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	transcript_name	strand	transcript_status	amino_acid_change	ucsc_cons	normal_depth	normal_vaf	tumor_depth	tumor_vaf	rna_depth	rna_vaf	polyphen	sift	condel	domain
DVL1	1855	genome.wustl.edu	37	1	1274812	1274812	+	Silent	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004421.2	-1	reviewed	p.P354	0.150	11	0%	10	40%	32	56.2%	-	-	-	superfamily_PDZ
CELA2A	63036	genome.wustl.edu	37	1	15788136	15788136	+	Silent	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033440.2	+1	reviewed	p.T70	0.647	97	0%	59	11.9%	0	-	-	-	-	HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,PatternScan_TRYPSIN_HIS
ARID1A	8289	genome.wustl.edu	37	1	27105553	27105553	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006015.4	+1	reviewed	p.R1722*	1.000	92	0%	110	40.9%	22	31.8%	-	-	-	NULL
CYP2J2	1573	genome.wustl.edu	37	1	60381745	60381745	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000775.2	-1	reviewed	p.S80G	0.112	160	0.6%	103	32%	6	50%	benign(0.014)	deleterious(0)	neutral(0.445)	HMMPfam_p450,superfamily_Cytochrome_P450
USH2A	7399	genome.wustl.edu	37	1	216166392	216166392	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_206933.2	-1	reviewed	p.V2259I	0.992	216	0%	161	34.8%	0	-	benign(0.004)	tolerated(1)	-	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
AADAC	13	genome.wustl.edu	37	3	151545849	151545849	+	Silent	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001086.2	+1	reviewed	p.V363	0.003	59	0%	49	26.5%	1	100%	-	-	-	HMMPfam_Abhydrolase_3,superfamily_alpha/beta-Hydrolases
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279	byCluster	TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.H1047R	1.000	128	0%	94	36.2%	8	12.5%	possibly_damaging(0.926)	deleterious(0.03)	deleterious(0.739)	HMMSmart_PI3Kc,superfamily_Kinase_like
INPP4B	8821	genome.wustl.edu	37	4	143130127	143130127	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001101669.1	-1	reviewed	p.R297*	1.000	194	0%	168	10.1%	6	0%	-	-	-	NULL
IRF2	3660	genome.wustl.edu	37	4	185320124	185320124	+	Silent	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000505067	-1	known	p.G147S	0.812	100	0%	64	26.6%	36	19.4%	-	-	-	NULL
GRAMD3	65983	genome.wustl.edu	37	5	125822612	125822612	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_023927.2	+1	validated	p.N369S	0.980	125	0%	120	35.8%	26	34.6%	benign(0.043)	tolerated(0.79)	neutral(0.004)	NULL
ALDH7A1	501	genome.wustl.edu	37	5	125930950	125930950	+	Missense_Mutation	SNP	C	C	T	rs144272515	by1000genomes	TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000447989	-1	known	p.A8T	1.000	7	0.000	9	0.667	0	-	benign(0.079)	-	-	NULL
PHF15	23338	genome.wustl.edu	37	5	133896438	133896438	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015288.4	+1	provisional	p.R159G	0.992	79	0%	42	28.6%	4	0%	benign(0.281)	tolerated(0.43)	neutral(0.099)	HMMPfam_EPL1
KDM3B	51780	genome.wustl.edu	37	5	137727125	137727125	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016604.3	+1	validated	p.T602fs	1.000	-	-	-	-	-	-	-	-	-	NULL
PCDHB6	56130	genome.wustl.edu	37	5	140531021	140531021	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018939.2	+1	reviewed	p.V395M	0.000	129	0%	137	35%	0	-	benign(0)	tolerated(0.22)	neutral(0.042)	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
SLC36A3	285641	genome.wustl.edu	37	5	150663636	150663636	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145017.1	-1	validated	p.A356T	1.000	96	0%	76	36.8%	0	-	possibly_damaging(0.674)	deleterious(0)	deleterious(0.684)	HMMPfam_Aa_trans
LOC100128588	100128588	genome.wustl.edu	37	6	112647806	112647806	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_001723020.1	-1	model	p.E49A	0.980	19	0%	36	41.7%	0	-	-	-	-	HMMPfam_G-patch,HMMSmart_SM00443
ADCY8	114	genome.wustl.edu	37	8	131955704	131955704	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001115.2	-1	reviewed	p.L416V	1.000	50	0%	30	13.3%	0	-	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase
GDA	9615	genome.wustl.edu	37	9	74828843	74828843	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004293.3	+1	validated	p.D172Y	1.000	216	0%	260	35.4%	10	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Amidohydro_1,superfamily_Metallo-dependent hydrolases
CELP	1057	genome.wustl.edu	37	9	135962470	135962502	+	Splice_Site	DEL	CCCTCACAAGTGACTCTGAGGCTGCCCCCGTGT	CCCTCACAAGTGACTCTGAGGCTGCCCCCGTGT	-	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	CCCTCACAAGTGACTCTGAGGCTGCCCCCGTGT	CCCTCACAAGTGACTCTGAGGCTGCCCCCGTGT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000421286	+1	known	NULL	0.034:0.026:0.020:0.015:0.001:0.000:0.000:0.000:0.000:0.000:0.000	-	-	-	-	-	-	-	-	-	-
