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
ABCC9	10060	broad.mit.edu	36	12	21961247	21961247	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0189-01	TCGA-06-0189-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:21961247T>C	uc001rfh.1	-	c.464A>G	c.(463-465)TAC>TGC	p.Y155C	ABCC9_uc001rfi.1_Missense_Mutation_p.Y155C|ABCC9_uc001rfj.1_Missense_Mutation_p.Y155C	NM_020297	NP_064693	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	155	Extracellular (Potential).				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)	4					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.121951	54.987883	89.407535	30	216	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21961247	21961247	60	12	T	C	C	57	57	ABCC9	C	4	4
C13orf33	84935	broad.mit.edu	36	13	30378670	30378670	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0189-01	TCGA-06-0189-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:30378670C>G	uc001uth.2	+	c.18C>G	c.(16-18)TGC>TGG	p.C6W		NM_032849	NP_116238	Q5VYS4	CM033_HUMAN	hypothetical protein LOC84935	6											0		Lung SC(185;0.0281)												0.333333	7.677126	7.981835	4	8	CC		KEEP	---	---	---	---	capture		all cancers(112;0.00914)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.0559)|GBM - Glioblastoma multiforme(144;0.244)	Missense_Mutation	SNP	30378670	30378670	1774	13	C	G	G	27	27	C13orf33	G	3	3
PLA2G4E	123745	broad.mit.edu	36	15	40085608	40085608	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0189-01	TCGA-06-0189-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:40085608C>T	uc001zow.1	-	c.310G>A	c.(310-312)GTG>ATG	p.V104M		NM_001080490	NP_001073959	C9JK77	C9JK77_HUMAN	phospholipase A2, group IVE	104					phospholipid catabolic process						0		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)												0.105263	12.149808	32.751256	14	119	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)	Missense_Mutation	SNP	40085608	40085608	12431	15	C	T	T	19	19	PLA2G4E	T	1	1
CACNA1H	8912	broad.mit.edu	36	16	1197300	1197300	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0189-01	TCGA-06-0189-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1197300G>A	uc002cks.1	+	c.2932G>A	c.(2932-2934)GTG>ATG	p.V978M	CACNA1H_uc002ckt.1_Missense_Mutation_p.V978M|CACNA1H_uc002cku.1_5'Flank|CACNA1H_uc010brj.1_5'Flank|CACNA1H_uc002ckv.1_5'Flank	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	978	II.|Extracellular (Potential).				axon guidance|muscle contraction|muscle organ development|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)									0.181818	7.987107	10.079394	4	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1197300	1197300	2661	16	G	A	A	40	40	CACNA1H	A	1	1
KRT12	3859	broad.mit.edu	36	17	36274709	36274709	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0189-01	TCGA-06-0189-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36274709C>T	uc002hvk.2	-	c.682G>A	c.(682-684)GTA>ATA	p.V228I		NM_000223	NP_000214	Q99456	K1C12_HUMAN	keratin 12	228	Rod.|Coil 1B.				visual perception	intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)												0.108108	15.193995	37.725867	16	132	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36274709	36274709	8764	17	C	T	T	19	19	KRT12	T	1	1
HMCN1	83872	broad.mit.edu	36	1	184081798	184081798	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0189-01	TCGA-06-0189-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:184081798A>T	uc001grq.1	+	c.286A>T	c.(286-288)ATT>TTT	p.I96F		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1	96	VWFA.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.10989	10.980751	24.689963	10	81	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184081798	184081798	7511	1	A	T	T	4	4	HMCN1	T	4	4
UXS1	80146	broad.mit.edu	36	2	106128128	106128128	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0189-01	TCGA-06-0189-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:106128128T>C	uc002tdn.1	-	c.422A>G	c.(421-423)GAG>GGG	p.E141G	UXS1_uc002tdm.1_Missense_Mutation_p.E136G|UXS1_uc002tdo.1_Missense_Mutation_p.E79G	NM_025076	NP_079352	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	136	NAD.|Lumenal (Potential).				cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2														0.207921	54.897971	62.908849	21	80	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106128128	106128128	17674	2	T	C	C	54	54	UXS1	C	4	4
NCKAP5	344148	broad.mit.edu	36	2	133258283	133258283	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0189-01	TCGA-06-0189-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:133258283A>C	uc002ttp.1	-	c.2571T>G	c.(2569-2571)TTT>TTG	p.F857L	NCKAP5_uc002ttq.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	857							protein binding				0														0.076923	6.607559	47.088427	17	204	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	133258283	133258283	10622	2	A	C	C	5	5	NCKAP5	C	4	4
