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
UBR4	23352	genome.wustl.edu	37	1	19415445	19415445	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020765.2	-1	validated	p.P4746	0.949	52	0%	31	74.2%	23	73.9%	-	-	-	superfamily_ARM repeat
GNL2	29889	genome.wustl.edu	37	1	38041275	38041275	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013285.2	-1	validated	p.R355L	1.000	180	0%	279	18.3%	34	17.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_MMR_HSR1,superfamily_P-loop containing nucleoside triphosphate hydrolases
SZT2	23334	genome.wustl.edu	37	1	43902924	43902924	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015284.2	+1	predicted	p.D1140	0.959	225	0.4%	312	20.8%	23	21.7%	-	-	-	NULL
ADORA3	140	genome.wustl.edu	37	1	112045872	112045872	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020683.6	-1	reviewed	p.C35	1.000	132	0%	120	26.7%	5	0%	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
PDE4DIP	9659	genome.wustl.edu	37	1	144857694	144857694	+	Silent	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014644.4	-1	validated	p.G2120	0.975	453	0%	448	13.2%	1	0%	unknown(0)	-	-	NULL
NOTCH2NL	388677	genome.wustl.edu	37	1	145281658	145281658	+	Silent	SNP	C	C	A	rs67153225		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_203458.3	+1	validated	p.T196	1.000	337	0%	306	11.8%	183	3.8%	-	-	-	HMMSmart_SM00181,superfamily_EGF/Laminin
FMO5	2330	genome.wustl.edu	37	1	146658804	146658804	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001461.2	-1	reviewed	p.H426R	1.000	90	0%	119	38.7%	0	-	benign(0.12)	tolerated(0.31)	neutral(0.036)	HMMPfam_FMO-like
OR6N2	81442	genome.wustl.edu	37	1	158746588	158746588	+	Missense_Mutation	SNP	C	C	T	rs186539843	by1000genomes	TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005278.1	-1	provisional	p.V280I	0.998	222	0%	285	39.6%	0	-	possibly_damaging(0.947)	tolerated(0.1)	deleterious(0.677)	HMMPfam_7tm_1,superfamily_SSF81321
XPR1	9213	genome.wustl.edu	37	1	180849412	180849412	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004736.3	+1	validated	p.R670H	1.000	221	0%	277	41.9%	196	54%	benign(0.002)	tolerated(0.1)	neutral(0.286)	NULL
ENSG00000207472	0	genome.wustl.edu	37	1	182951421	182951422	+	RNA	INS	-	-	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000384741	-1	novel	NULL	0.102:0.108	-	-	-	-	-	-	-	-	-	-
KIF14	9928	genome.wustl.edu	37	1	200587334	200587334	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014875.2	-1	validated	p.S173C	0.000	175	0%	236	40.3%	2	0%	benign(0.11)	deleterious(0)	neutral(0.453)	NULL
SYT2	127833	genome.wustl.edu	37	1	202574721	202574721	+	Splice_Site	SNP	A	A	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001136504.1	-1	validated	e1+2	1.000	147	0%	156	22.4%	0	-	-	-	-	-
USH2A	7399	genome.wustl.edu	37	1	215853681	215853681	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_206933.2	-1	reviewed	p.P4035R	1.000	227	0%	236	41.9%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
ENAH	55740	genome.wustl.edu	37	1	225707077	225707077	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001008493.1	-1	validated	p.R209C	0.998	284	0%	280	23.9%	38	39.4%	unknown(0)	deleterious(0.01)	-	NULL
KIAA1383	54627	genome.wustl.edu	37	1	232941441	232941441	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019090.2	+1	validated	p.P224	0.000	16	0%	13	46.2%	0	-	-	-	-	NULL
ZNF496	84838	genome.wustl.edu	37	1	247463987	247463987	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032752.1	-1	provisional	p.R533Q	0.934	61	0%	74	23%	69	50.7%	probably_damaging(0.992)	tolerated(0.15)	deleterious(0.689)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667
OR2M7	391196	genome.wustl.edu	37	1	248487037	248487037	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004691.1	-1	provisional	p.Y278*	0.811	228	0%	307	31.9%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
