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
PLEKHN1	84069	genome.wustl.edu	37	1	905935	905935	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032129.2	+1	validated	p.A122V	0.793	10	0%	12	41.7%	1	0%	possibly_damaging(0.527)	tolerated(0.06)	deleterious(0.500)	HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729
C1orf159	54991	genome.wustl.edu	37	1	1019487	1019487	+	Missense_Mutation	SNP	T	T	C	rs147852840	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000379339	-1	known	p.M286V	0.000	5	0.000	8	0.750	2	0%	unknown(0)	deleterious(0)	-	NULL
TP73	7161	genome.wustl.edu	37	1	3646013	3646013	+	Splice_Site	DEL	G	G	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005427.2	+1	reviewed	e9+1	1.000	-	-	-	-	-	-	-	-	-	-
CEP104	9731	genome.wustl.edu	37	1	3740038	3740038	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014704.3	-1	validated	p.A818V	1.000	114	0%	113	43.4%	36	41.6%	possibly_damaging(0.869)	tolerated(0.1)	deleterious(0.623)	NULL
PHF13	148479	genome.wustl.edu	37	1	6680349	6680349	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153812.2	+1	validated	p.R210*	1.000	18	0%	10	60%	12	50%	-	-	-	NULL
SLC2A5	6518	genome.wustl.edu	37	1	9097982	9097982	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003039.2	-1	validated	p.V426M	0.980	20	0.000	9	0.667	10	10%	probably_damaging(0.982)	deleterious(0)	deleterious(0.871)	HMMPfam_Sugar_tr,superfamily_MFS_gen_substrate_transporter
CLSTN1	22883	genome.wustl.edu	37	1	9811715	9811715	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001009566.1	-1	validated	p.N155	0.976	59	0%	61	50.8%	30	53.3%	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
PRDM2	7799	genome.wustl.edu	37	1	14105787	14105787	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012231.4	+1	reviewed	p.R499	0.122	131	0%	128	32.8%	3	33.3%	-	-	-	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
CTRC	11330	genome.wustl.edu	37	1	15771139	15771139	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007272.2	+1	reviewed	p.Q178*	1.000	47	0%	66	43.9%	0	-	-	-	-	HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases
AGMAT	79814	genome.wustl.edu	37	1	15909853	15909853	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024758.3	-1	validated	p.L104F	0.976	23	0%	35	51.4%	6	50%	probably_damaging(0.958)	deleterious(0)	deleterious(0.846)	HMMPfam_Arginase,superfamily_SSF52768
LOC645317	645317	genome.wustl.edu	37	1	15931403	15931403	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_934920.4	+1	model	p.P140	0.921	43	0%	49	53.1%	1	0%	-	-	-	HMMPfam_CHCH
SPEN	23013	genome.wustl.edu	37	1	16256920	16256920	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015001.2	+1	reviewed	p.A1395	0.118	264	0%	279	45.5%	0	-	-	-	-	NULL
ARHGEF19	128272	genome.wustl.edu	37	1	16534495	16534495	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153213.3	-1	provisional	p.R213Q	0.221	17	0%	18	27.8%	21	66.6%	possibly_damaging(0.883)	deleterious(0.02)	deleterious(0.728)	NULL
C1orf201	90529	genome.wustl.edu	37	1	24706160	24706160	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178122.3	-1	predicted	p.A102T	1.000	159	0%	98	44.9%	6	66.6%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	NULL
CNKSR1	10256	genome.wustl.edu	37	1	26514789	26514789	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006314.2	+1	reviewed	p.R507*	0.291	26	0%	29	31%	37	24.3%	-	-	-	NULL
GPATCH3	63906	genome.wustl.edu	37	1	27219197	27219197	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000445019	-1	known	p.S49L	0.000	201	0.5%	228	50.4%	28	46.4%	-	-	-	NULL
SLC9A1	6548	genome.wustl.edu	37	1	27429791	27429791	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003047.3	-1	validated	p.R500W	1.000	22	0%	22	59.1%	9	66.6%	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMPfam_Na_H_Exchanger
PHACTR4	65979	genome.wustl.edu	37	1	28786746	28786746	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_023923.3	+1	reviewed	p.R82*	1.000	86	0%	67	47.8%	5	0%	-	-	-	HMMSmart_RPEL
PTPRU	10076	genome.wustl.edu	37	1	29642617	29642617	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005704.3	+1	reviewed	p.R1166H	1.000	54	0%	22	59.1%	12	25%	probably_damaging(0.996)	deleterious(0.01)	deleterious(0.867)	superfamily_(Phosphotyrosine protein) phosphatases II
LCK	3932	genome.wustl.edu	37	1	32745764	32745764	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001042771.1	+1	reviewed	p.G427E	1.000	34	0%	62	45.2%	4	25%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)
CSMD2	114784	genome.wustl.edu	37	1	34128645	34128645	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052896.3	-1	validated	p.R1327H	1.000	129	0%	104	46.2%	0	-	probably_damaging(0.974)	tolerated(0.15)	deleterious(0.657)	HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain
SFPQ	6421	genome.wustl.edu	37	1	35654848	35654848	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005066.2	-1	validated	p.D517	1.000	127	0%	80	38.8%	375	44.5%	-	-	-	superfamily_RNA-binding domain RBD
TFAP2E	339488	genome.wustl.edu	37	1	36060128	36060128	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178548.3	+1	validated	p.G394S	1.000	141	0%	181	41.4%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_TF_AP-2
MRPS15	64960	genome.wustl.edu	37	1	36923545	36923545	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031280.3	-1	reviewed	p.E141	0.992	205	0%	144	40.3%	414	43.4%	-	-	-	HMMPfam_Ribosomal_S15,superfamily_S15/NS1 RNA-binding domain
GRIK3	2899	genome.wustl.edu	37	1	37324832	37324832	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000831.3	-1	reviewed	p.Y327	0.774	62	0%	52	34.6%	0	-	-	-	-	HMMPfam_ANF_receptor,superfamily_SSF53822
SCMH1	22955	genome.wustl.edu	37	1	41512120	41512120	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031694.2	-1	validated	p.T476I	0.105	46	0%	57	50.9%	39	51.2%	possibly_damaging(0.799)	tolerated(0.09)	deleterious(0.597)	NULL
SZT2	23334	genome.wustl.edu	37	1	43891763	43891763	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015284.2	+1	predicted	p.L153P	1.000	111	0%	71	40.8%	0	-	probably_damaging(0.962)	tolerated(0.17)	neutral(0.464)	NULL
MUTYH	4595	genome.wustl.edu	37	1	45799121	45799121	+	Silent	SNP	G	G	A	rs121908380	byCluster;byFrequency	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000448481	-1	known	p.R102*	0.791	79	0%	114	43.9%	29	41.3%	-	-	-	superfamily_DNA-glycosylase
OSBPL9	114883	genome.wustl.edu	37	1	52251549	52251549	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000447887	+1	known	p.C650R	1.000	279	0%	196	41.8%	41	46.3%	-	-	-	HMMPfam_Oxysterol_BP
NRD1	4898	genome.wustl.edu	37	1	52280280	52280280	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002525.2	-1	validated	p.V589A	1.000	168	0%	127	38.6%	19	47.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Peptidase_M16_C
CC2D1B	200014	genome.wustl.edu	37	1	52827212	52827213	+	In_Frame_Ins	INS	-	-	TCC	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032449.1	-1	validated	p.98in_frame_insE	0.997:0.999	-	-	-	-	-	-	-	-	-	NULL
FAM159A	348378	genome.wustl.edu	37	1	53122589	53122589	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001042693.1	+1	validated	p.Q150H	0.001	292	0.3%	250	48.4%	3	33.3%	probably_damaging(0.981)	deleterious(0)	deleterious(0.870)	NULL
DIO1	1733	genome.wustl.edu	37	1	54359887	54359887	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039715.1	+1	reviewed	p.G2R	0.994	111	0%	120	38.3%	0	-	possibly_damaging(0.886)	deleterious(0.01)	deleterious(0.752)	NULL
KANK4	163782	genome.wustl.edu	37	1	62734038	62734038	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181712.4	-1	validated	p.Q718*	0.006	25	0%	31	48.4%	16	25%	-	-	-	NULL
IL12RB2	3595	genome.wustl.edu	37	1	67838135	67838135	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001559.2	+1	reviewed	p.Y492	0.000	307	0%	247	24.7%	1	0%	-	-	-	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
SRSF11	9295	genome.wustl.edu	37	1	70697950	70697950	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000370949	+1	known	p.G53*	1.000	103	0%	80	46.3%	7	14.2%	-	-	-	NULL
SSX2IP	117178	genome.wustl.edu	37	1	85113137	85113137	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014021.3	-1	reviewed	p.V608	0.101	246	0%	166	50%	22	27.2%	-	-	-	NULL
LRRC8B	23507	genome.wustl.edu	37	1	90058350	90058350	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001134476.1	+1	validated	p.G720	1.000	351	0%	248	41.1%	4	75%	-	-	-	HMMSmart_LRR_TYP,superfamily_SSF52058
PALMD	54873	genome.wustl.edu	37	1	100152744	100152744	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017734.4	+1	validated	p.K171	1.000	91	0%	57	36.8%	2	50%	-	-	-	NULL
KIAA1324	57535	genome.wustl.edu	37	1	109742532	109742532	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020775.3	+1	validated	p.A853V	0.021	74	0%	91	40.7%	849	49.8%	benign(0.001)	tolerated(0.22)	neutral(0.042)	superfamily_Mannose 6-phosphate receptor domain
CELSR2	1952	genome.wustl.edu	37	1	109814989	109814989	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001408.2	+1	reviewed	p.S2672	0.335	75	0%	60	45%	46	54.3%	-	-	-	NULL
CELSR2	1952	genome.wustl.edu	37	1	109815318	109815318	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001408.2	+1	reviewed	p.S2704N	0.005	38	0%	34	17.6%	43	23.2%	possibly_damaging(0.494)	tolerated(0.43)	neutral(0.178)	NULL
PSRC1	84722	genome.wustl.edu	37	1	109824253	109824253	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001032291.2	-1	reviewed	p.S169	0.003	87	0%	71	53.5%	37	48.6%	-	-	-	NULL
GPR61	83873	genome.wustl.edu	37	1	110086063	110086063	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031936.4	+1	validated	p.R140H	1.000	53	0%	65	43.1%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like
GSTM4	2948	genome.wustl.edu	37	1	110199040	110199040	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000850.4	+1	reviewed	p.I10S	1.000	77	0%	68	42.6%	50	28%	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	HMMPfam_GST_N,superfamily_Thioredoxin-like
KCNA3	3738	genome.wustl.edu	37	1	111216076	111216076	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002232.3	-1	reviewed	p.P452	0.949	144	0%	71	22.5%	1	0%	-	-	-	HMMPfam_Ion_trans,superfamily_SSF81324
KCNA3	3738	genome.wustl.edu	37	1	111216708	111216708	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002232.3	-1	reviewed	p.L242	1.000	107	0%	47	21.3%	0	-	-	-	-	superfamily_SSF81324
LRIG2	9860	genome.wustl.edu	37	1	113636070	113636070	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014813.1	+1	provisional	p.P133	1.000	150	0.7%	79	40.5%	1	0%	-	-	-	superfamily_SSF52047
SV2A	9900	genome.wustl.edu	37	1	149881044	149881044	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014849.3	-1	validated	p.W420L	1.000	94	0%	63	52.4%	0	-	benign(0.008)	tolerated(0.67)	neutral(0.003)	HMMPfam_MFS_1,superfamily_MFS general substrate transporter
ANP32E	81611	genome.wustl.edu	37	1	150204166	150204166	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030920.3	-1	validated	p.N51	0.994	116	0%	94	38.3%	62	51.6%	-	-	-	superfamily_L domain-like
ADAMTSL4	54507	genome.wustl.edu	37	1	150529441	150529441	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019032.4	+1	reviewed	p.G592	0.658	169	0%	48	39.6%	0	-	-	-	-	HMMPfam_ADAM_spacer1
RPTN	126638	genome.wustl.edu	37	1	152128002	152128002	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001122965.1	-1	validated	p.Q525*	0.792	1577	0%	1771	44%	0	-	-	-	-	NULL
FLG	2312	genome.wustl.edu	37	1	152276312	152276312	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002016.1	-1	reviewed	p.Q3684*	0.000	504	0%	556	43%	0	-	-	-	-	NULL
FLG2	388698	genome.wustl.edu	37	1	152324558	152324559	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	TG	TG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001014342.2	-1	provisional	p.H1901fs	0.000:0.000	-	-	-	-	-	-	-	-	-	NULL
CRNN	49860	genome.wustl.edu	37	1	152383073	152383073	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016190.2	-1	reviewed	p.A162V	0.001	241	0%	322	46.6%	0	-	possibly_damaging(0.808)	deleterious(0)	deleterious(0.748)	NULL
RXFP4	339403	genome.wustl.edu	37	1	155911908	155911908	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181885.2	+1	validated	p.S136	0.179	19	0%	39	35.9%	7	85.7%	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
BCAN	63827	genome.wustl.edu	37	1	156628449	156628449	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021948.3	+1	validated	p.R851H	1.000	54	0%	56	53.6%	0	-	probably_damaging(1)	tolerated(0.08)	deleterious(0.800)	HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain
DEDD	9191	genome.wustl.edu	37	1	161092286	161092286	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039711.1	-1	reviewed	p.Y203C	1.000	119	0%	150	44.7%	34	76.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
GPR161	23432	genome.wustl.edu	37	1	168066278	168066278	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153832.1	-1	provisional	p.T189	0.000	63	0%	80	46.3%	2	100%	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
