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
EXOSC10	5394	genome.wustl.edu	37	1	11158135	11158135	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001998.1	-1	validated	p.R64*	1.000	106	0%	127	28.3%	1	100%	-	-	-	HMMPfam_PMC2NT
PUM1	9698	genome.wustl.edu	37	1	31465245	31465245	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001020658.1	-1	reviewed	p.Q384*	1.000	256	0%	520	32.1%	5	20%	-	-	-	NULL
COL16A1	1307	genome.wustl.edu	37	1	32157635	32157635	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001856.3	-1	reviewed	p.K410Q	1.000	51	0%	41	41.5%	2	0%	unknown(0)	tolerated(0.09)	-	HMMPfam_Collagen
USP33	23032	genome.wustl.edu	37	1	78207369	78207369	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015017.3	-1	validated	p.R36Q	0.997	80	0%	78	35.9%	0	-	possibly_damaging(0.516)	tolerated(0.05)	deleterious(0.519)	NULL
DPYD	1806	genome.wustl.edu	37	1	98058899	98058899	+	Missense_Mutation	SNP	C	C	T	rs72549306	byCluster	TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000110.3	-1	reviewed	p.V335M	1.000	134	0%	153	50.3%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Pyr_redox_2,superfamily_SSF51971
STXBP3	6814	genome.wustl.edu	37	1	109340814	109340814	+	Silent	SNP	T	T	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007269.2	+1	validated	p.T468	0.829	326	0%	356	45.2%	10	40%	-	-	-	HMMPfam_Sec1,superfamily_Sec1-like
BCL2L15	440603	genome.wustl.edu	37	1	114429241	114429241	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001010922.2	-1	validated	p.R56P	1.000	124	0%	187	43.3%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
CEP350	9857	genome.wustl.edu	37	1	180000560	180000560	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014810.4	+1	reviewed	p.S1219Y	0.406	55	0%	101	23.8%	0	-	probably_damaging(0.955)	deleterious(0)	deleterious(0.843)	NULL
TPR	7175	genome.wustl.edu	37	1	186331435	186331435	+	Silent	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003292.2	-1	reviewed	p.L258	1.000	90	0%	88	36.4%	0	-	-	-	-	NULL
SERTAD4	56256	genome.wustl.edu	37	1	210415592	210415592	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019605.3	+1	validated	p.N327K	0.488	122	0%	115	46.1%	0	-	benign(0.026)	tolerated(1)	neutral(0.001)	NULL
OBSCN	84033	genome.wustl.edu	37	1	228461239	228461239	+	Missense_Mutation	SNP	C	C	T	rs189809636	by1000genomes	TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098623.1	+1	reviewed	p.H1710Y	0.763	8	0.000	9	0.667	0	-	benign(0.025)	deleterious(0.05)	neutral(0.346)	HMMSmart_SM00406,HMMSmart_SM00409,superfamily_Immunoglobulin
LOC644006	644006	genome.wustl.edu	37	1	231157656	231157656	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_929433.4	+1	model	p.L100F	0.924	65	0%	76	52.6%	0	-	-	-	-	NULL
APOB	338	genome.wustl.edu	37	2	21235038	21235038	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000384.2	-1	reviewed	p.L1568M	0.999	211	0%	395	31.1%	0	-	probably_damaging(0.991)	-	-	NULL
ATAD2B	54454	genome.wustl.edu	37	2	24033196	24033196	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017552.1	-1	validated	p.S815*	1.000	53	0%	127	30.7%	0	-	-	-	-	superfamily_P-loop containing nucleoside triphosphate hydrolases
OTOF	9381	genome.wustl.edu	37	2	26725223	26725223	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_194248.2	-1	reviewed	p.D219N	1.000	31	0%	65	35.4%	0	-	probably_damaging(0.959)	deleterious(0)	deleterious(0.847)	NULL
BIRC6	57448	genome.wustl.edu	37	2	32733118	32733118	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016252.3	+1	reviewed	p.V3258F	1.000	99	0%	197	22.8%	1	0%	benign(0.002)	tolerated(0.05)	neutral(0.345)	superfamily_Galactose-binding domain-like
MSH2	4436	genome.wustl.edu	37	2	47657080	47657089	+	Frame_Shift_Del	DEL	GGTAACAAGT	GGTAACAAGT	-	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	GGTAACAAGT	GGTAACAAGT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000251.1	+1	reviewed	p.G426fs	1.000	-	-	-	-	-	-	-	-	-	HMMPfam_MutS_III,HMMSmart_MUTSd,superfamily_DNA_repair_MutS_domIII