HPCAL1	3241	genome.wustl.edu	37	2	10559978	10559978	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002149.2	+1	reviewed	p.K32R	1.000	73	0%	111	24.3%	122	35.2%	benign(0)	tolerated(0.18)	neutral(0.056)	superfamily_EF-hand
ADCY3	109	genome.wustl.edu	37	2	25062800	25062800	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004036.3	-1	reviewed	p.D433N	1.000	94	0%	91	24.2%	24	37.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase,PatternScan_GUANYLATE_CYCLASE_1
SOCS5	9655	genome.wustl.edu	37	2	46986362	46986362	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014011.4	+1	reviewed	p.H231	1.000	48	0%	92	29.3%	2	50%	-	-	-	NULL
UBTFL6	643615	genome.wustl.edu	37	2	98253113	98253113	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_001714896.2	-1	model	p.E380K	0.116	283	0%	435	26.4%	0	-	-	-	-	NULL
C1QL2	165257	genome.wustl.edu	37	2	119915425	119915425	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182528.3	-1	validated	p.D141H	0.776	14	0%	23	52.2%	0	-	benign(0.238)	tolerated(0.1)	neutral(0.310)	NULL
MBD5	55777	genome.wustl.edu	37	2	149227494	149227494	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018328.4	+1	reviewed	p.Q661L	1.000	207	0%	208	23.6%	13	23%	probably_damaging(0.976)	deleterious(0.01)	deleterious(0.824)	NULL
CPS1	1373	genome.wustl.edu	37	2	211540487	211540487	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001122633.1	+1	reviewed	p.N1405	0.993	119	0%	122	37.7%	2	50%	-	-	-	HMMPfam_MGS,superfamily_Methylglyoxal synthase-like
PER2	8864	genome.wustl.edu	37	2	239159207	239159207	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022817.2	-1	reviewed	p.Y1151C	1.000	228	0%	281	33.5%	4	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
UPK1B	7348	genome.wustl.edu	37	3	118906821	118906821	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006952.3	+1	reviewed	p.A90V	1.000	217	0%	215	27.9%	40	50%	benign(0)	tolerated(1)	-	HMMPfam_Tetraspannin
COL6A5	256076	genome.wustl.edu	37	3	130187863	130187863	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000512836	+1	known	p.P590L	1.000	296	0%	316	41.8%	0	-	-	-	-	HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like
PLSCR2	57047	genome.wustl.edu	37	3	146177698	146177698	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000497985	-1	known	p.V71	0.000	454	0%	440	25.5%	1	0%	-	-	-	NULL
MME	4311	genome.wustl.edu	37	3	154884781	154884781	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000902.3	+1	reviewed	p.H584R	1.000	476	0%	541	48.8%	3	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	"PatternScan_ZINC_PROTEASE,HMMPfam_Peptidase_M13,superfamily_Metalloproteases (""zincins"") catalytic domain"
PIK3CA	5290	genome.wustl.edu	37	3	178927980	178927980	+	Missense_Mutation	SNP	T	T	C	rs121913272		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.C420R	1.000	109	0%	182	51.6%	8	37.5%	probably_damaging(0.992)	tolerated(0.24)	deleterious(0.485)	HMMSmart_C2,HMMPfam_PI3K_C2,HMMSmart_PI3K_C2,superfamily_C2_CaLB
NIPAL1	152519	genome.wustl.edu	37	4	48032178	48032178	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207330.1	+1	provisional	p.V119L	1.000	381	0%	440	28.6%	1	0%	benign(0.001)	tolerated(0.3)	neutral(0.029)	HMMPfam_DUF803,superfamily_SSF103481
YTHDC1	91746	genome.wustl.edu	37	4	69184261	69184261	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031732.2	-1	validated	p.G600	1.000	234	0%	222	33.3%	210	39%	-	-	-	NULL
ABCG2	9429	genome.wustl.edu	37	4	89052285	89052285	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004827.2	-1	reviewed	p.T153	0.000	427	0%	460	38.9%	0	-	-	-	-	HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases
ANKRD50	57182	genome.wustl.edu	37	4	125592000	125592000	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020337.2	-1	validated	p.D811V	1.000	201	0%	194	46.9%	10	50%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Ank,superfamily_ANK
TIGD4	201798	genome.wustl.edu	37	4	153691274	153691274	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145720.2	-1	reviewed	p.E295*	1.000	170	0%	197	26.9%	0	-	-	-	-	HMMPfam_DDE
FHDC1	85462	genome.wustl.edu	37	4	153897117	153897117	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033393.2	+1	validated	p.R892W	0.997	23	0%	19	26.3%	3	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
RBM46	166863	genome.wustl.edu	37	4	155720031	155720031	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144979.3	+1	validated	p.Y239*	1.000	77	0%	95	26.3%	0	-	-	-	-	HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928
CDKN2AIP	55602	genome.wustl.edu	37	4	184367453	184367453	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017632.2	+1	provisional	p.G206*	0.136	174	0%	137	25.5%	26	42.3%	-	-	-	NULL
BRD9	65980	genome.wustl.edu	37	5	879974	879974	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_023924.4	-1	validated	p.S262L	1.000	327	0%	756	10.1%	93	15%	probably_damaging(0.998)	tolerated(0.31)	deleterious(0.501)	NULL
DROSHA	29102	genome.wustl.edu	37	5	31486602	31486602	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013235.4	-1	validated	p.P637R	1.000	229	0%	459	21.4%	8	12.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
CWC27	10283	genome.wustl.edu	37	5	64314116	64314116	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005869.2	+1	validated	p.K463Q	1.000	128	0%	83	75.9%	5	100%	probably_damaging(0.99)	tolerated(0.38)	neutral(0.459)	NULL
PCDHA2	56146	genome.wustl.edu	37	5	140176463	140176463	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018905.2	+1	reviewed	p.D638	0.002	95	0%	84	73.8%	0	-	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
OR2B3	442184	genome.wustl.edu	37	6	29054301	29054301	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005226.2	-1	validated	p.G242E	0.626	113	0%	228	24.6%	0	-	probably_damaging(0.988)	deleterious(0)	deleterious(0.882)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
GNL1	2794	genome.wustl.edu	37	6	30515142	30515142	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005275.3	-1	validated	p.P422H	1.000	142	0%	220	19.5%	156	20.5%	possibly_damaging(0.945)	deleterious(0)	deleterious(0.834)	HMMPfam_MMR_HSR1,superfamily_P-loop containing nucleoside triphosphate hydrolases
VPS52	6293	genome.wustl.edu	37	6	33219411	33219411	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022553.4	-1	reviewed	p.R637W	1.000	153	0%	279	19.4%	47	25.5%	probably_damaging(0.99)	deleterious(0)	deleterious(0.886)	NULL
GRM4	2914	genome.wustl.edu	37	6	34101142	34101142	+	Silent	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000841.1	-1	reviewed	p.R44	0.993	38	0%	46	21.7%	0	-	-	-	-	superfamily_Periplasmic binding protein-like I
TNFRSF21	27242	genome.wustl.edu	37	6	47252121	47252121	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014452.3	-1	reviewed	p.V266L	1.000	544	0%	813	18.6%	337	25.2%	possibly_damaging(0.466)	deleterious(0.02)	deleterious(0.536)	NULL
IMPG1	3617	genome.wustl.edu	37	6	76715183	76715183	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001563.2	-1	provisional	p.A319E	0.000	374	0.5%	591	22.8%	0	-	benign(0.011)	tolerated(1)	neutral(0.001)	HMMPfam_SEA,HMMSmart_SEA,superfamily_SSF82671
ZNF292	23036	genome.wustl.edu	37	6	87966983	87966983	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015021.1	+1	validated	p.N1212	0.848	81	0%	209	25.8%	7	28.5%	-	-	-	NULL
MANEA	79694	genome.wustl.edu	37	6	96034487	96034487	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024641.2	+1	validated	p.N58Y	0.007	187	0%	303	20.5%	0	-	benign(0)	tolerated(0.06)	neutral(0.323)	NULL