KIFAP3	22920	genome.wustl.edu	37	1	169930291	169930291	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014970.2	-1	reviewed	p.R690H	1.000	156	0%	113	47.8%	27	37%	probably_damaging(0.998)	tolerated(0.05)	deleterious(0.820)	HMMPfam_KAP
SEC16B	89866	genome.wustl.edu	37	1	177930832	177930832	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033127.2	-1	validated	p.R227H	0.934	64	0%	52	36.5%	3	0%	benign(0.006)	tolerated(0.67)	neutral(0.003)	NULL
KCNT2	343450	genome.wustl.edu	37	1	196342344	196342344	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198503.2	-1	validated	p.A443	1.000	166	0%	50	52%	0	-	-	-	-	HMMPfam_BK_channel_a,superfamily_NAD(P)-binding Rossmann-fold domains
KIF21B	23046	genome.wustl.edu	37	1	200956183	200956183	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017596.2	-1	provisional	p.D1185	1.000	91	0%	77	41.6%	0	-	-	-	-	superfamily_WD40_like
KIF21B	23046	genome.wustl.edu	37	1	200977986	200977986	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017596.2	-1	provisional	p.L120I	1.000	132	0%	116	48.3%	0	-	probably_damaging(0.987)	tolerated(0.21)	deleterious(0.480)	HMMPfam_Kinesin,HMMSmart_KISc,superfamily_SSF52540
TMEM81	388730	genome.wustl.edu	37	1	205053387	205053387	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_203376.1	-1	validated	p.L21S	0.003	163	0%	131	49.6%	2	50%	benign(0.008)	deleterious(0.01)	neutral(0.406)	NULL
SLC45A3	85414	genome.wustl.edu	37	1	205632155	205632155	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033102.2	-1	validated	p.A255V	0.993	15	0%	16	56.2%	4	50%	benign(0.005)	deleterious(0.05)	neutral(0.345)	superfamily_MFS general substrate transporter
FAIM3	9214	genome.wustl.edu	37	1	207087160	207087160	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142472.1	-1	validated	p.A106V	0.000	153	0%	249	54.6%	0	-	benign(0)	tolerated(1)	-	HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin
C1orf65	164127	genome.wustl.edu	37	1	223568645	223568645	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152610.2	+1	validated	p.L610	0.000	94	0%	67	52.2%	0	-	-	-	-	NULL
LOC100130093	100130093	genome.wustl.edu	37	1	227920568	227920568	+	RNA	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_024485.1	+1	validated	NULL	0.001	11	0%	13	46.2%	1	100%	-	-	-	-
OBSCN	84033	genome.wustl.edu	37	1	228520620	228520620	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098623.1	+1	reviewed	p.A5238T	1.000	17	0%	16	56.2%	0	-	probably_damaging(0.955)	tolerated(0.06)	deleterious(0.721)	NULL
OBSCN	84033	genome.wustl.edu	37	1	228563735	228563735	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098623.1	+1	reviewed	p.D7605N	0.999	19	0%	19	47.4%	5	20%	benign(0.355)	tolerated(0.06)	neutral(0.435)	HMMSmart_SM00060,superfamily_Fibronectin type III
DISC1	27185	genome.wustl.edu	37	1	231837748	231837748	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018662.2	+1	reviewed	p.V365	0.758	73	0%	27	44.4%	1	0%	-	-	-	NULL
KIAA1804	84451	genome.wustl.edu	37	1	233514835	233514835	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032435.2	+1	validated	p.A695T	0.348	178	0%	138	41.3%	0	-	benign(0)	tolerated(0.5)	neutral(0.010)	NULL
LYST	1130	genome.wustl.edu	37	1	235926125	235926125	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000081.2	-1	reviewed	p.R2050W	0.966	183	0%	139	27.3%	0	-	possibly_damaging(0.9)	-	-	NULL
ACTN2	88	genome.wustl.edu	37	1	236902683	236902683	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001103.2	+1	reviewed	p.L320	1.000	218	0%	254	50%	0	-	-	-	-	HMMPfam_Spectrin,superfamily_Spectrin repeat
OR2M5	127059	genome.wustl.edu	37	1	248309055	248309055	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004690.1	+1	provisional	p.C202	0.000	652	0%	681	41.4%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
KCNF1	3754	genome.wustl.edu	37	2	11053432	11053432	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002236.4	+1	reviewed	p.I294V	1.000	16	0.000	4	1.000	0	-	probably_damaging(0.971)	deleterious(0.01)	deleterious(0.819)	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
GREB1	9687	genome.wustl.edu	37	2	11758553	11758553	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014668.3	+1	reviewed	p.G1184	0.136	12	0%	18	55.6%	16	37.5%	-	-	-	NULL
GREB1	9687	genome.wustl.edu	37	2	11780546	11780546	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014668.3	+1	reviewed	p.R1939L	1.000	144	0%	150	48%	31	41.9%	probably_damaging(0.992)	deleterious(0.02)	deleterious(0.831)	NULL
CIB4	130106	genome.wustl.edu	37	2	26818053	26818053	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001029881.1	-1	provisional	p.R107C	1.000	62	0%	58	48.3%	0	-	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	HMMSmart_EFh,HMMPfam_efhand,superfamily_SSF47473
ALK	238	genome.wustl.edu	37	2	29606606	29606606	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004304.3	-1	reviewed	p.C425Y	1.000	79	0%	82	41.5%	0	-	probably_damaging(0.983)	deleterious(0)	deleterious(0.873)	NULL
BIRC6	57448	genome.wustl.edu	37	2	32640284	32640284	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016252.3	+1	reviewed	p.A642V	1.000	139	0%	127	47.2%	0	-	benign(0.253)	tolerated(0.15)	neutral(0.267)	NULL
LHCGR	3973	genome.wustl.edu	37	2	48925908	48925908	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000233.3	-1	reviewed	p.P238S	1.000	229	0%	145	35.2%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_L domain-like
GPR75	10936	genome.wustl.edu	37	2	54081089	54081089	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006794.2	-1	validated	p.P269A	1.000	62	0%	71	39.4%	0	-	probably_damaging(0.998)	tolerated(0.32)	deleterious(0.498)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
CCDC88A	55704	genome.wustl.edu	37	2	55561787	55561787	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135597.1	-1	validated	p.Q724*	1.000	237	0%	94	38.3%	0	-	-	-	-	NULL
NAT8	9027	genome.wustl.edu	37	2	73868263	73868263	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003960.3	-1	reviewed	p.A165T	0.999	107	0%	103	42.7%	0	-	possibly_damaging(0.936)	deleterious(0.01)	deleterious(0.787)	HMMPfam_Acetyltransf_1,superfamily_Acyl_CoA_acyltransferase
PCGF1	84759	genome.wustl.edu	37	2	74733345	74733345	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032673.2	-1	validated	p.S129	0.991	92	0%	119	42.9%	43	53.4%	-	-	-	NULL
POLR1A	25885	genome.wustl.edu	37	2	86305239	86305239	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015425.3	-1	validated	p.Q419*	1.000	114	0%	91	41.8%	3	0%	-	-	-	HMMSmart_SM00663,superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase
LYG1	129530	genome.wustl.edu	37	2	99912133	99912133	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_174898.2	-1	validated	p.M1V	0.912	247	0%	170	45.3%	8	62.5%	unknown(0)	deleterious(0)	-	NULL
CHST10	9486	genome.wustl.edu	37	2	101009817	101009817	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004854.3	-1	validated	p.E321*	1.000	284	0%	198	45.5%	8	37.5%	-	-	-	HMMPfam_Sulfotransfer_2
IL1RL2	8808	genome.wustl.edu	37	2	102842362	102842362	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003854.2	+1	reviewed	p.P332	0.680	61	0%	53	49.1%	0	-	-	-	-	superfamily_SSF48726
IL1RL2	8808	genome.wustl.edu	37	2	102851709	102851709	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003854.2	+1	reviewed	p.L550	0.001	54	0%	58	34.5%	2	100%	-	-	-	NULL
NCK2	8440	genome.wustl.edu	37	2	106471637	106471637	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004720.2	+1	reviewed	p.R40W	1.000	50	0%	49	55.1%	38	47.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_SH3_1,HMMSmart_SH3,superfamily_SH3
LIMS1	3987	genome.wustl.edu	37	2	109294484	109294487	+	Splice_Site	DEL	GTAA	GTAA	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	GTAA	GTAA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004987.3	+1	reviewed	e7+1	1.000:1.000	-	-	-	-	-	-	-	-	-	-
POLR1B	84172	genome.wustl.edu	37	2	113315619	113315619	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019014.4	+1	validated	p.E431K	1.000	98	0%	41	41.5%	1	100%	probably_damaging(0.99)	deleterious(0.01)	deleterious(0.847)	superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase
POLR1B	84172	genome.wustl.edu	37	2	113330184	113330184	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019014.4	+1	validated	p.S707L	1.000	173	0%	95	40%	5	60%	benign(0.07)	deleterious(0.03)	neutral(0.369)	HMMPfam_RNA_pol_Rpb2_6,superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase
SLC20A1	6574	genome.wustl.edu	37	2	113416607	113416608	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	AG	AG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005415.3	+1	provisional	p.R332fs	0.023:0.531	-	-	-	-	-	-	-	-	-	HMMPfam_PHO4
PTPN4	5775	genome.wustl.edu	37	2	120677746	120677746	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002830.2	+1	reviewed	p.L310	1.000	237	0%	147	48.3%	3	0%	-	-	-	HMMPfam_FERM_C,superfamily_SSF50729
MYO7B	4648	genome.wustl.edu	37	2	128327424	128327424	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080527.1	+1	provisional	p.T177	0.003	16	0%	61	31.1%	0	-	-	-	-	HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases
LOC653269	653269	genome.wustl.edu	37	2	131220767	131220767	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_928585.2	-1	model	p.I950	1.000	56	0%	79	46.8%	0	-	-	-	-	HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain
MCM6	4175	genome.wustl.edu	37	2	136624275	136624275	+	Silent	SNP	A	A	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005915.4	-1	reviewed	p.A213	0.776	253	0%	203	38.4%	20	45%	-	-	-	HMMSmart_SM00350,superfamily_Nucleic acid-binding proteins
THSD7B	80731	genome.wustl.edu	37	2	138425349	138425349	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080427.1	+1	provisional	p.R1524*	0.999	21	0%	19	31.6%	0	-	-	-	-	NULL
MBD5	55777	genome.wustl.edu	37	2	149247126	149247126	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018328.4	+1	reviewed	p.V1076I	0.000	129	0%	127	52%	3	0%	unknown(0)	deleterious(0)	-	NULL
KIF5C	3800	genome.wustl.edu	37	2	149854983	149854983	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000435030	+1	known	p.E724K	1.000	13	0.000	8	0.750	0	-	probably_damaging(0.997)	deleterious(0.01)	deleterious(0.872)	NULL
NR4A2	4929	genome.wustl.edu	37	2	157186121	157186121	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006186.3	-1	reviewed	p.R193H	1.000	40	0%	35	45.7%	2	0%	probably_damaging(0.999)	tolerated(0.09)	deleterious(0.787)	NULL
TANC1	85461	genome.wustl.edu	37	2	160053278	160053278	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033394.2	+1	validated	p.A1047T	1.000	32	0%	38	36.8%	8	37.5%	probably_damaging(0.997)	deleterious(0.02)	deleterious(0.849)	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat
SCN9A	6335	genome.wustl.edu	37	2	167108386	167108386	+	Missense_Mutation	SNP	G	G	A	rs190664764	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002977.3	-1	reviewed	p.R1110W	0.012	69	0%	55	34.5%	2	0%	possibly_damaging(0.732)	deleterious(0.01)	deleterious(0.673)	HMMPfam_Na_trans_assoc
SP3	6670	genome.wustl.edu	37	2	174774770	174774770	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003111.4	-1	reviewed	p.G749*	1.000	332	0%	160	43.1%	29	55.1%	-	-	-	NULL
COL3A1	1281	genome.wustl.edu	37	2	189867044	189867044	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000090.3	+1	reviewed	p.G804	0.257	56	0%	35	40%	53	0%	-	-	-	HMMPfam_Collagen
ASNSD1	54529	genome.wustl.edu	37	2	190530860	190530860	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019048.2	+1	validated	p.M1T	1.000	216	0%	120	40.8%	11	63.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
ANKRD44	91526	genome.wustl.edu	37	2	197943382	197943383	+	Frame_Shift_Ins	INS	-	-	TG	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000409153	-1	known	p.T566fs	0.000:0.001	-	-	-	-	-	-	-	-	-	superfamily_ANK
WDR12	55759	genome.wustl.edu	37	2	203760861	203760861	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018256.3	-1	reviewed	p.V179G	1.000	147	0%	121	47.9%	17	23.5%	benign(0.123)	deleterious(0)	neutral(0.455)	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40
TNS1	7145	genome.wustl.edu	37	2	218677119	218677119	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022648.4	-1	reviewed	p.L1564	1.000	47	0%	35	54.3%	3	66.6%	-	-	-	superfamily_SSF55550
ZNF142	7701	genome.wustl.edu	37	2	219508394	219508394	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001105537.1	-1	validated	p.P949S	0.013	215	0%	136	44.1%	5	40%	possibly_damaging(0.89)	deleterious(0)	deleterious(0.794)	NULL
CYP27A1	1593	genome.wustl.edu	37	2	219677340	219677340	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000784.3	+1	reviewed	p.V238M	0.001	349	0.3%	328	46%	43	48.8%	possibly_damaging(0.568)	tolerated(0.09)	deleterious(0.491)	HMMPfam_p450,superfamily_Cytochrome P450
ABCB6	10058	genome.wustl.edu	37	2	220078657	220078657	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000295750	-1	known	p.R338*	0.994	104	0%	102	47.1%	32	40.6%	possibly_damaging(0.749)	deleterious(0.04)	deleterious(0.624)	HMMPfam_ABC_membrane,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain
SPEG	10290	genome.wustl.edu	37	2	220353316	220353316	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005876.4	+1	validated	p.A2652V	0.977	32	0%	23	47.8%	0	-	possibly_damaging(0.842)	tolerated(0.36)	neutral(0.342)	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin
OBSL1	23363	genome.wustl.edu	37	2	220428170	220428170	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015311.2	-1	reviewed	p.R863C	0.974	54	0%	44	43.2%	210	50%	possibly_damaging(0.832)	deleterious(0)	deleterious(0.762)	HMMSmart_IG,HMMPfam_ig,superfamily_SSF48726
SCG2	7857	genome.wustl.edu	37	2	224463569	224463569	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003469.3	-1	reviewed	p.P144	0.001	738	0%	447	43%	0	-	-	-	-	HMMPfam_Granin
IRS1	3667	genome.wustl.edu	37	2	227660691	227660691	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005544.2	-1	reviewed	p.R922G	0.516	68	0%	44	38.6%	2	0%	probably_damaging(0.968)	tolerated(0.14)	deleterious(0.659)	NULL
SLC16A14	151473	genome.wustl.edu	37	2	230914620	230914620	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152527.4	-1	validated	p.G87D	1.000	148	0%	131	42%	2	100%	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	HMMPfam_MFS_1,superfamily_MFS general substrate transporter
CAB39	51719	genome.wustl.edu	37	2	231624754	231624754	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130849.1	+1	validated	p.A13V	1.000	95	0%	92	31.5%	6	33.3%	benign(0.023)	tolerated(0.2)	neutral(0.050)	HMMPfam_Mo25,superfamily_ARM repeat
CHRND	1144	genome.wustl.edu	37	2	233399886	233399886	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000751.1	+1	reviewed	p.C473Y	1.000	77	0%	54	24.1%	0	-	probably_damaging(0.998)	tolerated(0.18)	deleterious(0.530)	HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore
DGKD	8527	genome.wustl.edu	37	2	234344527	234344527	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152879.2	+1	reviewed	p.T217I	1.000	92	0%	61	47.5%	2	0%	probably_damaging(0.971)	deleterious(0)	deleterious(0.857)	superfamily_Cysteine-rich domain
SEC13	6396	genome.wustl.edu	37	3	10346791	10346791	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_183352.1	-1	reviewed	p.S212R	1.000	67	0%	66	47%	482	50.4%	probably_damaging(0.997)	deleterious(0.04)	deleterious(0.815)	HMMSmart_WD40,superfamily_WD40_like,HMMPfam_WD40
HRH1	3269	genome.wustl.edu	37	3	11300961	11300961	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000861.3	+1	reviewed	p.V80I	1.000	164	0%	153	43.8%	2	50%	probably_damaging(0.994)	tolerated(0.06)	deleterious(0.774)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
IQSEC1	9922	genome.wustl.edu	37	3	12950010	12950010	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014869.4	-1	validated	p.Q879R	1.000	33	0%	18	33.3%	4	25%	possibly_damaging(0.819)	deleterious(0.01)	deleterious(0.715)	NULL
FGD5	152273	genome.wustl.edu	37	3	14940265	14940265	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152536.3	+1	validated	p.S1029N	0.624	11	0%	10	60%	0	-	benign(0)	tolerated(0.56)	neutral(0.006)	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain)
FGD5	152273	genome.wustl.edu	37	3	14974177	14974177	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152536.3	+1	validated	p.L1431F	1.000	198	0%	146	38.4%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like
ZNF860	344787	genome.wustl.edu	37	3	32031756	32031756	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001137674.1	+1	provisional	p.G395	1.000	218	0%	154	44.8%	2	0%	-	-	-	superfamily_SSF57667
CCBP2	1238	genome.wustl.edu	37	3	42906895	42906895	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001296.4	+1	reviewed	p.A301T	0.999	442	0.5%	518	47.5%	2	0%	probably_damaging(0.995)	deleterious(0.03)	deleterious(0.822)	HMMPfam_7tm_1,superfamily_SSF81321
ZNF445	353274	genome.wustl.edu	37	3	44489342	44489342	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181489.5	-1	validated	p.H607	1.000	124	0%	126	49.2%	1	0%	-	-	-	PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667
FYCO1	79443	genome.wustl.edu	37	3	45996853	45996853	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024513.2	-1	validated	p.A1278T	0.886	137	0%	114	44.7%	3	0%	probably_damaging(0.998)	deleterious(0.03)	deleterious(0.839)	NULL
SETD2	29072	genome.wustl.edu	37	3	47164123	47164123	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014159.6	-1	reviewed	p.P668L	0.999	215	0%	121	37.2%	0	-	possibly_damaging(0.65)	tolerated(0.08)	deleterious(0.528)	NULL
PLXNB1	5364	genome.wustl.edu	37	3	48462318	48462318	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130082.1	-1	validated	p.A620T	0.137	39	0%	50	46%	25	32%	benign(0.003)	tolerated(0.4)	neutral(0.016)	NULL
PLXNB1	5364	genome.wustl.edu	37	3	48462729	48462729	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130082.1	-1	validated	p.G573V	1.000	107	0%	86	44.2%	18	50%	possibly_damaging(0.904)	deleterious(0)	deleterious(0.803)	NULL
CELSR3	1951	genome.wustl.edu	37	3	48698223	48698224	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	CT	CT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001407.2	-1	reviewed	p.E615fs	1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
LAMB2	3913	genome.wustl.edu	37	3	49162782	49162782	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002292.3	-1	reviewed	p.R875Q	1.000	71	0%	63	47.6%	38	47.3%	benign(0.031)	tolerated(1)	neutral(0.002)	PatternScan_EGF_LAM_1,superfamily_SSF57196
IP6K1	9807	genome.wustl.edu	37	3	49764848	49764848	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153273.3	-1	reviewed	p.R345W	0.941	23	0%	30	53.3%	10	50%	benign(0.003)	tolerated(0.06)	neutral(0.323)	HMMPfam_IPK,superfamily_SAICAR synthase-like
MON1A	84315	genome.wustl.edu	37	3	49948257	49948257	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032355.3	-1	validated	p.T322M	1.000	13	0%	15	46.7%	6	33.3%	probably_damaging(1)	deleterious(0.03)	deleterious(0.865)	HMMPfam_Mon1
TMEM115	11070	genome.wustl.edu	37	3	50392824	50392824	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007024.4	-1	validated	p.A336T	0.979	17	0%	24	37.5%	103	45.6%	benign(0)	tolerated(0.76)	neutral(0.001)	NULL
PCBP4	57060	genome.wustl.edu	37	3	51992316	51992316	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020418.3	-1	reviewed	p.A346T	0.976	22	0.000	8	0.500	68	38.2%	benign(0)	tolerated(0.12)	neutral(0.261)	NULL
GNL3	26354	genome.wustl.edu	37	3	52727456	52727456	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014366.4	+1	validated	p.T407I	0.786	321	0%	129	42.6%	172	42.4%	benign(0.246)	deleterious(0.02)	neutral(0.408)	NULL
ITIH4	3700	genome.wustl.edu	37	3	52854721	52854721	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002218.4	-1	reviewed	p.P587H	0.997	36	0%	27	44.4%	4	75%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PTPRG	5793	genome.wustl.edu	37	3	62216903	62216903	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002841.3	+1	reviewed	p.C765R	1.000	66	0%	64	35.9%	0	-	benign(0.255)	deleterious(0.05)	neutral(0.372)	NULL
CADPS	8618	genome.wustl.edu	37	3	62631414	62631414	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003716.3	-1	reviewed	p.A436	0.095	211	0%	179	43%	0	-	-	-	-	HMMPfam_C2
OR5H15	403274	genome.wustl.edu	37	3	97887622	97887622	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005515.1	+1	provisional	p.L27M	0.008	640	0%	420	42.1%	0	-	possibly_damaging(0.947)	deleterious(0.01)	deleterious(0.796)	superfamily_SSF81321
ZPLD1	131368	genome.wustl.edu	37	3	102153987	102153987	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_175056.1	+1	provisional	p.G10V	0.003	148	0%	62	43.5%	0	-	possibly_damaging(0.931)	-	-	NULL
CBLB	868	genome.wustl.edu	37	3	105422965	105422965	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_170662.3	-1	validated	p.A487V	0.184	99	0%	62	33.9%	9	44.4%	benign(0.011)	tolerated(0.07)	neutral(0.320)	NULL
GUCA1C	9626	genome.wustl.edu	37	3	108626930	108626930	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005459.3	-1	validated	p.M190T	0.004	126	0%	66	31.8%	0	-	benign(0)	tolerated(0.75)	neutral(0.002)	NULL
PLXND1	23129	genome.wustl.edu	37	3	129286424	129286427	+	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	TGTC	TGTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015103.2	-1	validated	p.D1332fs	1.000:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
AMOTL2	51421	genome.wustl.edu	37	3	134089809	134089809	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016201.2	-1	reviewed	p.R156H	1.000	6	0.000	10	0.800	7	42.8%	probably_damaging(1)	deleterious(0.05)	deleterious(0.845)	NULL
XRN1	54464	genome.wustl.edu	37	3	142031595	142031595	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019001.3	-1	validated	p.I1555V	0.985	329	0%	180	45.6%	2	50%	benign(0.012)	tolerated(0.39)	neutral(0.017)	NULL
AGTR1	185	genome.wustl.edu	37	3	148459561	148459561	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000685.4	+1	reviewed	p.L247F	1.000	219	0%	114	37.7%	0	-	benign(0.04)	tolerated(0.06)	neutral(0.325)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
TNIK	23043	genome.wustl.edu	37	3	170884920	170884920	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015028.2	-1	validated	p.H305N	1.000	47	0%	32	50%	3	0%	possibly_damaging(0.946)	deleterious(0)	deleterious(0.835)	superfamily_Protein kinase-like (PK-like)
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279	byCluster	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.H1047R	1.000	168	0%	153	37.3%	15	26.6%	possibly_damaging(0.926)	deleterious(0.03)	deleterious(0.739)	HMMSmart_PI3Kc,superfamily_Kinase_like
ACTL6A	86	genome.wustl.edu	37	3	179294018	179294018	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004301.3	+1	reviewed	p.R164C	1.000	143	0%	70	37.1%	36	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain
DVL3	1857	genome.wustl.edu	37	3	183882616	183882616	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004423.3	+1	reviewed	p.R166W	1.000	146	0%	70	38.6%	33	45.4%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Dishevelled
GP5	2814	genome.wustl.edu	37	3	194118305	194118305	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004488.2	-1	validated	p.G236E	0.015	167	0%	55	34.5%	0	-	probably_damaging(1)	deleterious(0.04)	deleterious(0.849)	HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058
CEP19	84984	genome.wustl.edu	37	3	196434521	196434523	+	In_Frame_Del	DEL	CTT	CTT	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	CTT	CTT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032898.3	-1	validated	p.K135in_frame_del	0.995:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
WHSC2	7469	genome.wustl.edu	37	4	1985323	1985323	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005663.3	-1	reviewed	p.E479K	1.000	43	0%	23	39.1%	87	44.8%	possibly_damaging(0.945)	deleterious(0.03)	deleterious(0.754)	NULL
DRD5	1816	genome.wustl.edu	37	4	9784937	9784937	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000798.4	+1	reviewed	p.D428	0.445	70	0%	67	49.3%	0	-	-	-	-	NULL
BEND4	389206	genome.wustl.edu	37	4	42119672	42119672	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207406.3	-1	validated	p.A490T	0.996	12	0%	11	54.5%	0	-	possibly_damaging(0.643)	deleterious(0)	deleterious(0.670)	HMMPfam_BEN
GNPDA2	132789	genome.wustl.edu	37	4	44713031	44713031	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138335.1	-1	provisional	p.L178S	1.000	193	0%	130	47.7%	11	45.4%	benign(0.126)	deleterious(0)	neutral(0.455)	HMMPfam_Glucosamine_iso,superfamily_NagB/RpiA/CoA transferase-like
LRRC66	339977	genome.wustl.edu	37	4	52862253	52862253	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001024611.1	-1	provisional	p.R312H	0.000	91	0%	58	44.8%	6	66.6%	benign(0)	tolerated(0.4)	neutral(0.016)	NULL
EXOC1	55763	genome.wustl.edu	37	4	56768654	56768654	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001024924.1	+1	reviewed	p.L828I	1.000	111	0%	74	45.9%	26	53.8%	probably_damaging(0.982)	deleterious(0)	deleterious(0.871)	HMMPfam_Sec3
EPHA5	2044	genome.wustl.edu	37	4	66361207	66361207	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004439.5	-1	reviewed	p.C322Y	1.000	282	0.4%	235	39.1%	0	-	probably_damaging(0.987)	deleterious(0)	deleterious(0.881)	NULL
COX18	285521	genome.wustl.edu	37	4	73927617	73927617	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173827.2	-1	validated	p.I247fs	0.002	-	-	-	-	-	-	-	-	-	HMMPfam_60KD_IMP
ENSG00000245879	0	genome.wustl.edu	37	4	74964407	74964407	+	RNA	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000500608	+1	known	NULL	0.997	103	0%	74	20.3%	2	100%	-	-	-	-
FRAS1	80144	genome.wustl.edu	37	4	79458198	79458198	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025074.6	+1	reviewed	p.N3713K	1.000	197	0%	156	53.2%	0	-	benign(0.001)	tolerated(0.21)	neutral(0.044)	NULL
WDFY3	23001	genome.wustl.edu	37	4	85594131	85594131	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014991.4	-1	reviewed	p.Q3491*	1.000	227	0%	149	47.7%	32	43.7%	-	-	-	HMMPfam_FYVE,HMMSmart_SM00064,superfamily_FYVE/PHD zinc finger
ARSJ	79642	genome.wustl.edu	37	4	114824027	114824027	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024590.3	-1	validated	p.Y401	0.922	222	0%	190	41.6%	2	100%	-	-	-	HMMPfam_Sulfatase,superfamily_Alkaline phosphatase-like