USP19	10869	genome.wustl.edu	37	3	49154344	49154344	+	Silent	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006677.1	-1	provisional	p.P213	0.003	49	0%	40	52.5%	2	0%	-	-	-	HMMPfam_DUF1872
SLMAP	7871	genome.wustl.edu	37	3	57857375	57857375	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007159.2	+1	validated	p.S383*	1.000	107	0%	120	38.3%	0	-	-	-	-	NULL
ATXN7	6314	genome.wustl.edu	37	3	63973759	63973759	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001128149.2	+1	reviewed	p.A374S	1.000	425	0%	403	44.7%	0	-	probably_damaging(0.999)	deleterious(0.04)	deleterious(0.839)	HMMPfam_SCA7
POLQ	10721	genome.wustl.edu	37	3	121200581	121200581	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_199420.3	-1	validated	p.L2017I	0.999	164	0%	208	36.1%	1	0%	probably_damaging(0.978)	deleterious(0.04)	deleterious(0.769)	superfamily_Ribonuclease H-like
NPHP3	27031	genome.wustl.edu	37	3	132413683	132413683	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153240.3	-1	reviewed	p.E766D	0.192	240	0%	252	42.9%	0	-	benign(0)	tolerated(0.09)	neutral(0.296)	NULL
PEX5L	51555	genome.wustl.edu	37	3	179576911	179576911	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016559.1	-1	provisional	p.A254G	0.989	198	0%	216	44.9%	0	-	benign(0.111)	tolerated(0.06)	neutral(0.331)	NULL
MUC20	200958	genome.wustl.edu	37	3	195460044	195460044	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152673.2	+1	reviewed	p.H524Q	0.000	29	0%	38	15.8%	119	0.8%	possibly_damaging(0.873)	tolerated(0.45)	neutral(0.351)	NULL
FBXW7	55294	genome.wustl.edu	37	4	153249384	153249384	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033632.2	-1	reviewed	p.R465H	1.000	341	0%	392	44.6%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40
STOX2	56977	genome.wustl.edu	37	4	184938282	184938282	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020225.1	+1	provisional	p.E876K	1.000	60	0%	55	50.9%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
LPCAT1	79888	genome.wustl.edu	37	5	1463855	1463855	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024830.3	-1	validated	p.P506T	0.000	129	0%	148	36.5%	4	0%	benign(0.001)	deleterious(0.03)	neutral(0.364)	NULL
RAI14	26064	genome.wustl.edu	37	5	34824014	34824014	+	Silent	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145525.1	+1	validated	p.N692	0.000	158	0%	208	37%	2	50%	-	-	-	NULL
VCAN	1462	genome.wustl.edu	37	5	82815532	82815532	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004385.4	+1	reviewed	p.Y469*	0.236	228	0%	293	48.5%	0	-	-	-	-	NULL
PCDHB16	57717	genome.wustl.edu	37	5	140562499	140562499	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020957.1	+1	reviewed	p.R122M	0.000	95	2.1%	89	38.2%	0	-	benign(0.002)	tolerated(0.06)	neutral(0.323)	PatternScan_CADHERIN_1,superfamily_Cadherin
OR12D3	81797	genome.wustl.edu	37	6	29236369	29236369	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000396806	-1	known	p.S273I	0.000	102	0%	123	51.2%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
NOTCH4	4855	genome.wustl.edu	37	6	32163293	32163293	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004557.3	-1	reviewed	p.R1978L	0.013	212	0%	192	41.1%	1	100%	possibly_damaging(0.83)	deleterious(0)	deleterious(0.760)	NULL
RING1	6015	genome.wustl.edu	37	6	33178980	33178980	+	Silent	SNP	A	A	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002931.3	+1	reviewed	p.T167	0.938	397	0%	292	40.1%	3	66.6%	-	-	-	NULL
GRIK2	2898	genome.wustl.edu	37	6	102503408	102503408	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021956.4	+1	reviewed	p.V839L	1.000	280	0%	265	39.6%	0	-	benign(0.045)	tolerated(0.15)	neutral(0.243)	HMMPfam_Lig_chan