SLC22A16	85413	genome.wustl.edu	37	6	110778151	110778152	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	AG	AG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033125.2	-1	provisional	p.S41fs	0.976:1.000	-	-	-	-	-	-	-	-	-	NULL
HDAC2	3066	genome.wustl.edu	37	6	114267320	114267322	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	AAG	AAG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000432975	-1	known	p.L28in_frame_del	0.639:0.636:0.050	-	-	-	-	-	-	-	-	-	NULL
NHSL1	57224	genome.wustl.edu	37	6	138893048	138893050	+	In_Frame_Del	DEL	TCT	TCT	-	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	TCT	TCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000342260	-1	known	p.MKKE1in_frame_del*	1.000	-	-	-	-	-	-	-	-	-	NULL
PHF14	9678	genome.wustl.edu	37	7	11068419	11068421	+	In_Frame_Del	DEL	CTG	CTG	-	rs150121849	by1000genomes	TCGA-D1-A16N-01	TCGA-D1-A16N-01	CTG	CTG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000303905	+1	known	p.L478in_frame_del	0.853:1.000:0.999	-	-	-	-	-	-	-	-	-	HMMSmart_PHD
PDE1C	5137	genome.wustl.edu	37	7	31920390	31920390	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005020.1	-1	provisional	p.V71A	1.000	401	0%	399	27.1%	0	-	probably_damaging(0.987)	deleterious(0)	deleterious(0.881)	NULL
GLI3	2737	genome.wustl.edu	37	7	42005919	42005919	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000168.5	-1	reviewed	p.L918	1.000	37	0%	37	45.9%	16	62.5%	-	-	-	NULL
SLC25A40	55972	genome.wustl.edu	37	7	87465641	87465641	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018843.2	-1	validated	p.C314G	1.000	148	0%	137	35.8%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_Mitochondrial carrier,HMMPfam_Mito_carr
ZC3HAV1	56829	genome.wustl.edu	37	7	138794068	138794068	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020119.3	-1	reviewed	p.P4T	0.942	15	0%	13	46.2%	12	75%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
CSMD1	64478	genome.wustl.edu	37	8	3072068	3072068	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033225.5	-1	validated	p.I1607M	0.968	271	0%	400	19.5%	0	-	benign(0)	tolerated(0.6)	neutral(0.004)	HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain
FGF17	8822	genome.wustl.edu	37	8	21904064	21904064	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003867.2	+1	reviewed	p.F93V	0.996	199	0%	302	30.5%	3	0%	probably_damaging(0.976)	deleterious(0)	deleterious(0.863)	HMMPfam_FGF,HMMSmart_SM00442,superfamily_Cytokine
NEFM	4741	genome.wustl.edu	37	8	24772127	24772127	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005382.2	+1	reviewed	p.R274H	1.000	94	1.1%	169	20.7%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Filament
CHCHD7	79145	genome.wustl.edu	37	8	57127228	57127228	+	Splice_Site	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001011668.1	+1	validated	e2+2	1.000	410	0%	625	20.2%	0	-	-	-	-	-
MIR124-2	406908	genome.wustl.edu	37	8	65291812	65291812	+	RNA	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000385081	+1	known	NULL	0.936	121	0%	200	24.5%	0	-	-	-	-	-
VPS13B	157680	genome.wustl.edu	37	8	100865681	100865681	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017890.3	+1	reviewed	p.A3380V	0.083	110	0%	188	25%	8	25%	benign(0.004)	tolerated(0.07)	neutral(0.319)	NULL
CSMD3	114788	genome.wustl.edu	37	8	113662441	113662441	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198123.1	-1	validated	p.L1048I	0.977	175	0%	285	29.1%	0	-	benign(0.053)	tolerated(0.77)	neutral(0.005)	HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain
FAM135B	51059	genome.wustl.edu	37	8	139163582	139163582	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015912.3	-1	validated	p.S1046P	0.999	131	0.8%	188	58.5%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