CAPN10	11132	broad.mit.edu	36	2	241183122	241183122	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0189-01	TCGA-06-0189-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:241183122C>G	uc002vzk.1	+	c.1006C>G	c.(1006-1008)CTC>GTC	p.L336V	CAPN10_uc002vzl.1_Missense_Mutation_p.L336V|CAPN10_uc002vzm.1_Intron|CAPN10_uc002vzn.1_Missense_Mutation_p.L208V|CAPN10_uc002vzo.1_Non-coding_Transcript|CAPN10_uc010fzg.1_Non-coding_Transcript|CAPN10_uc002vzp.1_Non-coding_Transcript|CAPN10_uc002vzq.1_Intron	NM_023083	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10 isoform a	336	Domain III 1.				actin cytoskeleton reorganization|cellular response to insulin stimulus|positive regulation of apoptosis|positive regulation of glucose import|positive regulation of insulin secretion|positive regulation of intracellular transport|proteolysis	cytosol|plasma membrane	calcium-dependent cysteine-type endopeptidase activity|cytoskeletal protein binding|SNARE binding			ovary(3)|large_intestine(2)|lung(1)	6		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)												0.184211	6.506372	10.103981	7	31	CC		KEEP	---	---	---	---	capture		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)	Missense_Mutation	SNP	241183122	241183122	2740	2	C	G	G	28	28	CAPN10	G	3	3
PLXND1	23129	broad.mit.edu	36	3	130807519	130807519	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0189-01	TCGA-06-0189-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:130807519G>C	uc003emx.2	-	c.654C>G	c.(652-654)AGC>AGG	p.S218R		NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	218	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1						Ovarian(97;366 1484 3738 22084 39045)								0.285714	9.108121	9.676937	4	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130807519	130807519	12553	3	G	C	C	34	34	PLXND1	C	3	3
MST1	4485	broad.mit.edu	36	3	49698920	49698920	+	Splice_Site_SNP	SNP	T	G	G			TCGA-06-0189-01	TCGA-06-0189-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49698920T>G	uc003cxg.1	-	c.806_splice	c.e8-1	p.G269_splice	MST1_uc010hkx.1_Intron	NM_020998	NP_066278			macrophage stimulating 1 (hepatocyte growth						proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1						GBM(110;181 1524 8005 22865 46297)								0.142857	9.550889	13.852839	5	30	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Splice_Site_SNP	SNP	49698920	49698920	10283	3	T	G	G	56	56	MST1	G	5	4
MDN1	23195	broad.mit.edu	36	6	90459560	90459560	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0189-01	TCGA-06-0189-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:90459560C>A	uc003pnn.1	-	c.9910G>T	c.(9910-9912)GAT>TAT	p.D3304Y		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	3304					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)	8		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)												0.2	7.894772	9.564924	4	16	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0193)	Missense_Mutation	SNP	90459560	90459560	9804	6	C	A	A	30	30	MDN1	A	3	3
ABCA13	154664	broad.mit.edu	36	7	48362609	48362609	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0189-01	TCGA-06-0189-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:48362609A>C	uc003toq.1	+	c.10502A>C	c.(10501-10503)TAC>TCC	p.Y3501S	ABCA13_uc010kys.1_Missense_Mutation_p.Y630S|ABCA13_uc003tos.1_Missense_Mutation_p.Y382S	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3556					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10														0.263158	6.53518	7.528512	5	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48362609	48362609	32	7	A	C	C	14	14	ABCA13	C	4	4
WBSCR27	155368	broad.mit.edu	36	7	72887030	72887030	+	Silent	SNP	C	T	T			TCGA-06-0189-01	TCGA-06-0189-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72887030C>T	uc003tzj.1	-	c.717G>A	c.(715-717)AGG>AGA	p.R239R		NM_152559	NP_689772	Q8N6F8	WBS27_HUMAN	Williams-Beuren syndrome chromosome region 27	239							methyltransferase activity			central_nervous_system(1)	1		Lung NSC(55;0.159)												0.1125	7.212218	19.082575	9	71	CC		KEEP	---	---	---	---	capture			Silent	SNP	72887030	72887030	17838	7	C	T	T	26	26	WBSCR27	T	2	2
TAF6	6878	broad.mit.edu	36	7	99543561	99543561	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0189-01	TCGA-06-0189-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99543561G>C	uc003uth.1	-	c.1751C>G	c.(1750-1752)GCC>GGC	p.A584G	AP4M1_uc003utd.2_Intron|TAF6_uc003utg.1_Missense_Mutation_p.A449G|TAF6_uc003uti.1_Missense_Mutation_p.A527G|TAF6_uc003utk.1_Missense_Mutation_p.A527G|TAF6_uc003utj.1_Missense_Mutation_p.A517G|TAF6_uc003utm.1_Missense_Mutation_p.A527G|TAF6_uc003utl.1_Missense_Mutation_p.A517G	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	527					negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|general RNA polymerase II transcription factor activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription initiation factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.297297	9.561825	11.097953	11	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99543561	99543561	16051	7	G	C	C	42	42	TAF6	C	3	3
NLGN4X	57502	broad.mit.edu	36	X	5831320	5831320	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0189-01	TCGA-06-0189-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:5831320T>G	uc010ndi.1	-	c.1510A>C	c.(1510-1512)ACC>CCC	p.T504P	NLGN4X_uc004crp.1_Missense_Mutation_p.T487P|NLGN4X_uc010ndh.1_Missense_Mutation_p.T467P|NLGN4X_uc004crq.1_Missense_Mutation_p.T467P|NLGN4X_uc004crr.1_Missense_Mutation_p.T467P|NLGN4X_uc010ndj.1_Missense_Mutation_p.T467P	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4	467	Extracellular (Potential).				brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|regulation of synaptic transmission|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	carboxylesterase activity|chloride ion binding|neurexin binding|protein homodimerization activity			large_intestine(1)|skin(1)	2														0.2	7.124748	10.194782	7	28	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5831320	5831320	10867	23	T	G	G	59	59	NLGN4X	G	4	4