COL10A1	1300	genome.wustl.edu	37	6	116442361	116442361	+	Silent	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000493.3	-1	reviewed	p.L306	0.253	54	0%	51	52.9%	1	0%	-	-	-	NULL
MAP3K5	4217	genome.wustl.edu	37	6	136972140	136972140	+	Silent	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005923.3	-1	reviewed	p.H590	0.785	22	0%	25	56%	1	0%	-	-	-	NULL
UTRN	7402	genome.wustl.edu	37	6	144835132	144835132	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007124.2	+1	reviewed	p.I1678L	1.000	199	0%	214	43.9%	0	-	possibly_damaging(0.663)	tolerated(0.51)	neutral(0.243)	HMMPfam_Spectrin,superfamily_Spectrin
SYTL3	94120	genome.wustl.edu	37	6	159084345	159084345	+	Silent	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001009991.2	+1	validated	p.R15	0.632	53	0%	58	46.6%	0	-	-	-	-	superfamily_FYVE/PHD zinc finger
FNDC1	84624	genome.wustl.edu	37	6	159650865	159650865	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032532.2	+1	validated	p.A400V	1.000	427	0%	425	40.7%	0	-	unknown(0)	deleterious(0.04)	-	HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like
SCIN	85477	genome.wustl.edu	37	7	12689092	12689092	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001112706.2	+1	validated	p.I628F	1.000	25	0%	24	37.5%	0	-	possibly_damaging(0.931)	deleterious(0.01)	deleterious(0.783)	HMMSmart_SM00262,HMMPfam_Gelsolin,superfamily_Actin depolymerizing proteins
SSPO	23145	genome.wustl.edu	37	7	149492657	149492657	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000378016	+1	known	p.N2146S	0.001	27	0%	33	33.3%	0	-	-	-	-	HMMPfam_F5_F8_type_C,HMMSmart_SM00231,superfamily_Galactose-binding domain-like
ABP1	26	genome.wustl.edu	37	7	150554356	150554356	+	Silent	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001091.2	+1	reviewed	p.P266	0.000	37	0%	34	41.2%	7	42.8%	-	-	-	superfamily_Amine oxidase N-terminal region
CSMD3	114788	genome.wustl.edu	37	8	113293531	113293531	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198123.1	-1	validated	p.R3127L	1.000	104	0%	149	28.9%	0	-	probably_damaging(0.997)	tolerated(0.57)	deleterious(0.472)	HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain
CSMD3	114788	genome.wustl.edu	37	8	114111160	114111160	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198123.1	-1	validated	p.S248T	1.000	94	0%	229	30.1%	0	-	unknown(0)	tolerated(0.75)	-	HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain
UGCG	7357	genome.wustl.edu	37	9	114695230	114695230	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003358.1	+1	reviewed	p.Y380N	1.000	142	0%	190	30.5%	1	0%	possibly_damaging(0.678)	deleterious(0)	deleterious(0.686)	NULL
LOC645954	645954	genome.wustl.edu	37	10	31001498	31001498	+	RNA	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_017086.3	+1	model	NULL	0.988	63	0%	99	46.5%	0	-	-	-	-	-
LRRC20	55222	genome.wustl.edu	37	10	72061120	72061120	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207119.1	-1	validated	p.P182H	0.037	61	0%	90	30%	1	0%	possibly_damaging(0.677)	deleterious(0)	deleterious(0.685)	NULL
PLCE1	51196	genome.wustl.edu	37	10	95790936	95790936	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016341.3	+1	reviewed	p.R45G	0.000	286	0%	290	41.4%	0	-	benign(0.01)	deleterious(0)	neutral(0.445)	NULL
NOLC1	9221	genome.wustl.edu	37	10	103917208	103917208	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004741.3	+1	validated	p.G113R	0.000	89	0%	112	45.5%	5	20%	unknown(0)	deleterious(0.03)	-	NULL
FAM160B1	57700	genome.wustl.edu	37	10	116606408	116606408	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020940.3	+1	validated	p.E497*	1.000	238	0%	264	50.4%	0	-	-	-	-	NULL
PTPRJ	5795	genome.wustl.edu	37	11	48146705	48146705	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002843.3	+1	reviewed	p.E354*	0.458	116	0%	131	46.6%	5	0%	-	-	-	HMMSmart_FN3