ANKRD50	57182	genome.wustl.edu	37	4	125590323	125590323	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020337.2	-1	validated	p.Q1370R	1.000	353	0%	263	39.2%	5	60%	probably_damaging(0.994)	deleterious(0.04)	deleterious(0.801)	NULL
FGA	2243	genome.wustl.edu	37	4	155505774	155505774	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000508.3	-1	reviewed	p.D701	0.853	206	0%	213	44.1%	0	-	-	-	-	HMMPfam_Fibrinogen_C,HMMSmart_SM00186,superfamily_Fibrinogen C-terminal domain-like
GRIA2	2891	genome.wustl.edu	37	4	158142953	158142953	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000826.3	+1	reviewed	p.N75D	1.000	82	0%	79	43%	0	-	benign(0.001)	tolerated(0.14)	neutral(0.249)	HMMPfam_ANF_receptor,superfamily_SSF53822
TLR3	7098	genome.wustl.edu	37	4	186997960	186997960	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003265.2	+1	reviewed	p.L63F	1.000	109	0%	134	47%	2	0%	benign(0.09)	deleterious(0.01)	neutral(0.412)	HMMPfam_LRR_1,superfamily_SSF52058
FAT1	2195	genome.wustl.edu	37	4	187524699	187524699	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005245.3	-1	reviewed	p.R3661C	1.000	61	0%	44	34.1%	23	34.7%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_Concanavalin A-like lectins/glucanases
FAT1	2195	genome.wustl.edu	37	4	187527266	187527266	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005245.3	-1	reviewed	p.N3436	0.124	165	0%	114	41.2%	14	50%	-	-	-	HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Cadherin-like
FAT1	2195	genome.wustl.edu	37	4	187539448	187539448	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005245.3	-1	reviewed	p.K2764N	0.999	352	0%	203	37.4%	8	37.5%	probably_damaging(0.999)	tolerated(0.1)	deleterious(0.777)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Cadherin-like
TRIML1	339976	genome.wustl.edu	37	4	189060900	189060900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178556.3	+1	provisional	p.P63L	0.011	50	0%	98	44.9%	0	-	possibly_damaging(0.925)	tolerated(0.23)	neutral(0.415)	superfamily_SSF57850
NSUN2	54888	genome.wustl.edu	37	5	6600070	6600070	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017755.4	-1	validated	p.C758Y	0.004	103	0%	143	46.2%	91	41.7%	benign(0.075)	deleterious(0.04)	neutral(0.354)	NULL
ANKH	56172	genome.wustl.edu	37	5	14769183	14769183	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_054027.4	-1	reviewed	p.V72M	1.000	135	0%	106	37.7%	19	57.8%	probably_damaging(0.996)	deleterious(0.03)	deleterious(0.826)	HMMPfam_ANKH
FBXL7	23194	genome.wustl.edu	37	5	15928198	15928198	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012304.3	+1	reviewed	p.K109N	0.968	61	0%	66	51.5%	0	-	benign(0.002)	tolerated(0.65)	neutral(0.003)	NULL
ZNF622	90441	genome.wustl.edu	37	5	16465474	16465474	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033414.2	-1	provisional	p.A101T	1.000	167	0%	122	42.6%	40	37.5%	benign(0.271)	tolerated(0.5)	neutral(0.039)	NULL
PDZD2	23037	genome.wustl.edu	37	5	32089450	32089450	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178140.2	+1	reviewed	p.T1966A	0.001	92	0%	130	43.1%	0	-	benign(0)	tolerated(1)	-	NULL
SNX18	112574	genome.wustl.edu	37	5	53814853	53814853	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052870.2	+1	reviewed	p.I357	0.852	32	0%	22	40.9%	4	50%	-	-	-	HMMPfam_PX,HMMSmart_SM00312,superfamily_PX domain
PDE4D	5144	genome.wustl.edu	37	5	58882193	58882193	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006203.4	-1	validated	p.H3	0.997	382	0%	221	43.9%	0	-	-	-	-	NULL
ZNF366	167465	genome.wustl.edu	37	5	71739932	71739932	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152625.1	-1	provisional	p.E629A	0.006	94	0%	82	45.1%	0	-	benign(0.036)	deleterious(0.02)	neutral(0.385)	NULL
POU5F2	134187	genome.wustl.edu	37	5	93076428	93076428	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153216.1	-1	provisional	p.A281V	0.000	41	0%	72	37.5%	0	-	-	-	-	superfamily_Homeodomain_like
MCTP1	79772	genome.wustl.edu	37	5	94248613	94248613	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000503301	-1	known	p.H236Y	1.000	223	0%	147	36.7%	0	-	-	-	-	HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)
PPIP5K2	23262	genome.wustl.edu	37	5	102484895	102484895	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015216.2	+1	provisional	p.R262	1.000	165	0%	98	38.8%	0	-	-	-	-	superfamily_SSF56059
FBXL17	64839	genome.wustl.edu	37	5	107521920	107521920	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000496714	-1	known	p.R150H	1.000	81	0%	31	38.7%	5	40%	probably_damaging(0.999)	deleterious(0.04)	deleterious(0.839)	superfamily_SSF52047
ZNF608	57507	genome.wustl.edu	37	5	123979362	123979363	+	Frame_Shift_Del	DEL	GA	GA	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	GA	GA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020747.2	-1	validated	p.P1380fs	1.000:0.996	-	-	-	-	-	-	-	-	-	NULL
RAPGEF6	51735	genome.wustl.edu	37	5	130883836	130883836	+	Silent	SNP	A	A	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016340.5	-1	validated	p.I133	1.000	204	0%	117	44.4%	0	-	-	-	-	NULL
FNIP1	96459	genome.wustl.edu	37	5	131007632	131007632	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000513722	-1	known	p.S629L	1.000	329	0%	233	38.2%	2	50%	-	-	-	NULL
HARS	3035	genome.wustl.edu	37	5	140057274	140057274	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002109.3	-1	reviewed	p.R232H	1.000	173	0%	116	41.4%	81	37%	benign(0.152)	deleterious(0.02)	neutral(0.397)	HMMPfam_tRNA-synt_2b,superfamily_SSF55681
PCDHA3	56145	genome.wustl.edu	37	5	140182516	140182516	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018906.2	+1	reviewed	p.S578	0.000	47	0%	72	44.4%	3	0%	-	-	-	HMMPfam_Cadherin,superfamily_Cadherin-like
PCDHA8	56140	genome.wustl.edu	37	5	140221198	140221198	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018911.2	+1	reviewed	p.R98W	0.001	171	0%	177	35%	0	-	benign(0.039)	deleterious(0.05)	neutral(0.347)	HMMSmart_SM00112,HMMPfam_Cadherin_2,superfamily_Cadherin-like
PCDHB5	26167	genome.wustl.edu	37	5	140517169	140517169	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015669.2	+1	reviewed	p.A718V	0.000	174	0%	238	44.5%	0	-	benign(0.135)	tolerated(0.06)	neutral(0.334)	NULL
PCDHB6	56130	genome.wustl.edu	37	5	140531614	140531614	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018939.2	+1	reviewed	p.G592	0.996	74	0%	142	40.1%	0	-	-	-	-	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
PCDHB16	57717	genome.wustl.edu	37	5	140563515	140563515	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020957.1	+1	reviewed	p.R461C	0.046	263	0%	259	37.8%	1	100%	benign(0.188)	deleterious(0.05)	neutral(0.363)	HMMPfam_Cadherin,superfamily_Cadherin
PCDHGA3	56112	genome.wustl.edu	37	5	140724459	140724459	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018916.3	+1	reviewed	p.K287E	0.107	94	0%	129	46.5%	0	-	benign(0.023)	tolerated(0.27)	neutral(0.035)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
PCDHGB6	56100	genome.wustl.edu	37	5	140789380	140789380	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018926.2	+1	reviewed	p.H537	0.234	19	0%	23	26.1%	1	0%	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
SPINK5	11005	genome.wustl.edu	37	5	147498547	147498547	+	Splice_Site	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127698.1	+1	reviewed	e24-2	0.056	114	0%	83	42.2%	0	-	-	-	-	-
ATP10B	23120	genome.wustl.edu	37	5	160115033	160115033	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025153.2	-1	validated	p.R17G	0.000	95	0%	118	50%	0	-	benign(0)	tolerated(0.21)	neutral(0.044)	NULL
FBXW11	23291	genome.wustl.edu	37	5	171337690	171337690	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012300.2	-1	reviewed	p.D87N	1.000	135	0%	89	32.6%	1	0%	benign(0.176)	tolerated(0.05)	neutral(0.361)	NULL
STC2	8614	genome.wustl.edu	37	5	172750287	172750287	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003714.2	-1	reviewed	p.A147	0.001	63	0%	63	49.2%	27	44.4%	-	-	-	HMMPfam_Stanniocalcin
N4BP3	23138	genome.wustl.edu	37	5	177547388	177547388	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015111.1	+1	validated	p.G180	0.004	10	0%	10	70%	8	25%	-	-	-	NULL
TBC1D9B	23061	genome.wustl.edu	37	5	179318540	179318540	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198868.2	-1	validated	p.R295W	1.000	37	0%	40	40%	18	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_GRAM,HMMSmart_SM00568
GCNT2	2651	genome.wustl.edu	37	6	10557032	10557032	+	Missense_Mutation	SNP	G	G	A	rs56318832		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001491.2	+1	reviewed	p.V126M	1.000	385	0%	369	44.2%	0	-	possibly_damaging(0.595)	deleterious(0.02)	deleterious(0.589)	HMMPfam_Branch
NEDD9	4739	genome.wustl.edu	37	6	11191425	11191425	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142393.1	-1	validated	p.P226L	0.999	62	0%	66	50%	4	25%	benign(0.002)	deleterious(0)	neutral(0.445)	NULL
GFOD1	54438	genome.wustl.edu	37	6	13365349	13365349	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018988.2	-1	provisional	p.G267R	1.000	16	0%	28	39.3%	4	100%	possibly_damaging(0.919)	tolerated(0.07)	deleterious(0.689)	superfamily_Glyceraldehyde-3-phosphate dehydrogenase-like C-terminal domain
CAP2	10486	genome.wustl.edu	37	6	17421798	17421798	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006366.2	+1	reviewed	p.M4I	1.000	171	0%	130	50.8%	0	-	benign(0.032)	tolerated(0.18)	neutral(0.058)	HMMPfam_CAP_N
NRSN1	140767	genome.wustl.edu	37	6	24145982	24145982	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080723.4	+1	validated	p.G132	1.000	158	0%	127	37.8%	0	-	-	-	-	NULL
HIST1H2BD	3017	genome.wustl.edu	37	6	26158501	26158501	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021063.2	+1	reviewed	p.K35R	1.000	142	0%	164	44.5%	65	40%	possibly_damaging(0.777)	tolerated(0.06)	deleterious(0.613)	HMMSmart_SM00427,HMMPfam_Histone,superfamily_Histone-fold
HIST1H2BE	8344	genome.wustl.edu	37	6	26184286	26184286	+	Missense_Mutation	SNP	C	C	T	rs191131837	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003523.2	+1	reviewed	p.S88L	1.000	120	0%	161	41%	4	0%	benign(0.036)	deleterious(0.03)	neutral(0.366)	HMMSmart_SM00427,HMMPfam_Histone,superfamily_Histone-fold
BTN2A2	10385	genome.wustl.edu	37	6	26392629	26392629	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006995.3	+1	reviewed	p.A336T	0.998	185	0%	156	46.8%	6	16.6%	probably_damaging(0.984)	deleterious(0)	deleterious(0.875)	HMMSmart_SM00589
ZNF391	346157	genome.wustl.edu	37	6	27369058	27369058	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001076781.1	+1	validated	p.K303	0.936	187	0%	153	36.6%	3	66.6%	-	-	-	superfamily_C2H2 and C2HC zinc fingers
OR2B2	81697	genome.wustl.edu	37	6	27879356	27879356	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033057.2	-1	validated	p.V248M	0.331	256	0%	281	42.3%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
PGBD1	84547	genome.wustl.edu	37	6	28268674	28268674	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032507.3	+1	reviewed	p.A348D	1.000	229	0%	186	39.8%	5	40%	probably_damaging(0.962)	tolerated(0.08)	deleterious(0.705)	NULL
RNF39	80352	genome.wustl.edu	37	6	30043429	30043429	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025236.3	-1	validated	p.P46	0.085	42	2.4%	51	39.2%	10	60%	-	-	-	NULL
VARS	7407	genome.wustl.edu	37	6	31753448	31753448	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006295.2	-1	reviewed	p.T388I	1.000	20	0%	22	45.5%	40	52.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_tRNA-synt_1,superfamily_Nucleotidylyl transferase
PPT2	9374	genome.wustl.edu	37	6	32130627	32130627	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138717.1	+1	reviewed	p.R276Q	1.000	200	0%	92	40.2%	7	85.7%	probably_damaging(0.989)	tolerated(0.36)	neutral(0.460)	HMMPfam_Palm_thioest,superfamily_alpha/beta-Hydrolases
COL11A2	1302	genome.wustl.edu	37	6	33147515	33147515	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080680.2	-1	reviewed	p.A476V	0.998	20	0%	26	34.6%	0	-	benign(0.036)	tolerated(0.15)	neutral(0.243)	NULL
ITPR3	3710	genome.wustl.edu	37	6	33646519	33646519	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002224.2	+1	validated	p.T1292M	1.000	6	0.000	6	0.833	26	73%	probably_damaging(1)	deleterious(0.03)	deleterious(0.865)	HMMPfam_RYDR_ITPR
SNRPC	6631	genome.wustl.edu	37	6	34735775	34735775	+	Splice_Site	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003093.2	+1	reviewed	e4+1	1.000	84	0%	64	45.3%	0	-	-	-	-	-
PGC	5225	genome.wustl.edu	37	6	41715044	41715044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002630.3	-1	reviewed	p.C10Y	1.000	39	0%	40	40%	0	-	benign(0.065)	deleterious(0.01)	neutral(0.410)	superfamily_Pept_Aspartic
CUL7	9820	genome.wustl.edu	37	6	43008685	43008685	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014780.4	-1	reviewed	p.L1258F	1.000	33	0%	32	50%	24	50%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	HMMPfam_Cullin,superfamily_Cullin_homology