INSL4	3641	genome.wustl.edu	37	9	5233789	5233789	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002195.1	+1	reviewed	p.R111H	0.000	191	0%	299	10.7%	0	-	possibly_damaging(0.807)	tolerated(0.16)	neutral(0.363)	NULL
PGM5	5239	genome.wustl.edu	37	9	71114229	71114229	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021965.3	+1	validated	p.Y522	0.997	190	0.5%	143	47.6%	7	57.1%	-	-	-	HMMPfam_PGM_PMM_IV,superfamily_Phosphoglucomutase C-terminal domain
GCNT1	2650	genome.wustl.edu	37	9	79117365	79117365	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001097633.1	+1	reviewed	p.V23A	0.621	132	0%	127	49.6%	2	100%	benign(0.001)	tolerated(0.4)	neutral(0.016)	NULL
SYK	6850	genome.wustl.edu	37	9	93650849	93650849	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003177.5	+1	reviewed	p.G592V	0.992	322	0%	215	47.4%	62	82.2%	benign(0.156)	tolerated(0.09)	neutral(0.310)	HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)
EPB41L4B	54566	genome.wustl.edu	37	9	111976038	111976038	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019114.3	-1	validated	p.E565V	0.994	240	0%	159	78.6%	0	-	probably_damaging(0.99)	deleterious(0)	deleterious(0.886)	NULL
EHMT1	79813	genome.wustl.edu	37	9	140637853	140637853	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000460843	+1	known	p.V285A	1.000	111	0%	85	48.2%	8	87.5%	probably_damaging(0.987)	deleterious(0)	deleterious(0.881)	NULL
WDFY4	57705	genome.wustl.edu	37	10	49939514	49939514	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020945.1	+1	validated	p.D497H	0.955	73	0%	37	78.4%	1	0%	benign(0.104)	tolerated(0.09)	neutral(0.304)	superfamily_ARM repeat
PTEN	5728	genome.wustl.edu	37	10	89692935	89692935	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.L140*	1.000	247	0%	194	73.7%	5	80%	-	-	-	HMMPfam_DSPc,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II
C10orf26	54838	genome.wustl.edu	37	10	104572427	104572427	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001083913.1	+1	validated	p.S144I	1.000	138	0%	91	53.8%	28	60.7%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	NULL
RBM20	282996	genome.wustl.edu	37	10	112581679	112581679	+	Splice_Site	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000465774	+1	known	NULL	1.000	97	0%	64	35.9%	0	-	-	-	-	-
ATRNL1	26033	genome.wustl.edu	37	10	117093845	117093845	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207303.2	+1	validated	p.C1031R	1.000	331	0%	172	51.7%	6	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMSmart_SM00181,superfamily_EGF/Laminin
MRGPRE	116534	genome.wustl.edu	37	11	3249426	3249428	+	In_Frame_Del	DEL	GCA	GCA	-	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	GCA	GCA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039165.2	-1	validated	p.L200in_frame_del	0.003:0.008:0.062	-	-	-	-	-	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
MRGPRE	116534	genome.wustl.edu	37	11	3249607	3249623	+	Frame_Shift_Del	DEL	GGTGGTCAGGTGGCGTG	GGTGGTCAGGTGGCGTG	-	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	GGTGGTCAGGTGGCGTG	GGTGGTCAGGTGGCGTG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039165.2	-1	validated	p.P135fs	0.009:0.008:0.000:0.000:0.012:0.003:0.001:0.000:0.004:0.051:0.044:0.039:0.002:0.001:0.005:0.052:0.587	-	-	-	-	-	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
OR51T1	401665	genome.wustl.edu	37	11	4903148	4903148	+	Missense_Mutation	SNP	A	A	G	rs34690738		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004759.1	+1	provisional	p.T34A	0.991	300	0%	283	25.1%	0	-	possibly_damaging(0.787)	deleterious(0.03)	deleterious(0.659)	NULL
EIF3F	8665	genome.wustl.edu	37	11	8014442	8014442	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003754.2	+1	validated	p.T175M	1.000	106	0%	100	20%	353	22.9%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Mov34,HMMSmart_JAB_MPN
