|protein transport	cleavage furrow|endoplasmic reticulum membrane|Golgi cisterna membrane|lipid particle|membrane fraction|midbody	metal ion binding|phosphatidylinositol transporter activity			lung(2)|central_nervous_system(1)	3						GBM(28;144 709 4607 5525)								0.35	9.607795	10.100969	7	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67022304	67022304	12374	11	G	C	C	42	42	PITPNM1	C	3	3
TPSAB1	7177	broad.mit.edu	36	16	1231602	1231602	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0240-01	TCGA-06-0240-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1231602T>C	uc010brl.1	+	c.421T>C	c.(421-423)TCC>CCC	p.S141P	TPSAB1_uc002ckz.1_Missense_Mutation_p.S134P|TPSAB1_uc002cla.2_Missense_Mutation_p.S125P	NM_003294	NP_003285	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1 precursor	134	Peptidase S1.				defense response|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)												0.333333	7.495379	7.790907	4	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1231602	1231602	16967	16	T	C	C	54	54	TPSAB1	C	4	4
LRRC29	26231	broad.mit.edu	36	16	65799426	65799426	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0240-01	TCGA-06-0240-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65799426C>A	uc002esd.1	-	c.354G>T	c.(352-354)TTG>TTT	p.L118F	LRRC29_uc002ese.1_Missense_Mutation_p.L118F|LRRC29_uc002esf.1_Missense_Mutation_p.L118F|LRRC29_uc002esg.2_Missense_Mutation_p.L118F	NM_012163	NP_036295	Q8WV35	LRC29_HUMAN	F-box and leucine-rich repeat protein 9	118	LRR 4.										0		Ovarian(137;0.0563)												0.375	11.415752	11.645462	6	10	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)	Missense_Mutation	SNP	65799426	65799426	9358	16	C	A	A	21	21	LRRC29	A	3	3
FBF1	85302	broad.mit.edu	36	17	71422480	71422480	+	Silent	SNP	G	C	C			TCGA-06-0240-01	TCGA-06-0240-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71422480G>C	uc002jqc.2	-	c.2712C>G	c.(2710-2712)GCC>GCG	p.A904A	FBF1_uc002jqa.1_Intron|FBF1_uc002jqb.2_Intron|FBF1_uc010dgr.1_Silent_p.A215A	NM_001080542	NP_001074011	A6NLR5	A6NLR5_HUMAN	Fas (TNFRSF6) binding factor 1	904											0														0.444444	8.788844	8.814224	4	5	GG		KEEP	---	---	---	---	capture			Silent	SNP	71422480	71422480	5931	17	G	C	C	39	39	FBF1	C	3	3
SUV420H2	84787	broad.mit.edu	36	19	60550580	60550580	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0240-01	TCGA-06-0240-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60550580T>G	uc002qkj.2	+	c.1340T>G	c.(1339-1341)GTG>GGG	p.V447G	SUV420H2_uc002qkl.1_Missense_Mutation_p.V332G	NM_032701	NP_116090	Q86Y97	SV422_HUMAN	suppressor of variegation 4-20 homolog 2	447					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding				0	Breast(117;0.191)													0.5	12.7765	12.7765	8	8	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)	Missense_Mutation	SNP	60550580	60550580	15935	19	T	G	G	59	59	SUV420H2	G	4	4
KIAA0754	643314	broad.mit.edu	36	1	39651915	39651915	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0240-01	TCGA-06-0240-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39651915G>A	uc009vvt.1	+	c.3391G>A	c.(3391-3393)GCC>ACC	p.A1131T	MACF1_uc009vvo.1_Intron|MACF1_uc009vvp.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc009vvr.1_Intron|MACF1_uc009vvs.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	995	Ala-rich.|10.										0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)												0.222222	7.119926	8.377829	4	14	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		Missense_Mutation	SNP	39651915	39651915	8499	1	G	A	A	38	38	KIAA0754	A	1	1
STAG2	10735	broad.mit.edu	36	X	123023301	123023301	+	Splice_Site_SNP	SNP	G	T	T			TCGA-06-0240-01	TCGA-06-0240-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:123023301G>T	uc004eua.1	+	c.1535_splice	c.e17-1	p.A512_splice	STAG2_uc004etz.2_Splice_Site_SNP_p.A512_splice|STAG2_uc004eub.1_Splice_Site_SNP_p.A512_splice|STAG2_uc004euc.1_Splice_Site_SNP_p.A512_splice|STAG2_uc004eud.1_Splice_Site_SNP_p.A512_splice|STAG2_uc004eue.1_Splice_Site_SNP_p.A512_splice	NM_001042749	NP_001036215			stromal antigen 2 isoform a						cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5														0.272727	6.31876	6.832059	3	8	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	123023301	123023301	15761	23	G	T	T	34	34	STAG2	T	5	3
SPTBN4	57731	broad.mit.edu	36	19	45768289	45768290	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-0240-01	TCGA-06-0240-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45768289_45768290insA	uc002ony.1	+	c.7134_7135insA	c.(7132-7137)CCCAAGfs	p.P2378fs	SPTBN4_uc002onz.1_Frame_Shift_Ins_p.P2378fs|SPTBN4_uc010egx.1_Frame_Shift_Ins_p.P1121fs|SPTBN4_uc010eha.1_5'Flank	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	2378_2379					actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)	4			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)											0.38			5	8				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	45768289	45768290	15635	19	-	A	A	21	21	SPTBN4	A	5	5
MUC4	4585	broad.mit.edu	36	3	196996768	196996769	+	In_Frame_Ins	INS	-	GAT	GAT			TCGA-06-0240-01	TCGA-06-0240-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:196996768_196996769insGAT	uc010hzt.1	-	c.6077_6078insATC	c.(6076-6078)TCC>TCATCC	p.2026_2026S>SS	MUC4_uc003fvo.1_Intron|MUC4_uc003fvp.1_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	798	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)										0.40			4	6				---	---	---	---	capture_indel			In_Frame_Ins	INS	196996768	196996769	10372	3	-	GAT	GAT	47	47	MUC4	GAT	5	5
MAFA	389692	broad.mit.edu	36	8	144583097	144583099	+	In_Frame_Del	DEL	TGG	-	-			TCGA-06-0240-01	TCGA-06-0240-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144583097_144583099delTGG	uc003yyc.1	-	c.621_623delCCA	c.(619-624)CACCAT>CAT	p.207_208HH>H		NM_201589	NP_963883	Q8NHW3	MAFA_HUMAN	v-maf musculoaponeurotic fibrosarcoma oncogene	207_208	His-rich.				insulin secretion|nitric oxide mediated signal transduction|response to glucose stimulus	nucleus	protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)											0.45			5	6				---	---	---	---	capture_indel			In_Frame_Del	DEL	144583097	144583099	9534	8	TGG	-	-	51	51	MAFA	-	5	5