MRPL2	51069	genome.wustl.edu	37	6	43023660	43023660	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015950.3	-1	reviewed	p.R202	0.984	46	0%	59	39%	129	48.8%	-	-	-	HMMPfam_Ribosomal_L2_C,superfamily_Transl_SH3_like
TCTE1	202500	genome.wustl.edu	37	6	44247986	44247986	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182539.3	-1	validated	p.R480W	0.917	75	0%	43	55.8%	0	-	benign(0.382)	-	-	superfamily_SSF52047
PKHD1	5314	genome.wustl.edu	37	6	51524037	51524037	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138694.3	-1	reviewed	p.S3629	0.000	325	0%	243	44.9%	0	-	-	-	-	NULL
TRAM2	9697	genome.wustl.edu	37	6	52370482	52370482	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012288.3	-1	reviewed	p.V264M	0.999	119	0%	109	53.2%	1	100%	possibly_damaging(0.843)	deleterious(0.01)	deleterious(0.729)	HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724
DST	667	genome.wustl.edu	37	6	56329501	56329501	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000370769	-1	known	p.T7345A	1.000	43	0%	41	41.5%	0	-	benign(0.349)	-	-	NULL
DST	667	genome.wustl.edu	37	6	56470905	56470905	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000370769	-1	known	p.A2630fs	0.000	-	-	-	-	-	-	-	-	-	NULL
COL12A1	1303	genome.wustl.edu	37	6	75828890	75828890	+	Missense_Mutation	SNP	G	G	A	rs141593495	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004370.5	-1	reviewed	p.T2408M	0.992	128	0%	114	48.2%	3	0%	probably_damaging(0.999)	-	-	HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like
MDN1	23195	genome.wustl.edu	37	6	90468058	90468058	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014611.1	-1	provisional	p.R873Q	1.000	53	0%	29	44.8%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMSmart_SM00382,HMMPfam_AAA_5,superfamily_P-loop containing nucleoside triphosphate hydrolases
MICAL1	64780	genome.wustl.edu	37	6	109773563	109773563	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022765.3	-1	validated	p.I240V	1.000	78	0%	52	53.8%	4	50%	possibly_damaging(0.871)	deleterious(0)	deleterious(0.783)	superfamily_FAD/NAD(P)-binding domain
SOGA3	387104	genome.wustl.edu	37	6	127796470	127796470	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001012279.2	-1	validated	p.R901C	0.008	16	0%	30	43.3%	0	-	probably_damaging(0.997)	deleterious(0.01)	deleterious(0.872)	NULL
MAP3K5	4217	genome.wustl.edu	37	6	136913359	136913359	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005923.3	-1	reviewed	p.T1059	0.005	260	0.4%	167	44.3%	5	20%	-	-	-	NULL
UTRN	7402	genome.wustl.edu	37	6	145161876	145161876	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007124.2	+1	reviewed	p.A3393V	0.052	55	0%	44	50%	18	16.6%	benign(0.02)	tolerated(0.57)	neutral(0.007)	NULL
PLEKHG1	57480	genome.wustl.edu	37	6	151121977	151121977	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001029884.1	+1	provisional	p.R251Q	1.000	134	0%	111	52.3%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain)
SYTL3	94120	genome.wustl.edu	37	6	159084396	159084396	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001009991.2	+1	validated	p.E32D	1.000	32	0%	39	46.2%	3	33.3%	possibly_damaging(0.574)	tolerated(0.33)	neutral(0.221)	superfamily_FYVE/PHD zinc finger
IGF2R	3482	genome.wustl.edu	37	6	160494395	160494395	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000876.2	+1	reviewed	p.C1614Y	1.000	70	0%	68	41.2%	9	55.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_CIMR,superfamily_Mannose 6-phosphate receptor domain
SLC22A3	6581	genome.wustl.edu	37	6	160831809	160831809	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021977.2	+1	reviewed	p.D302E	0.556	116	0.9%	82	36.6%	0	-	benign(0)	tolerated(1)	-	HMMPfam_MFS_1,superfamily_MFS general substrate transporter
MAP3K4	4216	genome.wustl.edu	37	6	161470229	161470229	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005922.2	+1	reviewed	p.A309T	0.761	278	0%	214	48.1%	3	0%	benign(0.153)	tolerated(0.32)	neutral(0.037)	NULL
GPR146	115330	genome.wustl.edu	37	7	1097715	1097715	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138445.2	+1	provisional	p.D188	0.993	12	0%	14	64.3%	10	40%	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
SDK1	221935	genome.wustl.edu	37	7	4167089	4167089	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152744.3	+1	validated	p.V1300	0.605	182	0%	187	44.4%	0	-	-	-	-	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
PAPOLB	56903	genome.wustl.edu	37	7	4900522	4900522	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020144.4	-1	validated	p.P307H	1.000	391	0.3%	308	39.6%	0	-	benign(0.217)	tolerated(0.15)	neutral(0.263)	HMMPfam_PAP_central,superfamily_SSF81631
RSPH10B	222967	genome.wustl.edu	37	7	6005297	6005297	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173565.3	-1	validated	p.A101T	0.998	136	0%	87	31%	0	-	probably_damaging(0.966)	tolerated(0.11)	deleterious(0.679)	HMMPfam_MORN,superfamily_SSF82185
NUPL2	11097	genome.wustl.edu	37	7	23221797	23221798	+	In_Frame_Ins	INS	-	-	CGGCAGCAACCG	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007342.2	+1	validated	p.35in_frame_insRQQP	0.999:1.000	-	-	-	-	-	-	-	-	-	NULL
MPP6	51678	genome.wustl.edu	37	7	24720081	24720081	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016447.2	+1	provisional	p.T463M	1.000	423	0%	292	45.9%	5	40%	probably_damaging(0.973)	deleterious(0.05)	deleterious(0.760)	HMMPfam_Guanylate_kin,HMMSmart_SM00072,superfamily_P-loop containing nucleoside triphosphate hydrolases
HOXA7	3204	genome.wustl.edu	37	7	27194634	27194634	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006896.3	-1	reviewed	p.A196V	0.020	50	0%	54	40.7%	24	54.1%	unknown(0)	tolerated(0.11)	-	NULL
BMPER	168667	genome.wustl.edu	37	7	34118685	34118685	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_133468.3	+1	validated	p.L432P	1.000	92	0%	91	49.5%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_VWD,HMMSmart_VWD
ELMO1	9844	genome.wustl.edu	37	7	37250990	37250990	+	Splice_Site	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014800.9	-1	reviewed	e12+1	1.000	110	0%	64	37.5%	1	100%	-	-	-	-
GLI3	2737	genome.wustl.edu	37	7	42065865	42065865	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000168.5	-1	reviewed	p.P392H	1.000	34	0%	25	48%	0	-	benign(0.253)	deleterious(0.04)	neutral(0.375)	NULL
HECW1	23072	genome.wustl.edu	37	7	43519303	43519303	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015052.3	+1	validated	p.R1065Q	1.000	295	0%	294	43.5%	0	-	possibly_damaging(0.575)	deleterious(0.01)	deleterious(0.603)	NULL
POLM	27434	genome.wustl.edu	37	7	44113231	44113231	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013284.2	-1	validated	p.P464L	0.249	100	0%	123	39.8%	11	45.4%	benign(0.001)	tolerated(0.16)	neutral(0.059)	HMMSmart_POLXc,superfamily_SSF81301
PKD1L1	168507	genome.wustl.edu	37	7	47898467	47898467	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138295.2	-1	reviewed	p.A1389V	0.003	100	0%	112	44.6%	0	-	benign(0.33)	deleterious(0.02)	deleterious(0.486)	NULL
COBL	23242	genome.wustl.edu	37	7	51111097	51111097	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000452534	-1	known	p.*439R	0.000	82	0%	65	46.2%	5	20%	-	-	-	NULL
VSTM2A	222008	genome.wustl.edu	37	7	54617692	54617692	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182546.2	+1	validated	p.R155C	0.980	56	0%	25	44%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
LANCL2	55915	genome.wustl.edu	37	7	55467774	55467774	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018697.3	+1	validated	p.V219M	0.999	182	0%	41	43.9%	29	37.9%	probably_damaging(0.99)	deleterious(0.01)	deleterious(0.847)	HMMPfam_LANC_like
ENSG00000249319	0	genome.wustl.edu	37	7	65553846	65553846	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000450043	+1	known	p.R26*	0.000	17	0%	15	46.7%	86	48.8%	-	-	-	HMMPfam_Lyase_1,superfamily_L-aspartase-like
PHTF2	57157	genome.wustl.edu	37	7	77539710	77539710	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127357.1	+1	validated	p.A220T	1.000	122	0%	97	50.5%	5	0%	possibly_damaging(0.929)	tolerated(1)	neutral(0.376)	NULL
FZD1	8321	genome.wustl.edu	37	7	90895830	90895831	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	TG	TG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003505.1	+1	reviewed	p.V546fs	0.485:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_Frizzled
KRIT1	889	genome.wustl.edu	37	7	91855911	91855913	+	In_Frame_Del	DEL	GAG	GAG	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	GAG	GAG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004912.3	-1	reviewed	p.P358in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat
PON1	5444	genome.wustl.edu	37	7	94931624	94931624	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000446.5	-1	reviewed	p.V268M	0.996	153	0%	113	45.1%	0	-	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	superfamily_Calcium-dependent phosphotriesterase
TECPR1	25851	genome.wustl.edu	37	7	97853019	97853019	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015395.1	-1	provisional	p.G901E	1.000	34	0%	13	38.5%	9	22.2%	probably_damaging(0.993)	deleterious(0.01)	deleterious(0.856)	HMMSmart_SM00694
AZGP1	563	genome.wustl.edu	37	7	99569369	99569369	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001185.3	-1	validated	p.G113R	0.083	150	0%	120	40%	40	5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_MHC_I,superfamily_MHC antigen-recognition domain
MCM7	4176	genome.wustl.edu	37	7	99693413	99693413	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005916.3	-1	reviewed	p.R527*	0.995	145	0%	181	45.3%	277	10.4%	-	-	-	HMMPfam_MCM,HMMSmart_SM00350,superfamily_P-loop containing nucleoside triphosphate hydrolases
STAG3	10734	genome.wustl.edu	37	7	99794894	99794894	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012447.2	+1	validated	p.H353Y	1.000	1027	0%	927	34.8%	0	-	benign(0.001)	tolerated(0.26)	neutral(0.034)	superfamily_ARM repeat
STAG3	10734	genome.wustl.edu	37	7	99802988	99802988	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012447.2	+1	validated	p.S1073	0.998	101	0%	116	44.8%	0	-	-	-	-	superfamily_ARM repeat
ZAN	7455	genome.wustl.edu	37	7	100382434	100382434	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003386.1	+1	reviewed	p.M2271L	0.337	21	0%	28	50%	0	-	probably_damaging(0.999)	deleterious(0.02)	deleterious(0.873)	NULL
CDHR3	222256	genome.wustl.edu	37	7	105658505	105658506	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152750.4	+1	validated	p.S548fs	0.004:0.000	-	-	-	-	-	-	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
DNAJB9	4189	genome.wustl.edu	37	7	108213373	108213373	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012328.1	+1	provisional	p.R83Q	0.999	135	0%	81	53.1%	12	66.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DnaJ,superfamily_Chaperone J-domain,PatternScan_DNAJ_1
PPP1R3A	5506	genome.wustl.edu	37	7	113558547	113558547	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002711.3	-1	reviewed	p.H169Y	0.996	177	0%	79	45.6%	0	-	benign(0)	tolerated(0.69)	neutral(0.002)	HMMPfam_CBM_21
GPR37	2861	genome.wustl.edu	37	7	124386654	124386654	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005302.2	-1	provisional	p.T589	0.998	156	0.6%	114	38.6%	1	0%	-	-	-	superfamily_Family A G protein-coupled receptor-like
OPN1SW	611	genome.wustl.edu	37	7	128415620	128415620	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001708.2	-1	reviewed	p.N75	0.085	111	0%	312	26.6%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
FLNC	2318	genome.wustl.edu	37	7	128481545	128481545	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001458.4	+1	reviewed	p.C682Y	1.000	97	0%	53	41.5%	0	-	benign(0.247)	deleterious(0.01)	neutral(0.431)	HMMSmart_SM00557,superfamily_E set domains,HMMPfam_Filamin
IRF5	3663	genome.wustl.edu	37	7	128582196	128582196	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098629.1	+1	reviewed	p.L21	1.000	46	0%	60	45%	0	-	-	-	-	HMMPfam_IRF,HMMSmart_IRF,superfamily_SSF46785
FAM40B	57464	genome.wustl.edu	37	7	129098142	129098142	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020704.2	+1	validated	p.E375D	1.000	29	0%	33	39.4%	1	0%	benign(0.001)	tolerated(0.34)	neutral(0.023)	NULL
CNOT4	4850	genome.wustl.edu	37	7	135106940	135106940	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013316.2	-1	validated	p.V113I	1.000	223	0%	149	41.6%	7	28.5%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928
KIAA1549	57670	genome.wustl.edu	37	7	138603602	138603602	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020910.2	-1	validated	p.A207V	0.000	281	0%	288	48.6%	0	-	benign(0.013)	tolerated(0.4)	neutral(0.017)	NULL
TRBV7-4	28594	genome.wustl.edu	37	7	142176751	142176751	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000390369	-1	known	p.L14	0.911	147	0%	125	44.8%	0	-	-	-	-	NULL
PRSS1	5644	genome.wustl.edu	37	7	142460750	142460750	+	Missense_Mutation	SNP	G	G	T	rs189270875	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002769.3	+1	reviewed	p.G208V	0.954	124	0%	145	36.6%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys
C7orf34	135927	genome.wustl.edu	37	7	142636705	142636705	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178829.4	+1	validated	p.W21*	0.000	47	0%	31	32.3%	0	-	-	-	-	NULL