ACCSL	390110	genome.wustl.edu	37	11	44073241	44073241	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031854.2	+1	validated	p.A248	0.011	732	0%	717	44.4%	0	-	-	-	-	HMMPfam_Aminotran_1_2,superfamily_PLP-dependent transferases
ARHGAP1	392	genome.wustl.edu	37	11	46700689	46700689	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004308.2	-1	provisional	p.A406	0.009	336	0%	358	13.7%	75	20%	-	-	-	HMMPfam_RhoGAP,HMMSmart_RhoGAP,superfamily_Rho_GAP
ALKBH8	91801	genome.wustl.edu	37	11	107431621	107431621	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000417449	-1	known	p.A2D	0.019	173	0%	189	30.7%	3	0%	unknown(0)	-	-	NULL
NPAT	4863	genome.wustl.edu	37	11	108061222	108061222	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002519.2	-1	validated	p.M99T	1.000	269	0%	325	29.8%	2	50%	possibly_damaging(0.722)	deleterious(0.01)	deleterious(0.667)	NULL
GPRC5A	9052	genome.wustl.edu	37	12	13061271	13061271	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003979.3	+1	reviewed	p.V30I	1.000	72	0%	104	35.6%	7	42.8%	benign(0.009)	tolerated(0.23)	neutral(0.042)	NULL
COL2A1	1280	genome.wustl.edu	37	12	48374742	48374742	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001844.4	-1	reviewed	p.G825R	1.000	76	0%	66	43.9%	15	40%	unknown(0)	deleterious(0)	-	HMMPfam_Collagen
ADCY6	112	genome.wustl.edu	37	12	49162494	49162494	+	Silent	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015270.3	-1	reviewed	p.T1129	1.000	137	0.7%	176	14.8%	18	16.6%	-	-	-	HMMPfam_Guanylate_cyc,HMMSmart_SM00044,superfamily_Adenylyl and guanylyl cyclase catalytic domain
ASIC1	41	genome.wustl.edu	37	12	50474357	50474357	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020039.2	+1	reviewed	p.I428F	1.000	219	0%	239	27.2%	2	0%	benign(0.002)	tolerated(0.29)	neutral(0.029)	HMMPfam_ASC
KRT73	319101	genome.wustl.edu	37	12	53011883	53011883	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_175068.2	-1	reviewed	p.K142N	0.998	199	0%	212	36.3%	0	-	possibly_damaging(0.82)	deleterious(0)	deleterious(0.755)	HMMPfam_Filament
SOAT2	8435	genome.wustl.edu	37	12	53499744	53499744	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003578.3	+1	reviewed	p.G130D	0.923	102	0%	109	25.7%	0	-	probably_damaging(0.992)	deleterious(0.01)	deleterious(0.853)	NULL
ACACB	32	genome.wustl.edu	37	12	109689902	109689902	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001093.3	+1	reviewed	p.R1948*	1.000	148	0%	155	26.5%	9	0%	-	-	-	HMMPfam_Carboxyl_trans,superfamily_ClpP/crotonase
OAS2	4939	genome.wustl.edu	37	12	113442836	113442836	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016817.2	+1	reviewed	p.N426I	0.000	204	0%	266	46.6%	36	55.5%	possibly_damaging(0.832)	deleterious(0.01)	deleterious(0.723)	HMMPfam_NTP_transf_2,superfamily_Nucleotidyltransferase
POLE	5426	genome.wustl.edu	37	12	133249804	133249804	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006231.2	-1	validated	p.Y473	0.768	280	0%	294	22.1%	67	44.7%	-	-	-	HMMSmart_POLBc,superfamily_RNaseH_fold
ENSG00000187721	0	genome.wustl.edu	37	13	19601018	19601018	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000433887	-1	known	p.Q84H	0.784	26	0%	22	72.7%	0	-	possibly_damaging(0.823)	deleterious(0)	deleterious(0.756)	HMMPfam_GTF2I
RB1	5925	genome.wustl.edu	37	13	48947629	48947629	+	Splice_Site	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000321.2	+1	reviewed	e12+1	1.000	135	0%	88	78.4%	0	-	-	-	-	-
PCDH9	5101	genome.wustl.edu	37	13	67205537	67205537	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_203487.2	-1	reviewed	p.R1049C	1.000	106	0%	65	12.3%	0	-	possibly_damaging(0.912)	deleterious(0)	deleterious(0.808)	NULL
