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	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	c_position_WU	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	annotation_errors_WU
CDH1	999	genome.wustl.edu	37	16	68849628	68849628	+	Nonsense_Mutation	SNP	C	C	T	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	16	68849628	68849628	C	T	SNP	CDH1	NM_004360	human	genbank	57_37b	+1	reviewed	nonsense	c.1531	p.Q511*	0.000	superfamily_Cadherin-like,HMMPfam_Cadherin,HMMSmart_SM00112	superfamily_Cadherin-like,HMMPfam_Cadherin_pro,HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_C	-	no_errors
ENSG00000245029	0	genome.wustl.edu	37	1	16889985	16889985	+	RNA	SNP	T	T	C	rs6603880	byCluster;byFrequency;by2Hit2Allele	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	16889985	16889985	T	C	SNP	ENSG00000245029	ENST00000500210	human	ensembl	57_37b	+1	novel	rna	NULL	NULL	0.040	-	-	-	
EPB41L4A	64097	genome.wustl.edu	37	5	111506043	111506043	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	5	111506043	111506043	C	T	SNP	EPB41L4A	NM_022140	human	genbank	57_37b	-1	validated	missense	c.1694	p.G565E	0.993	NULL	HMMSmart_SM00295,superfamily_Ubiquitin-like,HMMPfam_FERM_N,PatternScan_FERM_1,superfamily_Second domain of FERM,HMMPfam_FERM_M,PatternScan_FERM_2,superfamily_PH domain-like,HMMPfam_FERM_C,HMMPfam_FA	-	no_errors
ESPL1	9700	genome.wustl.edu	37	12	53682322	53682323	+	Frame_Shift_Del	DEL	GT	GT	-	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	GT	GT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	12	53682322	53682323	GT	-	DEL	ESPL1	NM_012291	human	genbank	57_37b	+1	validated	frame_shift_del	c.4547_4548	p.G1517fs	0.126:0.120	NULL	HMMPfam_Peptidase_C50	(deletion:cds_exon[53682322,53682483])	no_errors
FTSJ3	117246	genome.wustl.edu	37	17	61898202	61898202	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	17	61898202	61898202	T	C	SNP	FTSJ3	NM_017647	human	genbank	57_37b	-1	reviewed	missense	c.2069	p.N690S	1.000	HMMPfam_Spb1_C	superfamily_S-adenosyl-L-methionine-dependent methyltransferases,HMMPfam_FtsJ,HMMPfam_Spb1_C	-	no_errors
FXYD5	53827	genome.wustl.edu	37	19	35649292	35649292	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	19	35649292	35649292	G	A	SNP	FXYD5	NM_014164	human	genbank	57_37b	+1	reviewed	nonsense	c.188	p.W63*	0.000	NULL	HMMPfam_ATP1G1_PLM_MAT8,PatternScan_FXYD	-	no_errors
GPR56	9289	genome.wustl.edu	37	16	57691314	57691314	+	Missense_Mutation	SNP	C	C	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	16	57691314	57691314	C	A	SNP	GPR56	NM_001145771	human	genbank	57_37b	+1	reviewed	missense	c.1197	p.H399Q	1.000	NULL	HMMPfam_GPS,HMMSmart_SM00303,HMMPfam_7tm_2,PatternScan_AMP_BINDING	-	no_errors
GRM1	2911	genome.wustl.edu	37	6	146720226	146720226	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	6	146720226	146720226	G	A	SNP	GRM1	NM_000838	human	genbank	57_37b	+1	reviewed	missense	c.2051	p.R684H	1.000	HMMPfam_7tm_3	superfamily_SSF53822,HMMPfam_ANF_receptor,PatternScan_G_PROTEIN_RECEP_F3_1,HMMPfam_NCD3G,PatternScan_G_PROTEIN_RECEP_F3_2,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_3,HMMPfam_GluR_Homer-bdg	-	no_errors
HK1	3098	genome.wustl.edu	37	10	71154851	71154851	+	Nonsense_Mutation	SNP	C	C	T	rs113021525	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	10	71154851	71154851	C	T	SNP	HK1	NM_033497	human	genbank	57_37b	+1	reviewed	nonsense	c.2377	p.Q793*	1.000	HMMPfam_Hexokinase_2,superfamily_SSF53067	superfamily_SSF53067,HMMPfam_Hexokinase_1,PatternScan_HEXOKINASES,HMMPfam_Hexokinase_2	-	