LOC728377	728377	genome.wustl.edu	37	7	143979564	143979564	+	RNA	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_078379.1	-1	model	NULL	0.997	426	0.2%	395	17%	2	0%	-	-	-	-
ZNF862	643641	genome.wustl.edu	37	7	149559061	149559061	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001099220.1	+1	provisional	p.A938T	0.000	113	0%	70	35.7%	9	33.3%	benign(0)	deleterious(0.03)	neutral(0.364)	NULL
GIMAP1	170575	genome.wustl.edu	37	7	150417776	150417776	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_130759.2	+1	reviewed	p.A228	0.001	17	0%	18	38.9%	2	0%	-	-	-	HMMPfam_AIG1,superfamily_P-loop containing nucleoside triphosphate hydrolases
GALNT11	63917	genome.wustl.edu	37	7	151810418	151810418	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022087.2	+1	validated	p.E390K	1.000	157	0%	169	47.3%	102	52.9%	benign(0.021)	tolerated(0.22)	neutral(0.043)	superfamily_Nucleotide-diphospho-sugar transferases
MLL3	58508	genome.wustl.edu	37	7	151874769	151874769	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_170606.2	-1	reviewed	p.H2590R	0.988	114	0%	107	45.8%	1	100%	probably_damaging(0.998)	-	-	NULL
ESYT2	57488	genome.wustl.edu	37	7	158560398	158560398	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020728.2	-1	validated	p.V339I	0.993	98	0%	113	37.2%	5	0%	benign(0.183)	tolerated(0.37)	neutral(0.036)	NULL
TUSC3	7991	genome.wustl.edu	37	8	15517024	15517024	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006765.2	+1	reviewed	p.M145I	1.000	164	0%	91	48.4%	0	-	benign(0.006)	tolerated(0.11)	neutral(0.272)	HMMPfam_OST3_OST6,superfamily_Thioredoxin-like
EFHA2	286097	genome.wustl.edu	37	8	16921706	16921706	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181723.2	+1	validated	p.P165	0.761	218	0%	160	51.2%	0	-	-	-	-	NULL
STC1	6781	genome.wustl.edu	37	8	23702305	23702305	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003155.2	-1	reviewed	p.R241H	1.000	88	0%	129	41.9%	13	23%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_Stanniocalcin
NEFM	4741	genome.wustl.edu	37	8	24774948	24774948	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005382.2	+1	reviewed	p.K527R	1.000	63	0%	44	36.4%	0	-	unknown(0)	tolerated(0.13)	-	NULL
PTK2B	2185	genome.wustl.edu	37	8	27309038	27309038	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000397497	+1	known	p.R558C	0.000	29	0%	29	37.9%	0	-	benign(0.029)	deleterious(0.03)	neutral(0.366)	NULL
ADAM9	8754	genome.wustl.edu	37	8	38934903	38934903	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003816.2	+1	reviewed	p.N618	1.000	163	0%	123	54.5%	32	40.6%	-	-	-	HMMSmart_SM00608
PRKDC	5591	genome.wustl.edu	37	8	48761804	48761804	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000314191	-1	known	p.C2396W	1.000	197	0%	258	43.4%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_ARM repeat
RGS20	8601	genome.wustl.edu	37	8	54791979	54791979	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_170587.2	+1	validated	p.P109	0.633	36	0%	17	35.3%	0	-	-	-	-	NULL
CHD7	55636	genome.wustl.edu	37	8	61768742	61768742	+	Missense_Mutation	SNP	C	C	T	rs189926848	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017780.2	+1	reviewed	p.T2382M	0.472	29	0%	21	42.9%	12	33.3%	benign(0)	tolerated(0.17)	neutral(0.059)	NULL
CHD7	55636	genome.wustl.edu	37	8	61778287	61778287	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017780.2	+1	reviewed	p.A2930V	1.000	138	0%	110	36.4%	25	60%	possibly_damaging(0.797)	deleterious(0.03)	deleterious(0.664)	NULL
COPS5	10987	genome.wustl.edu	37	8	67968764	67968764	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006837.2	-1	reviewed	p.H217Y	1.000	69	0%	39	15.4%	86	12.7%	probably_damaging(0.999)	tolerated(0.13)	deleterious(0.743)	NULL
IL7	3574	genome.wustl.edu	37	8	79650847	79650847	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000880.2	-1	reviewed	p.A84	1.000	168	0%	75	37.3%	0	-	-	-	-	HMMPfam_IL7,HMMSmart_SM00127
FABP5	2171	genome.wustl.edu	37	8	82196201	82196201	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001444.1	+1	reviewed	p.L116I	0.201	70	0%	48	56.2%	65	46.1%	benign(0.211)	deleterious(0.05)	neutral(0.366)	HMMPfam_Lipocalin,superfamily_Lipocalins
UBR5	51366	genome.wustl.edu	37	8	103297490	103297490	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015902.4	-1	reviewed	p.R1854H	1.000	168	0%	151	42.4%	11	45.4%	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	NULL
LRP12	29967	genome.wustl.edu	37	8	105509713	105509713	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013437.4	-1	reviewed	p.A356V	1.000	120	0%	108	41.7%	1	100%	probably_damaging(0.996)	deleterious(0.01)	deleterious(0.867)	HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain
TG	7038	genome.wustl.edu	37	8	133906046	133906046	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003235.4	+1	reviewed	p.L958P	0.890	197	0%	237	41.4%	0	-	possibly_damaging(0.854)	deleterious(0)	deleterious(0.774)	NULL
ZFAT	57623	genome.wustl.edu	37	8	135622826	135622826	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020863.3	-1	reviewed	p.R174Q	0.342	216	0.5%	137	34.3%	0	-	probably_damaging(0.974)	deleterious(0)	deleterious(0.861)	NULL
COL22A1	169044	genome.wustl.edu	37	8	139890148	139890148	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152888.1	-1	validated	p.A168V	0.996	13	0%	25	48%	0	-	unknown(0)	tolerated(0.07)	-	HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like
COMMD5	28991	genome.wustl.edu	37	8	146076199	146076199	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001081003.1	-1	validated	p.S175	0.126	12	0%	19	52.6%	60	50%	-	-	-	HMMPfam_HCaRG
KIAA1432	57589	genome.wustl.edu	37	9	5763200	5763200	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020829.2	+1	validated	p.R646*	1.000	316	0%	357	47.3%	2	50%	-	-	-	NULL
UHRF2	115426	genome.wustl.edu	37	9	6413516	6413516	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152896.1	+1	reviewed	p.D9G	1.000	10	0%	19	21.1%	1	0%	possibly_damaging(0.631)	deleterious(0.03)	deleterious(0.585)	HMMPfam_ubiquitin,HMMSmart_SM00213,superfamily_Ubiquitin-like
KLHL9	55958	genome.wustl.edu	37	9	21333395	21333395	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018847.2	-1	validated	p.M488I	1.000	436	0%	434	38%	17	52.9%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain
TOPORS	10210	genome.wustl.edu	37	9	32543128	32543128	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005802.3	-1	reviewed	p.D465	0.006	230	0%	224	44.6%	9	66.6%	-	-	-	NULL
KIF24	347240	genome.wustl.edu	37	9	34297019	34297019	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_194313.2	-1	validated	p.N303D	1.000	23	0%	27	51.9%	0	-	benign(0.016)	tolerated(0.15)	neutral(0.241)	HMMPfam_Kinesin,HMMSmart_SM00129,superfamily_P-loop containing nucleoside triphosphate hydrolases
GRHPR	9380	genome.wustl.edu	37	9	37432012	37432012	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012203.1	+1	reviewed	p.V248I	0.995	59	0%	44	38.6%	360	45.2%	benign(0.342)	tolerated(0.52)	neutral(0.116)	HMMPfam_2-Hacid_dh,HMMPfam_2-Hacid_dh_C,PatternScan_D_2_HYDROXYACID_DH_3,superfamily_NAD(P)-binding Rossmann-fold domains
MCART1	92014	genome.wustl.edu	37	9	37888304	37888304	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033412.3	-1	validated	p.R82C	1.000	182	0%	208	45.2%	4	25%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_Mitoch_carrier,HMMPfam_Mito_carr
FAM74A3	728495	genome.wustl.edu	37	9	40716026	40716026	+	RNA	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_026801.1	+1	predicted	NULL	0.968	64	0%	77	54.5%	0	-	-	-	-	-
FAM75A6	389730	genome.wustl.edu	37	9	43626190	43626191	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145196.1	-1	predicted	p.T832fs	0.000:0.000	-	-	-	-	-	-	-	-	-	NULL
DAPK1	1612	genome.wustl.edu	37	9	90296405	90296405	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004938.2	+1	reviewed	p.S696	0.011	183	0%	148	38.5%	12	25%	-	-	-	superfamily_SSF52540
C9orf79	286234	genome.wustl.edu	37	9	90502203	90502203	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178828.4	+1	validated	p.P934L	0.000	71	0%	54	53.7%	0	-	benign(0)	tolerated(1)	-	NULL
ASPN	54829	genome.wustl.edu	37	9	95237021	95237022	+	In_Frame_Ins	INS	-	-	TCC	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017680.3	-1	validated	p.53in_frame_insE	0.936:0.967	-	-	-	-	-	-	-	-	-	superfamily_SSF52058
ABCA1	19	genome.wustl.edu	37	9	107566905	107566905	+	Splice_Site	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005502.2	-1	reviewed	e31+2	0.999	189	0%	87	34.5%	0	-	-	-	-	-
CTNNAL1	8727	genome.wustl.edu	37	9	111714732	111714732	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003798.2	-1	provisional	p.D558N	1.000	132	0%	126	40.5%	65	56.9%	probably_damaging(1)	tolerated(0.12)	deleterious(0.760)	superfamily_alpha-catenin/vinculin
SUSD1	64420	genome.wustl.edu	37	9	114905868	114905868	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000374263	-1	known	p.H137Y	0.938	206	0%	181	44.8%	1	0%	benign(0.119)	deleterious(0.02)	neutral(0.393)	HMMSmart_EGF_CA,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_SSF57196
PTBP3	9991	genome.wustl.edu	37	9	115060116	115060116	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000374257	-1	known	p.V10	0.996	214	0%	115	52.2%	2	100%	-	-	-	NULL
C5	727	genome.wustl.edu	37	9	123760010	123760010	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001735.2	-1	reviewed	p.E869K	0.693	130	0%	119	46.2%	1	100%	benign(0)	tolerated(0.88)	-	NULL
OR1B1	347169	genome.wustl.edu	37	9	125391204	125391204	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004450.1	-1	provisional	p.A204V	0.019	151	0%	198	46%	0	-	possibly_damaging(0.815)	tolerated(1)	neutral(0.307)	HMMPfam_7tm_1,superfamily_SSF81321
WDR38	401551	genome.wustl.edu	37	9	127618537	127618538	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	CT	CT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001045476.1	+1	provisional	p.L143fs	0.067:0.069	-	-	-	-	-	-	-	-	-	HMMSmart_WD40,superfamily_WD40_like,HMMPfam_WD40
GAPVD1	26130	genome.wustl.edu	37	9	128061313	128061313	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015635.2	+1	validated	p.A38V	1.000	156	0%	126	42.1%	2	50%	probably_damaging(0.996)	tolerated(0.1)	deleterious(0.748)	NULL
FPGS	2356	genome.wustl.edu	37	9	130569337	130569337	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004957.4	+1	reviewed	p.R158C	0.999	30	0%	39	41%	97	52.5%	benign(0.011)	tolerated(0.11)	neutral(0.272)	superfamily_MurD-like peptide ligases catalytic domain
ODF2	4957	genome.wustl.edu	37	9	131262462	131262462	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002540.3	+1	reviewed	p.N782	0.370	171	0%	133	33.8%	95	50.5%	-	-	-	NULL
LRRC8A	56262	genome.wustl.edu	37	9	131670714	131670714	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127244.1	+1	reviewed	p.A424V	1.000	28	0%	26	46.2%	20	40%	benign(0.001)	deleterious(0.02)	neutral(0.383)	NULL
ASB6	140459	genome.wustl.edu	37	9	132400170	132400170	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017873.2	-1	reviewed	p.P389S	1.000	50	0%	34	50%	35	51.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_SOCS_box,HMMSmart_SM00253
TOR1B	27348	genome.wustl.edu	37	9	132571717	132571717	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014506.1	+1	provisional	p.R289M	0.542	121	0%	104	45.2%	6	16.6%	benign(0.214)	tolerated(0.2)	neutral(0.070)	HMMPfam_Torsin,superfamily_SSF52540
LAMC3	10319	genome.wustl.edu	37	9	133914614	133914614	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006059.3	+1	reviewed	p.S421L	0.992	19	0%	31	51.6%	2	0%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,PatternScan_EGF_LAM_1,superfamily_SSF57196
GTF3C5	9328	genome.wustl.edu	37	9	135933232	135933232	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001122823.1	+1	validated	p.G482	0.000	30	0.000	5	0.800	119	46.2%	-	-	-	NULL
GBGT1	26301	genome.wustl.edu	37	9	136029008	136029008	+	Missense_Mutation	SNP	G	G	A	rs189095621	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021996.4	-1	validated	p.R334C	1.000	32	0%	16	43.8%	4	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Glyco_transf_6,superfamily_Nucleotide-diphospho-sugar transferases
BRD3	8019	genome.wustl.edu	37	9	136901326	136901326	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007371.3	-1	reviewed	p.P588	0.001	28	0%	31	61.3%	20	60%	-	-	-	NULL
UBAC1	10422	genome.wustl.edu	37	9	138836987	138836987	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016172.2	-1	validated	p.A255T	0.016	37	0%	32	37.5%	37	24.3%	benign(0)	tolerated(0.74)	neutral(0.002)	NULL
NOTCH1	4851	genome.wustl.edu	37	9	139395086	139395086	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017617.3	-1	reviewed	p.S1951N	1.000	11	0%	13	30.8%	6	33.3%	benign(0.298)	deleterious(0.01)	deleterious(0.498)	HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK
CACNA1B	774	genome.wustl.edu	37	9	141014730	141014730	+	Silent	SNP	G	G	A	rs187721569	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000718.2	+1	validated	p.S2048	0.000	4	0.000	6	0.667	0	-	-	-	-	NULL