TBC1D4	9882	genome.wustl.edu	37	13	75936666	75936666	+	Silent	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014832.2	-1	validated	p.N192	0.069	161	0%	113	44.2%	10	70%	-	-	-	superfamily_PH domain-like
YY1	7528	genome.wustl.edu	37	14	100705788	100705790	+	In_Frame_Del	DEL	CCA	CCA	-	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	CCA	CCA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003403.3	+1	reviewed	p.H73in_frame_del	0.016:0.090:0.106	-	-	-	-	-	-	-	-	-	NULL
HERC2	8924	genome.wustl.edu	37	15	28408246	28408246	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004667.4	-1	reviewed	p.Y3580	0.997	55	0%	30	43.3%	16	50%	-	-	-	NULL
JMJD7-PLA2G4B	8681	genome.wustl.edu	37	15	42131176	42131176	+	RNA	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_015346.1	+1	validated	NULL	0.173	74	0%	47	48.9%	0	-	-	-	-	-
GABPB1	2553	genome.wustl.edu	37	15	50578281	50578281	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005254.5	-1	reviewed	p.E340A	1.000	282	0%	198	75.3%	10	100%	benign(0.123)	deleterious(0)	neutral(0.455)	NULL
ZNF768	79724	genome.wustl.edu	37	16	30535975	30535975	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024671.3	-1	validated	p.R496C	1.000	63	0%	46	39.1%	117	59.8%	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667
CMTM2	146225	genome.wustl.edu	37	16	66613719	66613719	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144673.2	+1	reviewed	p.R70H	0.062	73	0%	42	47.6%	0	-	probably_damaging(0.999)	deleterious(0.05)	deleterious(0.836)	NULL
INPP5K	51763	genome.wustl.edu	37	17	1413080	1413080	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016532.3	-1	reviewed	p.R92H	0.999	97	0%	89	58.4%	13	53.8%	probably_damaging(1)	tolerated(0.08)	deleterious(0.800)	HMMSmart_SM00128,HMMPfam_Exo_endo_phos,superfamily_DNase I-like
SPATA22	84690	genome.wustl.edu	37	17	3372583	3372583	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032598.4	-1	validated	p.T13A	1.000	184	0%	142	47.9%	0	-	probably_damaging(0.979)	deleterious(0)	deleterious(0.867)	NULL
TRPV3	162514	genome.wustl.edu	37	17	3436060	3436060	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145068.2	-1	reviewed	p.R319H	0.847	195	0%	94	45.7%	4	75%	benign(0.038)	tolerated(0.24)	neutral(0.040)	superfamily_Ankyrin repeat
TP53	7157	genome.wustl.edu	37	17	7577565	7577565	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000546.4	-1	reviewed	p.N239S	1.000	166	0%	93	75.3%	228	96.4%	benign(0.236)	deleterious(0.02)	neutral(0.407)	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53
MYH2	4620	genome.wustl.edu	37	17	10447073	10447073	+	Silent	SNP	G	G	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001100112.1	-1	reviewed	p.A232	1.000	301	0%	202	49%	0	-	-	-	-	HMMPfam_Myosin_head,HMMSmart_MYSc,superfamily_SSF52540
MAP2K4	6416	genome.wustl.edu	37	17	12011162	12011184	+	Frame_Shift_Del	DEL	AATATGTATATAGTGTATTAGAT	AATATGTATATAGTGTATTAGAT	-	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	AATATGTATATAGTGTATTAGAT	AATATGTATATAGTGTATTAGAT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003010.2	+1	reviewed	p.K190fs	1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999:1.000:1.000:1.000:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase
TRIM16	10626	genome.wustl.edu	37	17	15535954	15535954	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006470.3	-1	reviewed	p.T295I	0.157	311	0%	212	9.9%	13	15.3%	probably_damaging(0.983)	tolerated(0.07)	deleterious(0.748)	NULL
DRG2	1819	genome.wustl.edu	37	17	18003953	18003953	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001388.3	+1	reviewed	p.Q204R	1.000	159	0%	109	54.1%	57	54.3%	benign(0.004)	tolerated(0.55)	neutral(0.007)	superfamily_P-loop containing nucleoside triphosphate hydrolases
RNF112	7732	genome.wustl.edu	37	17	19316905	19316905	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007148.4	+1	reviewed	p.V246M	1.000	157	0%	78	10.3%	0	-	-	-	-	HMMPfam_GBP,superfamily_SSF52540