C11orf9	745	genome.wustl.edu	37	11	61539128	61539128	+	Silent	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127392.1	+1	validated	p.P299	0.999	114	0%	72	44.4%	0	-	-	-	-	NULL
SLC22A25	387601	genome.wustl.edu	37	11	62995935	62995935	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_199352.3	-1	validated	p.D168E	1.000	151	0%	180	36.1%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_MFS_1,superfamily_MFS general substrate transporter
SYVN1	84447	genome.wustl.edu	37	11	64900985	64900985	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_172230.2	-1	reviewed	p.Y30N	1.000	59	0%	76	35.5%	8	37.5%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
RNF214	257160	genome.wustl.edu	37	11	117152119	117152119	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001077239.1	+1	validated	p.R412P	1.000	235	0%	216	48.1%	7	71.4%	probably_damaging(0.97)	deleterious(0.01)	deleterious(0.818)	NULL
CHD4	1108	genome.wustl.edu	37	12	6701600	6701600	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001273.2	-1	reviewed	p.K969N	1.000	331	0.3%	408	59.1%	6	50%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_SNF2_N
MCRS1	10445	genome.wustl.edu	37	12	49953511	49953511	+	Splice_Site	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001012300.1	-1	validated	e10+1	1.000	47	0%	43	41.9%	2	100%	-	-	-	-
ACVR1B	91	genome.wustl.edu	37	12	52379078	52379078	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004302.3	+1	reviewed	p.D361G	0.996	118	0%	138	25.4%	2	0%	probably_damaging(0.961)	tolerated(0.1)	deleterious(0.691)	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase
CCT2	10576	genome.wustl.edu	37	12	69990984	69990984	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006431.2	+1	reviewed	p.G344E	1.000	255	0.4%	385	61%	72	51.3%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Cpn60_TCP1,superfamily_GroEL equatorial domain-like,superfamily_GroEL apical domain-like,superfamily_GroEL-intermediate domain like
PRKAB1	5564	genome.wustl.edu	37	12	120110179	120110179	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006253.4	+1	reviewed	p.R78P	1.000	118	0%	93	41.9%	0	-	possibly_damaging(0.628)	tolerated(0.26)	neutral(0.253)	NULL
LRRC43	254050	genome.wustl.edu	37	12	122670797	122670797	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098519.1	+1	validated	p.A158T	1.000	45	0%	33	30.3%	0	-	probably_damaging(0.98)	tolerated(0.13)	deleterious(0.676)	superfamily_Outer arm dynein light chain 1
DNAJC15	29103	genome.wustl.edu	37	13	43643082	43643082	+	Silent	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013238.2	+1	validated	p.R59	0.962	92	0%	80	38.8%	51	3.9%	-	-	-	NULL
LIPC	3990	genome.wustl.edu	37	15	58840773	58840773	+	Splice_Site	SNP	T	T	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000236.2	+1	reviewed	e6+2	1.000	21	0%	21	47.6%	0	-	-	-	-	-
GRIN2A	2903	genome.wustl.edu	37	16	10274194	10274194	+	Silent	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000833.3	-1	reviewed	p.A25	0.992	46	0%	34	61.8%	0	-	-	-	-	superfamily_Periplasmic binding protein-like I
MYH11	4629	genome.wustl.edu	37	16	15813109	15813109	+	Silent	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001040114.1	-1	reviewed	p.L1720	1.000	110	0%	116	50%	1	0%	-	-	-	HMMPfam_Myosin_tail_1
GTF3C1	2975	genome.wustl.edu	37	16	27503657	27503657	+	Splice_Site	SNP	A	A	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001520.3	-1	validated	e19+2	1.000	80	0%	98	45.9%	1	100%	-	-	-	-
HYDIN	54768	genome.wustl.edu	37	16	71098642	71098642	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032821.2	-1	validated	p.D726V	0.126	80	0%	44	90.9%	0	-	probably_damaging(0.999)	tolerated(0.07)	deleterious(0.809)	NULL
ZFHX3	463	genome.wustl.edu	37	16	72821683	72821683	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006885.3	-1	reviewed	p.Q3498*	1.000	49	0%	21	81%	1	100%	-	-	-	NULL