PTEN	5728	genome.wustl.edu	37	10	89692896	89692896	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.G127V	1.000	186	0%	191	38.7%	28	46.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II
PTEN	5728	genome.wustl.edu	37	10	89692935	89692935	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.L140*	1.000	135	0%	151	39.7%	31	19.3%	-	-	-	HMMPfam_DSPc,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II
KRAS	3845	genome.wustl.edu	37	12	25380275	25380275	+	Missense_Mutation	SNP	T	T	G	rs17851045	byCluster	TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033360.2	-1	reviewed	p.Q61H	1.000	135	0%	138	72.5%	10	90%	benign(0.006)	deleterious(0.01)	neutral(0.406)	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases
ZMYM2	7750	genome.wustl.edu	37	13	20579371	20579372	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003453.2	+1	validated	p.T432fs	1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_zf-FCS,HMMSmart_TRASH
NFATC4	4776	genome.wustl.edu	37	14	24843125	24843126	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	TG	TG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000424781	+1	known	p.C575fs	0.091:0.104	-	-	-	-	-	-	-	-	-	NULL
AKAP6	9472	genome.wustl.edu	37	14	33291977	33291977	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004274.4	+1	reviewed	p.S1653I	1.000	67	0%	45	28.9%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
APBA2	321	genome.wustl.edu	37	15	29346180	29346180	+	Silent	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005503.3	+1	reviewed	p.S31	0.004	41	0%	23	39.1%	11	63.6%	-	-	-	NULL
BNC1	646	genome.wustl.edu	37	15	83932868	83932868	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001717.3	-1	reviewed	p.V379I	1.000	185	0%	185	39.5%	0	-	benign(0.366)	deleterious(0)	deleterious(0.561)	PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2
GUCY2D	3000	genome.wustl.edu	37	17	7918688	7918688	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000180.3	+1	reviewed	p.P938S	1.000	33	0%	25	56%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase
KANSL1	284058	genome.wustl.edu	37	17	44248470	44248470	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015443.2	-1	validated	p.T347I	1.000	97	0%	74	43.2%	7	28.5%	probably_damaging(0.999)	tolerated(0.12)	deleterious(0.751)	NULL
KAT7	11143	genome.wustl.edu	37	17	47903466	47903466	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007067.3	+1	provisional	p.R529C	1.000	157	0%	167	31.7%	15	53.3%	probably_damaging(0.994)	deleterious(0)	deleterious(0.897)	HMMPfam_MOZ_SAS,superfamily_Acyl-CoA N-acyltransferases (Nat)
RNF213	57674	genome.wustl.edu	37	17	78282928	78282928	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020954.2	+1	validated	p.S871F	0.999	98	0%	90	12.2%	0	-	probably_damaging(0.976)	deleterious(0)	deleterious(0.863)	NULL
ENSG00000175388	0	genome.wustl.edu	37	18	10773471	10773471	+	Silent	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000383408	-1	known	p.S171	0.535	151	0%	120	10%	0	-	-	-	-	NULL
WDR83OS	51398	genome.wustl.edu	37	19	12780184	12780184	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016145.3	-1	validated	p.P12S	1.000	61	0%	36	25%	216	44.9%	benign(0)	tolerated(0.19)	neutral(0.050)	HMMPfam_UPF0139
PEG3	5178	genome.wustl.edu	37	19	57328030	57328030	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006210.2	-1	reviewed	p.R594C	0.008	180	0%	142	39.4%	0	-	probably_damaging(0.988)	tolerated(0.07)	deleterious(0.756)	NULL
C20orf11	54994	genome.wustl.edu	37	20	61576260	61576260	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017896.2	+1	validated	p.K228R	1.000	56	0%	70	37.1%	52	26.9%	possibly_damaging(0.871)	tolerated(0.15)	deleterious(0.580)	NULL
KRTAP21-3	100288323	genome.wustl.edu	37	21	32091035	32091035	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000444335	-1	known	p.G15S	0.000	128	0%	108	37%	0	-	possibly_damaging(0.848)	-	-	NULL
DSCAM	1826	genome.wustl.edu	37	21	41719671	41719671	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001389.3	-1	validated	p.D379G	1.000	193	0%	168	35.7%	0	-	benign(0)	deleterious(0.03)	neutral(0.364)	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin
MIR106A	406899	genome.wustl.edu	37	X	133304300	133304300	+	RNA	SNP	T	T	G	novel		TCGA-B5-A0JS-01A-11D-A10B-09	TCGA-B5-A0JS-10A-01D-A10O-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000384870	-1	known	NULL	1.000	79	0%	73	35.6%	0	-	-	-	-	-