DIP2C	22982	genome.wustl.edu	37	10	436261	436261	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014974.2	-1	reviewed	p.P479	0.033	131	0%	117	39.3%	0	-	-	-	-	HMMPfam_AMP-binding,superfamily_SSF56801
FAM208B	54906	genome.wustl.edu	37	10	5791578	5791578	+	Missense_Mutation	SNP	G	G	A	rs45596231	byFrequency;by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017782.4	+1	validated	p.S2065N	0.000	167	0%	109	41.3%	11	45.4%	benign(0.102)	tolerated(0.22)	neutral(0.050)	NULL
FAM171A1	221061	genome.wustl.edu	37	10	15255162	15255162	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001010924.1	-1	validated	p.E809*	0.994	65	0%	68	47.1%	65	61.5%	-	-	-	HMMPfam_UPF0560
PLXDC2	84898	genome.wustl.edu	37	10	20466006	20466006	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032812.7	+1	provisional	p.E321G	1.000	258	0%	112	35.7%	1	0%	probably_damaging(0.998)	tolerated(0.32)	deleterious(0.498)	NULL
ENSG00000099251	0	genome.wustl.edu	37	10	38647276	38647276	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000356314	+1	known	p.A24	0.062	32	0%	41	39%	1	0%	-	-	-	HMMPfam_adh_short,superfamily_NAD(P)-binding Rossmann-fold domains
SYT15	83849	genome.wustl.edu	37	10	46968715	46968715	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031912.3	-1	reviewed	p.A74D	0.001	53	0%	37	18.9%	0	-	benign(0)	deleterious(0.01)	neutral(0.406)	NULL
GPRIN2	9721	genome.wustl.edu	37	10	46999914	46999914	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014696.3	+1	validated	p.C345Y	1.000	28	0%	29	20.7%	1	0%	probably_damaging(0.981)	deleterious(0.01)	deleterious(0.831)	NULL
FRMPD2	143162	genome.wustl.edu	37	10	49446049	49446049	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001018071.3	-1	reviewed	p.L302	0.049	166	0%	124	43.5%	1	0%	-	-	-	NULL
ARID5B	84159	genome.wustl.edu	37	10	63661940	63661940	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032199.2	+1	validated	p.L15S	1.000	129	0%	98	42.9%	0	-	benign(0.029)	tolerated(0.3)	neutral(0.030)	NULL
ARID5B	84159	genome.wustl.edu	37	10	63852312	63852312	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032199.2	+1	validated	p.A1030	0.000	103	0%	90	44.4%	6	50%	-	-	-	NULL
HK1	3098	genome.wustl.edu	37	10	71136805	71136805	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033497.2	+1	reviewed	p.R335*	0.998	129	0%	90	48.9%	17	5.8%	-	-	-	HMMPfam_Hexokinase_2,superfamily_SSF53067
CDH23	64072	genome.wustl.edu	37	10	73563053	73563053	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022124.5	+1	reviewed	p.A2583V	1.000	18	0%	23	47.8%	0	-	probably_damaging(1)	tolerated(0.11)	deleterious(0.772)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
PPP3CB	5532	genome.wustl.edu	37	10	75231318	75231318	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142353.1	-1	validated	p.S193C	1.000	255	0%	138	34.1%	5	20%	benign(0)	tolerated(1)	-	HMMPfam_Metallophos,HMMSmart_PP2Ac,superfamily_SSF56300
SAMD8	142891	genome.wustl.edu	37	10	76924436	76924436	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144660.2	+1	validated	p.T204	0.960	163	0%	116	37.1%	8	50%	-	-	-	NULL
POLR3A	11128	genome.wustl.edu	37	10	79769401	79769401	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007055.3	-1	validated	p.F601	1.000	170	0%	219	34.7%	1	100%	-	-	-	HMMPfam_RNA_pol_Rpb1_3,superfamily_SSF64484
GLUD1	2746	genome.wustl.edu	37	10	88836378	88836378	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005271.3	-1	reviewed	p.V161I	1.000	187	0%	64	32.8%	16	56.2%	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	HMMPfam_ELFV_dehydrog_N,superfamily_SSF53223
PTEN	5728	genome.wustl.edu	37	10	89692904	89692904	+	Nonsense_Mutation	SNP	C	C	T	rs121909224	byCluster	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.R130*	1.000	282	0%	225	39.1%	5	60%	-	-	-	HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II
PTEN	5728	genome.wustl.edu	37	10	89720741	89720741	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.Q298*	1.000	314	0%	212	45.8%	13	30.7%	-	-	-	superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_PTEN_C2
IFIT5	24138	genome.wustl.edu	37	10	91177167	91177167	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012420.2	+1	validated	p.L71F	0.001	140	0%	152	53.3%	3	33.3%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_TPR_1,HMMSmart_TPR,superfamily_SSF48452
PCGF5	84333	genome.wustl.edu	37	10	93008435	93008435	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032373.3	+1	provisional	p.R93	0.998	762	0%	439	44%	0	-	-	-	-	superfamily_RING/U-box
PLCE1	51196	genome.wustl.edu	37	10	95994018	95994018	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016341.3	+1	reviewed	p.S721	0.026	169	0.6%	119	40.3%	0	-	-	-	-	HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF
SLIT1	6585	genome.wustl.edu	37	10	98761034	98761034	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371070	-1	known	p.R1439H	0.973	32	0%	32	43.8%	0	-	benign(0.238)	tolerated(0.59)	neutral(0.029)	NULL
ABCC2	1244	genome.wustl.edu	37	10	101560266	101560266	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000392.3	+1	reviewed	p.C385	1.000	340	0%	325	47.4%	0	-	-	-	-	HMMPfam_ABC_membrane,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain
GBF1	8729	genome.wustl.edu	37	10	104123022	104123022	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004193.1	+1	provisional	p.T628S	0.973	59	0%	44	45.5%	3	0%	benign(0)	tolerated(0.75)	neutral(0.002)	NULL
SUFU	51684	genome.wustl.edu	37	10	104309851	104309851	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016169.3	+1	reviewed	p.V148M	1.000	66	0%	64	51.6%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_SUFU,superfamily_Suppressor of Fused N-terminal domain
CCDC147	159686	genome.wustl.edu	37	10	106125669	106125669	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001008723.1	+1	validated	p.M232T	1.000	99	0%	97	47.4%	0	-	benign(0.309)	tolerated(0.17)	neutral(0.155)	NULL
SORCS1	114815	genome.wustl.edu	37	10	108427525	108427525	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001013031.1	-1	reviewed	p.C742Y	1.000	67	0%	37	40.5%	0	-	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMSmart_VPS10
NRAP	4892	genome.wustl.edu	37	10	115391645	115391645	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198060.2	-1	validated	p.A571T	1.000	345	0.6%	205	42.9%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Nebulin,HMMSmart_SM00227
PPAPDC1A	196051	genome.wustl.edu	37	10	122278345	122278345	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001030059.1	+1	validated	p.A86V	1.000	166	0%	81	38.3%	0	-	benign(0.022)	deleterious(0.01)	neutral(0.407)	HMMPfam_PAP2,HMMSmart_SM00014,superfamily_Acid phosphatase/Vanadium-dependent haloperoxidase
RIC8A	60626	genome.wustl.edu	37	11	212920	212920	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021932.4	+1	provisional	p.E438K	0.961	41	0%	33	57.6%	124	51.6%	possibly_damaging(0.659)	tolerated(0.18)	neutral(0.289)	HMMPfam_Ric8
MUC5B	727897	genome.wustl.edu	37	11	1264230	1264230	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002458.1	+1	validated	p.S2043	0.002	133	0.8%	172	48.8%	26	26.9%	-	-	-	NULL
KRTAP5-1	387264	genome.wustl.edu	37	11	1605933	1605933	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005922.1	-1	validated	p.C183R	0.071	125	0%	132	27.3%	5	20%	unknown(0)	deleterious(0)	-	PatternScan_4FE4S_FER_1
TNNT3	7140	genome.wustl.edu	37	11	1959705	1959705	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006757.3	+1	reviewed	p.G254S	1.000	7	0.000	11	0.364	0	-	probably_damaging(0.998)	tolerated(0.19)	deleterious(0.524)	NULL
DCHS1	8642	genome.wustl.edu	37	11	6646599	6646599	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003737.2	-1	reviewed	p.R2326C	1.000	94	0%	45	40%	3	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
EIF4G2	1982	genome.wustl.edu	37	11	10823260	10823260	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000429377	-1	known	p.S527L	1.000	247	0%	187	41.2%	176	31.8%	possibly_damaging(0.925)	deleterious(0.01)	deleterious(0.779)	NULL
USP47	55031	genome.wustl.edu	37	11	11951042	11951044	+	In_Frame_Del	DEL	ATT	ATT	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	ATT	ATT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017944.3	+1	validated	p.Y417in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_UCH,superfamily_Cysteine proteinases
MICALCL	84953	genome.wustl.edu	37	11	12313763	12313763	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032867.2	+1	validated	p.S16	0.005	162	0%	164	45.7%	0	-	-	-	-	NULL
LDHC	3948	genome.wustl.edu	37	11	18434390	18434390	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002301.4	+1	reviewed	p.K42	1.000	117	0%	113	41.6%	0	-	-	-	-	HMMPfam_Ldh_1_N,superfamily_NAD(P)-bd
LDHC	3948	genome.wustl.edu	37	11	18436758	18436758	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002301.4	+1	reviewed	p.D52N	1.000	113	0%	77	50.6%	0	-	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	HMMPfam_Ldh_1_N,superfamily_NAD(P)-bd
EIF3M	10480	genome.wustl.edu	37	11	32615480	32615480	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006360.3	+1	provisional	p.R201Q	1.000	87	0%	57	36.8%	269	52.4%	probably_damaging(0.992)	deleterious(0.01)	deleterious(0.853)	NULL
CHST1	8534	genome.wustl.edu	37	11	45672090	45672090	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003654.4	-1	validated	p.Y128	0.645	33	0%	52	46.2%	2	50%	-	-	-	HMMPfam_Sulfotransfer_1,superfamily_SSF52540
SLC35C1	55343	genome.wustl.edu	37	11	45832387	45832387	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018389.4	+1	reviewed	p.T199I	1.000	14	0.000	8	0.500	23	73.9%	benign(0.001)	tolerated(0.29)	neutral(0.029)	HMMPfam_TPT
PACSIN3	29763	genome.wustl.edu	37	11	47199520	47199520	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016223.4	-1	reviewed	p.L413M	1.000	18	0.000	8	0.625	314	50.9%	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	HMMPfam_SH3_1,HMMSmart_SH3,superfamily_SH3
OR4C2P	119750	genome.wustl.edu	37	11	48441911	48441911	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000428162	+1	known	p.G39D	0.941	116	0%	115	47%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
OR8K3	219473	genome.wustl.edu	37	11	56086683	56086683	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005202.1	+1	provisional	p.R301*	0.000	117	0%	91	45.1%	0	-	-	-	-	superfamily_SSF81321
OR5M10	390167	genome.wustl.edu	37	11	56345167	56345167	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004741.1	-1	provisional	p.E11K	0.314	178	0%	164	34.1%	0	-	possibly_damaging(0.877)	deleterious(0)	deleterious(0.786)	superfamily_SSF81321
APLNR	187	genome.wustl.edu	37	11	57003463	57003463	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005161.4	-1	reviewed	p.S339N	0.890	41	0%	55	45.5%	3	0%	benign(0.098)	tolerated(0.08)	neutral(0.307)	superfamily_SSF81321
ZDHHC5	25921	genome.wustl.edu	37	11	57466083	57466083	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015457.2	+1	validated	p.R392H	1.000	167	0%	133	42.1%	87	48.2%	benign(0.004)	tolerated(0.09)	neutral(0.296)	NULL
MS4A13	503497	genome.wustl.edu	37	11	60292794	60292794	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001012417.2	+1	validated	p.Q101*	0.999	98	0%	38	42.1%	0	-	-	-	-	HMMPfam_CD20
SLC22A9	114571	genome.wustl.edu	37	11	63177326	63177326	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080866.2	+1	validated	p.Q552*	0.000	151	0%	88	44.3%	0	-	-	-	-	NULL
STIP1	10963	genome.wustl.edu	37	11	63962067	63962067	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006819.2	+1	validated	p.R160*	0.414	37	0%	35	37.1%	83	6%	-	-	-	HMMSmart_STI1,superfamily_SSF48452
RASGRP2	10235	genome.wustl.edu	37	11	64503388	64503388	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098670.1	-1	reviewed	p.R387H	0.999	11	0.000	9	0.444	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00147,superfamily_Ras GEF
NAALADL1	10004	genome.wustl.edu	37	11	64812878	64812878	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005468.2	-1	validated	p.L696	1.000	12	0%	14	50%	0	-	-	-	-	HMMPfam_TFR_dimer,superfamily_Transferrin receptor ectodomain C-terminal domain
CORO1B	57175	genome.wustl.edu	37	11	67208702	67208702	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001018070.1	-1	validated	p.A217V	0.995	18	0%	11	45.5%	253	49.4%	benign(0.002)	deleterious(0.05)	neutral(0.345)	superfamily_WD40 repeat-like
ACY3	91703	genome.wustl.edu	37	11	67410358	67410358	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080658.1	-1	validated	p.S266N	0.570	9	0.000	24	0.458	41	31.7%	benign(0)	tolerated(0.64)	neutral(0.003)	HMMPfam_AstE_AspA
MRGPRD	116512	genome.wustl.edu	37	11	68748083	68748083	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198923.2	-1	validated	p.L125F	0.511	40	0%	58	43.1%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_7tm_1,superfamily_SSF81321
SERPINH1	871	genome.wustl.edu	37	11	75277520	75277520	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001235.2	+1	reviewed	p.T42	0.995	9	0.000	13	0.308	79	46.8%	-	-	-	HMMPfam_Serpin,superfamily_Serpins