TP53	7157	genome.wustl.edu	37	17	7578235	7578235	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000546.4	-1	reviewed	p.Y205C	0.989	211	0%	109	87.2%	5	100%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	superfamily_p53-like transcription factors,HMMPfam_P53
ACSF2	80221	genome.wustl.edu	37	17	48539624	48539624	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025149.4	+1	validated	p.E196G	1.000	86	0%	37	75.7%	2	50%	probably_damaging(1)	deleterious(0.03)	deleterious(0.865)	HMMPfam_AMP-binding,superfamily_SSF56801
TEX14	56155	genome.wustl.edu	37	17	56676936	56676936	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198393.2	-1	reviewed	p.E590D	0.011	127	0.8%	77	74%	0	-	benign(0.15)	deleterious(0.01)	neutral(0.419)	NULL
ZNF431	170959	genome.wustl.edu	37	19	21365601	21365601	+	Silent	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_133473.2	+1	validated	p.N165	0.002	275	0%	248	33.1%	0	-	-	-	-	NULL
ZNF99	7652	genome.wustl.edu	37	19	22940411	22940411	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080409.1	-1	provisional	p.G676V	0.043	296	0.3%	306	34.6%	0	-	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667
LTBP4	8425	genome.wustl.edu	37	19	41118087	41118087	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000308370	+1	known	p.G830A	1.000	25	0%	22	86.4%	4	25%	probably_damaging(0.992)	deleterious(0.02)	deleterious(0.831)	HMMSmart_EGF_CA,superfamily_Grow_fac_recept,HMMPfam_EGF_CA
ARHGAP35	2909	genome.wustl.edu	37	19	47423229	47423229	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004491.4	+1	reviewed	p.R433*	0.723	193	0%	174	92.5%	0	-	-	-	-	HMMSmart_SM00441
PCSK2	5126	genome.wustl.edu	37	20	17434477	17434477	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002594.2	+1	reviewed	p.M326V	1.000	51	0%	66	42.4%	0	-	possibly_damaging(0.889)	deleterious(0)	deleterious(0.794)	HMMPfam_Peptidase_S8,superfamily_Subtilisin-like
ENSG00000211459	0	genome.wustl.edu	37	MT	1199	1199	+	RNA	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000389680	+1	known	NULL	NULL	65	1.5%	48	20.8%	2885	23.6%	-	-	-	-
ENSG00000210140	0	genome.wustl.edu	37	MT	5791	5791	+	RNA	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387405	-1	novel	NULL	NULL	78	0%	48	97.9%	2095	95.3%	-	-	-	-
ENSG00000210151	0	genome.wustl.edu	37	MT	7453	7453	+	RNA	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387416	-1	novel	NULL	NULL	94	0%	64	100%	7928	96.1%	-	-	-	-
HEPH	9843	genome.wustl.edu	37	X	65409629	65409629	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138737.3	+1	reviewed	p.H307Q	1.000	130	0%	180	45%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Cu-oxidase,superfamily_Cupredoxins
AWAT2	158835	genome.wustl.edu	37	X	69263462	69263462	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001002254.1	-1	reviewed	p.A113V	0.047	56	0%	50	56%	0	-	benign(0.103)	tolerated(0.49)	neutral(0.019)	HMMPfam_DAGAT
TEX11	56159	genome.wustl.edu	37	X	69945133	69945133	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003811.1	-1	reviewed	p.S317P	0.000	205	0%	249	41.8%	0	-	benign(0.278)	tolerated(0.35)	neutral(0.051)	HMMPfam_SPO22,superfamily_TPR-like
MAGT1	84061	genome.wustl.edu	37	X	77112976	77112980	+	Frame_Shift_Del	DEL	GAGCT	GAGCT	-	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	GAGCT	GAGCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032121.5	-1	reviewed	p.A168fs	1.000:1.000:1.000:1.000:0.989	-	-	-	-	-	-	-	-	-	HMMPfam_OST3_OST6,superfamily_Thioredoxin-like
FATE1	89885	genome.wustl.edu	37	X	150885858	150885858	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05A-01A-11W-A027-09	TCGA-AP-A05A-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033085.2	+1	reviewed	p.R74P	0.000	190	0.5%	277	30.7%	0	-	probably_damaging(0.998)	tolerated(0.11)	deleterious(0.746)	NULL