KIAA2013	90231	genome.wustl.edu	37	1	11985345	11985345	+	Frame_Shift_Del	DEL	T	T	-	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	11985345	11985345	T	-	DEL	KIAA2013	NM_138346	human	genbank	57_37b	-1	provisional	frame_shift_del	c.950	p.K317fs	1.000	HMMPfam_DUF2152	HMMPfam_DUF2152	(deletion:cds_exon[11985262,11986294])	no_errors
KRTAP3-2	83897	genome.wustl.edu	37	17	39155871	39155871	+	Missense_Mutation	SNP	T	T	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	17	39155871	39155871	T	A	SNP	KRTAP3-2	NM_031959	human	genbank	57_37b	-1	reviewed	missense	c.235	p.T79S	0.942	HMMPfam_Keratin_matx	HMMPfam_Keratin_matx	-	no_errors
LOC221710	221710	genome.wustl.edu	37	6	11094562	11094562	+	Frame_Shift_Del	DEL	G	G	-	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	6	11094562	11094562	G	-	DEL	LOC221710	NM_001135575	human	genbank	57_37b	+1	validated	frame_shift_del	c.16	p.L7fs	0.996	NULL	NULL	(deletion:cds_exon[11094547,11094622])	no_errors
ONECUT2	9480	genome.wustl.edu	37	18	55103477	55103479	+	In_Frame_Del	DEL	CAC	CAC	-	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	CAC	CAC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	18	55103477	55103479	CAC	-	DEL	ONECUT2	NM_004852	human	genbank	57_37b	+1	reviewed	in_frame_del	c.529_531	p.H180in_frame_del	1.000:1.000:1.000	NULL	HMMPfam_CUT,superfamily_Homeodomain-like,HMMSmart_SM00389,HMMPfam_Homeobox	(deletion:cds_exon[55102949,55104176])	no_errors
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3	178936091	178936091	G	A	SNP	PIK3CA	NM_006218	human	genbank	57_37b	+1	reviewed	missense	c.1633	p.E545K	1.000	superfamily_ARM-type_fold,HMMSmart_PI3Ka,HMMPfam_PI3Ka	HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B,superfamily_SSF54236,HMMPfam_PI3K_rbd,HMMSmart_PI3K_rbd,HMMSmart_PI3K_C2,superfamily_C2_CaLB,HMMSmart_C2,HMMPfam_PI3K_C2,superfamily_ARM-type_fold,HMMSmart_PI3Ka,HMMPfam_PI3Ka,superfamily_Kinase_like,HMMPfam_PI3_PI4_kinase,HMMSmart_PI3Kc,PatternScan_PI3_4_KINASE_1,PatternScan_PI3_4_KINASE_2	-	
PIKFYVE	200576	genome.wustl.edu	37	2	209212650	209212650	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	2	209212650	209212650	C	T	SNP	PIKFYVE	NM_015040	human	genbank	57_37b	+1	validated	silent	c.5277	p.S1759	1.000	NULL	"superfamily_FYVE/PHD zinc finger,HMMSmart_SM00064,HMMPfam_FYVE,superfamily_""Winged helix"" DNA-binding domain,HMMPfam_DEP,HMMSmart_SM00049,superfamily_GroEL-intermediate domain like,HMMPfam_Cpn60_TCP1,superfamily_GroEL apical domain-like,superfamily_SAICAR synthase-like,HMMSmart_SM00330,HMMPfam_PIP5K"	-	no_errors
PLEKHA4	57664	genome.wustl.edu	37	19	49363612	49363612	+	Silent	SNP	G	G	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	19	49363612	49363612	G	A	SNP	PLEKHA4	NM_020904	human	genbank	57_37b	-1	validated	silent	c.471	p.D157	0.157	NULL	superfamily_PH domain-like,HMMPfam_PH,HMMSmart_SM00233	-	no_errors
PRDM16	63976	genome.wustl.edu	37	1	3301795	3301795	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	3301795	3301795	G	A	SNP	PRDM16	NM_022114	human	genbank	57_37b	+1	reviewed	missense	c.518	p.R173H	0.991	superfamily_SET domain,HMMSmart_SM00317	superfamily_SET domain,HMMSmart_SM00317,superfamily_C2H2 and C2HC zinc fingers,HMMSmart_SM00355,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1	-	no_errors
PRND	23627	genome.wustl.edu	37	20	4705447	4705447	+	Missense_Mutation	SNP	C	C	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	20	4705447	4705447	C	A	SNP	PRND	NM_012409	human	genbank	57_37b	+1	reviewed	missense	c.250	p.Q84K	1.000	superfamily_Prion-like,HMMPfam_Prion	superfamily_Prion-like,HMMPfam_Prion	-	no_errors