KSR1	8844	genome.wustl.edu	37	17	25928932	25928932	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014238.1	+1	validated	p.G371	0.767	199	0%	151	56.3%	0	-	-	-	-	NULL
SGCA	6442	genome.wustl.edu	37	17	48247549	48247549	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000023.2	+1	reviewed	p.G265C	0.998	209	0%	131	46.6%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Sarcoglycan_2
BRIP1	83990	genome.wustl.edu	37	17	59820418	59820418	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032043.1	-1	reviewed	p.V779I	1.000	257	0%	160	10.6%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMSmart_SM00491
RPTOR	57521	genome.wustl.edu	37	17	78727893	78727893	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020761.2	+1	reviewed	p.C246	0.381	148	0%	113	12.4%	18	27.7%	-	-	-	NULL
GNAL	2774	genome.wustl.edu	37	18	11867209	11867209	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182978.2	+1	validated	p.W298*	1.000	581	0%	722	38.6%	8	50%	-	-	-	HMMPfam_G-alpha,superfamily_SSF52540
SLC14A2	8170	genome.wustl.edu	37	18	43247878	43247878	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007163.3	+1	validated	p.G600C	1.000	305	0%	342	28.7%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_UT
ZNF532	55205	genome.wustl.edu	37	18	56621000	56621000	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018181.4	+1	validated	p.Y1040C	1.000	139	0%	106	33%	92	29.3%	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2
ENSG00000207072	0	genome.wustl.edu	37	18	66526207	66526207	+	RNA	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000384344	+1	novel	NULL	0.000	43	0%	36	52.8%	0	-	-	-	-	-
ARID3A	1820	genome.wustl.edu	37	19	965062	965062	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005224.2	+1	reviewed	p.A394T	0.675	45	0%	36	33.3%	4	50%	benign(0.008)	tolerated(0.71)	neutral(0.002)	NULL
SAMD4B	55095	genome.wustl.edu	37	19	39847697	39847697	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018028.2	+1	provisional	p.I55N	1.000	89	0%	58	13.8%	105	13.3%	probably_damaging(0.984)	deleterious(0.01)	deleterious(0.836)	NULL
PTGIR	5739	genome.wustl.edu	37	19	47127140	47127140	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000960.3	-1	reviewed	p.V115M	0.981	4	0.000	6	0.833	2	0%	probably_damaging(0.994)	deleterious(0)	deleterious(0.897)	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321
PLCB4	5332	genome.wustl.edu	37	20	9453459	9453459	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000933.3	+1	reviewed	p.S1113G	1.000	221	0%	293	23.5%	7	0%	possibly_damaging(0.636)	tolerated(0.12)	deleterious(0.483)	NULL
NINL	22981	genome.wustl.edu	37	20	25459720	25459720	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025176.4	-1	validated	p.E680D	0.885	58	0%	56	32.1%	10	10%	probably_damaging(0.985)	tolerated(0.06)	deleterious(0.754)	NULL
RPRD1B	58490	genome.wustl.edu	37	20	36686026	36686026	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021215.3	+1	validated	p.P170T	1.000	123	0%	169	28.4%	3	33.3%	benign(0)	tolerated(0.23)	neutral(0.042)	NULL
RBM11	54033	genome.wustl.edu	37	21	15599471	15599471	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144770.3	+1	validated	p.Q235*	0.096	422	0%	441	27.7%	2	0%	-	-	-	NULL
GART	2618	genome.wustl.edu	37	21	34889432	34889432	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000819.4	-1	reviewed	p.T657	0.945	143	0%	154	22.7%	50	34%	-	-	-	HMMPfam_AIRS_C,superfamily_PurM C-terminal domain-like
NRK	203447	genome.wustl.edu	37	X	105167391	105167391	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16N-01	TCGA-D1-A16N-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198465.2	+1	validated	p.D964	0.006	226	0%	173	80.9%	0	-	-	-	-	NULL