PWP2	5822	genome.wustl.edu	37	21	45528869	45528869	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	21	45528869	45528869	C	T	SNP	PWP2	NM_005049	human	genbank	57_37b	+1	validated	missense	c.23	p.S8L	0.995	NULL	superfamily_Peptidase_S9A_N,HMMSmart_WD40,superfamily_WD40_like,HMMPfam_WD40,PatternScan_WD_REPEATS_1,HMMPfam_PWP2	-	no_errors
RNF19A	25897	genome.wustl.edu	37	8	101300149	101300149	+	Missense_Mutation	SNP	T	T	G	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	8	101300149	101300149	T	G	SNP	RNF19A	NM_015435	human	genbank	57_37b	-1	reviewed	missense	c.254	p.N85T	1.000	NULL	superfamily_RING/U-box,HMMSmart_SM00184,HMMPfam_zf-C3HC4,HMMPfam_IBR,HMMSmart_SM00647	-	no_errors
SHE	126669	genome.wustl.edu	37	1	154461722	154461722	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	154461722	154461722	G	A	SNP	SHE	NM_001010846	human	genbank	57_37b	-1	provisional	missense	c.829	p.R277W	0.000	NULL	superfamily_SSF55550,HMMSmart_SH2,HMMPfam_SH2	-	no_errors
SNX3	8724	genome.wustl.edu	37	6	108581992	108581992	+	Missense_Mutation	SNP	C	C	A	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	6	108581992	108581992	C	A	SNP	SNX3	NM_003795	human	genbank	57_37b	-1	reviewed	missense	c.134	p.R45L	1.000	superfamily_PX domain,HMMPfam_PX,HMMSmart_SM00312	superfamily_PX domain,HMMPfam_PX,HMMSmart_SM00312	-	no_errors
TRIM11	81559	genome.wustl.edu	37	1	228584379	228584380	+	Frame_Shift_Ins	INS	-	-	AC	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	228584379	228584380	-	AC	INS	TRIM11	ENST00000366699	human	ensembl	57_37b	-1	known	frame_shift_ins	c.1128_1127	p.T377fs	0.080:0.073	NULL	superfamily_SSF57850,HMMSmart_RING,HMMPfam_zf-C3HC4,PatternScan_ZF_RING_1,HMMPfam_zf-B_box,HMMSmart_BBOX	-	no_errors
TSPYL1	7259	genome.wustl.edu	37	6	116600774	116600774	+	Missense_Mutation	SNP	C	C	G	rs3749895	byCluster;byFrequency;by2Hit2Allele;by1000genomes	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	6	116600774	116600774	C	G	SNP	TSPYL1	NM_003309	human	genbank	57_37b	-1	reviewed	missense	c.220	p.A74P	0.000	NULL	HMMPfam_NAP	-	
WHSC1	7468	genome.wustl.edu	37	4	1954980	1954981	+	Frame_Shift_Ins	INS	-	-	G	novel	unknown	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	4	1954980	1954981	-	G	INS	WHSC1	ENST00000350915	human	ensembl	57_37b	+1	known	frame_shift_ins	c.111_112	p.S38fs	0.000:0.001	NULL	HMMSmart_PHD,HMMSmart_RING,superfamily_FYVE_PHD_ZnF,HMMPfam_PHD,PatternScan_ZF_PHD_1,superfamily_SSF63748,HMMPfam_PWWP,HMMSmart_PWWP,superfamily_SSF82199,HMMSmart_AWS,HMMPfam_SET,HMMSmart_SET,HMMSmart_PostSET	-	no_errors
YWHAE	7531	genome.wustl.edu	37	17	1248392	1248392	+	RNA	SNP	A	A	G	rs9393	byCluster;byFrequency;by2Hit2Allele;by1000genomes	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	17	1248392	1248392	A	G	SNP	YWHAE	NR_024058	human	genbank	57_37b	-1	reviewed	rna	NULL	NULL	1.000	-	-	-	
ZNF627	199692	genome.wustl.edu	37	19	11725413	11725413	+	Silent	SNP	G	G	A	rs12151212	byCluster;by1000genomes	TCGA-A2-A0EX-01A-21W-A050-09	TCGA-A2-A0EX-10A-01W-A055-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	19	11725413	11725413	G	A	SNP	ZNF627	NM_145295	human	genbank	57_37b	+1	validated	silent	c.75	p.Q25	0.648	superfamily_Krueppel-associated_box,HMMPfam_KRAB,HMMSmart_KRAB	superfamily_Krueppel-associated_box,HMMPfam_KRAB,HMMSmart_KRAB,HMMSmart_ZnF_C2H2,superfamily_SSF57667,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1	-	