SERPINH1	871	genome.wustl.edu	37	11	75277662	75277662	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001235.2	+1	reviewed	p.A90T	0.998	12	0%	14	57.1%	64	39%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Serpin,HMMSmart_SM00093,superfamily_Serpins
SERPINH1	871	genome.wustl.edu	37	11	75282833	75282833	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001235.2	+1	reviewed	p.L321P	1.000	49	0%	45	26.7%	249	34.1%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Serpin,HMMSmart_SM00093,superfamily_Serpins
MYO7A	4647	genome.wustl.edu	37	11	76871323	76871323	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000260.3	+1	reviewed	p.V399I	1.000	6	0.000	6	0.833	1	0%	benign(0.323)	deleterious(0.03)	neutral(0.466)	HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases
DLG2	1740	genome.wustl.edu	37	11	84027875	84027875	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000280241	-1	known	p.P105L	0.999	143	0%	170	47.6%	0	-	possibly_damaging(0.508)	deleterious(0.01)	deleterious(0.576)	HMMPfam_MAGUK_N_PEST
FAT3	120114	genome.wustl.edu	37	11	92599975	92599975	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001008781.2	+1	validated	p.G3909	1.000	20	0%	17	29.4%	0	-	-	-	-	HMMSmart_SM00282,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_2
KDM4D	55693	genome.wustl.edu	37	11	94730840	94730840	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018039.2	+1	validated	p.R102C	0.976	248	0%	215	44.2%	0	-	benign(0.133)	deleterious(0.05)	neutral(0.356)	NULL
MMP27	64066	genome.wustl.edu	37	11	102562587	102562587	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022122.2	-1	reviewed	p.S484	0.023	172	0%	67	37.3%	0	-	-	-	-	NULL
ATM	472	genome.wustl.edu	37	11	108186827	108186827	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000051.3	+1	reviewed	p.A2062V	1.000	135	0%	79	36.7%	2	0%	benign(0)	tolerated(1)	-	superfamily_ARM repeat
ATM	472	genome.wustl.edu	37	11	108216609	108216609	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000051.3	+1	reviewed	p.T2853M	1.000	412	0%	187	46.5%	6	16.6%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat
ZC3H12C	85463	genome.wustl.edu	37	11	110035624	110035624	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033390.1	+1	validated	p.R605Q	0.068	116	0%	154	45.5%	0	-	probably_damaging(0.987)	tolerated(0.21)	deleterious(0.480)	NULL
DCPS	28960	genome.wustl.edu	37	11	126174027	126174027	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014026.3	+1	validated	p.E18*	0.979	14	0%	27	63%	20	45%	-	-	-	NULL
DCP1B	196513	genome.wustl.edu	37	12	2062350	2062350	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152640.3	-1	validated	p.Q252H	0.000	88	2.3%	61	42.6%	6	83.3%	benign(0)	tolerated(0.61)	neutral(0.004)	NULL
CD9	928	genome.wustl.edu	37	12	6344728	6344728	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000382519	+1	known	p.E228K	0.000	43	0%	57	29.8%	1719	50.5%	unknown(0)	deleterious(0)	-	NULL
EMG1	10436	genome.wustl.edu	37	12	7080234	7080234	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000261406	+1	known	p.A49V	1.000	21	0%	16	50%	70	30%	-	-	-	HMMPfam_EMG1
CDKN1B	1027	genome.wustl.edu	37	12	12870837	12870837	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004064.3	+1	reviewed	p.E22*	1.000	17	0%	22	45.5%	45	40%	-	-	-	NULL
KRAS	3845	genome.wustl.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529	byCluster	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033360.2	-1	reviewed	p.G12D	1.000	68	0%	29	41.4%	5	40%	possibly_damaging(0.886)	deleterious(0)	deleterious(0.791)	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases
IPO8	10526	genome.wustl.edu	37	12	30843490	30843490	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006390.2	-1	reviewed	p.A36T	1.000	320	0%	145	35.2%	6	66.6%	possibly_damaging(0.465)	deleterious(0)	deleterious(0.598)	HMMPfam_IBN_N,superfamily_ARM-type_fold
DDX11	1663	genome.wustl.edu	37	12	31244705	31244705	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152438.1	+1	reviewed	p.A381V	0.716	28	0%	35	28.6%	44	36.3%	benign(0)	tolerated(0.82)	neutral(0.001)	HMMSmart_SM00488,HMMPfam_DEAD_2,superfamily_P-loop containing nucleoside triphosphate hydrolases
PFKM	5213	genome.wustl.edu	37	12	48535728	48535728	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000289.5	+1	reviewed	p.G511D	1.000	138	0%	151	41.1%	11	54.5%	probably_damaging(0.996)	tolerated(0.05)	deleterious(0.807)	HMMPfam_PFK,superfamily_Phosphofructokinase
ASIC1	41	genome.wustl.edu	37	12	50452691	50452691	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020039.2	+1	reviewed	p.L48M	1.000	56	0%	40	55%	5	60%	possibly_damaging(0.832)	deleterious(0.02)	deleterious(0.700)	HMMPfam_ASC
KRT1	3848	genome.wustl.edu	37	12	53070923	53070923	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006121.3	-1	reviewed	p.R392*	0.292	195	0%	204	49%	0	-	-	-	-	HMMPfam_Filament
ATF7	11016	genome.wustl.edu	37	12	53917071	53917071	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130059.1	-1	validated	p.Q419R	1.000	72	0%	64	48.4%	7	28.5%	benign(0.429)	tolerated(0.2)	neutral(0.189)	NULL
PDE1B	5153	genome.wustl.edu	37	12	54964070	54964070	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000924.3	+1	validated	p.A175T	0.997	189	0%	168	42.9%	0	-	benign(0)	tolerated(0.15)	neutral(0.241)	superfamily_SSF109604
WIBG	84305	genome.wustl.edu	37	12	56297213	56297213	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032345.2	-1	validated	p.R30Q	1.000	84	0%	78	38.5%	94	59.5%	probably_damaging(0.999)	deleterious(0.02)	deleterious(0.873)	HMMPfam_Mago-bind,superfamily_Pym (Within the bgcn gene intron protein WIBG) N-terminal domain
IKZF4	64375	genome.wustl.edu	37	12	56428877	56428877	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022465.3	+1	validated	p.R507Q	1.000	133	0%	212	43.4%	2	100%	possibly_damaging(0.73)	tolerated(0.23)	neutral(0.308)	NULL
ESYT1	23344	genome.wustl.edu	37	12	56532241	56532241	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015292.2	+1	validated	p.A797	0.015	29	0%	44	34.1%	64	46.8%	-	-	-	superfamily_C2 domain (Calcium/lipid-binding domain CaLB)
MON2	23041	genome.wustl.edu	37	12	62959121	62959121	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015026.2	+1	validated	p.Q1379	0.999	190	0%	126	40.5%	4	50%	-	-	-	superfamily_ARM-type_fold
LEMD3	23592	genome.wustl.edu	37	12	65634798	65634798	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014319.4	+1	reviewed	p.R746W	1.000	218	0.5%	163	46%	7	57.1%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_MAN1_C
IL26	55801	genome.wustl.edu	37	12	68619273	68619273	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018402.1	-1	reviewed	p.R60H	0.214	273	0.4%	267	43.4%	0	-	benign(0.001)	tolerated(0.45)	neutral(0.012)	superfamily_4_helix_cytokine,HMMSmart_IL10
NAV3	89795	genome.wustl.edu	37	12	78571410	78571410	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000228327	+1	known	p.V1720I	1.000	149	0%	62	40.3%	0	-	benign(0.069)	tolerated(0.23)	neutral(0.046)	NULL
OTOGL	283310	genome.wustl.edu	37	12	80613571	80613574	+	Frame_Shift_Del	DEL	TTTT	TTTT	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	TTTT	TTTT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002343203.1	+1	model	p.F15fs	0.783:0.235:0.100:0.000	-	-	-	-	-	-	-	-	-	NULL
PPFIA2	8499	genome.wustl.edu	37	12	81839382	81839382	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003625.2	-1	reviewed	p.K175E	1.000	118	0%	95	27.4%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
ENSG00000227825	0	genome.wustl.edu	37	12	98849257	98849257	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000370696	-1	known	p.R214Q	0.702	27	0%	28	50%	1	0%	-	-	-	NULL
WSCD2	9671	genome.wustl.edu	37	12	108620780	108620780	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014653.2	+1	validated	p.A273V	1.000	59	0%	61	37.7%	0	-	benign(0.418)	deleterious(0)	deleterious(0.580)	HMMPfam_WSC,HMMSmart_SM00321
SSH1	54434	genome.wustl.edu	37	12	109186539	109186539	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018984.3	-1	validated	p.D472	0.984	49	0%	45	37.8%	3	66.6%	-	-	-	NULL
TMEM116	89894	genome.wustl.edu	37	12	112369575	112369575	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138341.1	-1	provisional	p.Q196	1.000	161	0%	156	44.9%	10	50%	-	-	-	NULL
VSIG10	54621	genome.wustl.edu	37	12	118504457	118504459	+	In_Frame_Del	DEL	TCT	TCT	-	rs185858778	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	TCT	TCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019086.5	-1	validated	p.E536in_frame_del	0.026:0.096:0.110	-	-	-	-	-	-	-	-	-	NULL
CIT	11113	genome.wustl.edu	37	12	120150421	120150421	+	Silent	SNP	G	G	T	rs142811369	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007174.1	-1	validated	p.S1511	0.015	110	0%	124	46.8%	7	57.1%	-	-	-	HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like
KDM2B	84678	genome.wustl.edu	37	12	121987468	121987468	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032590.4	-1	reviewed	p.R158H	1.000	38	0%	49	36.7%	5	20%	probably_damaging(0.985)	deleterious(0.01)	deleterious(0.838)	superfamily_Clavaminate synthase-like
B3GNT4	79369	genome.wustl.edu	37	12	122691003	122691003	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030765.2	+1	reviewed	p.P69T	0.000	100	0%	61	41%	5	80%	benign(0)	deleterious(0.04)	neutral(0.349)	NULL
SFSWAP	6433	genome.wustl.edu	37	12	132211525	132211525	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004592.2	+1	reviewed	p.E291D	0.561	91	0%	78	39.7%	26	38.4%	benign(0.025)	tolerated(0.85)	neutral(0.002)	NULL
ZMYM2	7750	genome.wustl.edu	37	13	20632822	20632822	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003453.2	+1	validated	p.M867I	1.000	435	0%	318	41.2%	27	33.3%	possibly_damaging(0.478)	tolerated(0.08)	neutral(0.458)	NULL
GJB2	2706	genome.wustl.edu	37	13	20763690	20763690	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004004.5	-1	reviewed	p.G11R	1.000	96	0%	64	46.9%	14	50%	possibly_damaging(0.926)	deleterious(0.03)	deleterious(0.739)	HMMPfam_Connexin
PABPC3	5042	genome.wustl.edu	37	13	25671837	25671837	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030979.2	+1	validated	p.R501C	0.979	109	0.9%	148	41.9%	0	-	benign(0.005)	deleterious(0.04)	neutral(0.349)	superfamily_PABC (PABP) domain
FRY	10129	genome.wustl.edu	37	13	32783153	32783153	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_023037.2	+1	validated	p.D1394	0.077	128	0%	116	41.4%	0	-	-	-	-	NULL
CSNK1A1L	122011	genome.wustl.edu	37	13	37679199	37679199	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145203.5	-1	validated	p.T65	0.993	159	0%	168	44%	0	-	-	-	-	superfamily_Kinase_like,HMMPfam_Pkinase
LHFP	10186	genome.wustl.edu	37	13	39952645	39952645	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005780.2	-1	reviewed	p.G135D	1.000	77	0%	67	44.8%	8	25%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_L_HGMIC_fpl
SLC25A15	10166	genome.wustl.edu	37	13	41373280	41373280	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014252.3	+1	reviewed	p.T48I	0.581	130	0%	138	45.7%	29	41.3%	benign(0)	tolerated(1)	-	superfamily_Mitochondrial carrier,HMMPfam_Mito_carr
DIAPH3	81624	genome.wustl.edu	37	13	60453407	60453407	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001042517.1	-1	validated	p.R855W	1.000	138	0%	82	48.8%	10	80%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00498,HMMPfam_FH2,superfamily_Formin homology 2 domain (FH2 domain)
RBM26	64062	genome.wustl.edu	37	13	79940321	79940321	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022118.3	-1	validated	p.P382H	1.000	145	0%	103	43.7%	8	62.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
TM9SF2	9375	genome.wustl.edu	37	13	100153989	100153989	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004800.1	+1	provisional	p.P43	0.986	48	0%	49	57.1%	34	29.4%	-	-	-	NULL
NALCN	259232	genome.wustl.edu	37	13	101944628	101944628	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052867.2	-1	validated	p.R297C	1.000	173	0%	114	33.3%	0	-	probably_damaging(0.998)	deleterious(0.03)	deleterious(0.839)	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
LIG4	3981	genome.wustl.edu	37	13	108862191	108862191	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098268.1	-1	reviewed	p.R476W	0.998	207	0%	197	42.1%	2	50%	probably_damaging(0.991)	deleterious(0)	deleterious(0.889)	HMMPfam_DNA_ligase_A_C
MYO16	23026	genome.wustl.edu	37	13	109779690	109779690	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015011.1	+1	validated	p.A1259	0.005	22	0%	23	39.1%	0	-	-	-	-	NULL
IPO4	79711	genome.wustl.edu	37	14	24652526	24652526	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024658.3	-1	validated	p.E719D	1.000	20	0%	14	42.9%	88	53.4%	benign(0.176)	tolerated(0.54)	neutral(0.024)	superfamily_ARM repeat
NYNRIN	57523	genome.wustl.edu	37	14	24880575	24880575	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025081.2	+1	validated	p.T854M	0.894	331	0%	289	44.3%	7	14.2%	probably_damaging(0.973)	deleterious(0.04)	deleterious(0.764)	NULL
ENSG00000250370	0	genome.wustl.edu	37	14	31354988	31354988	+	RNA	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000503907	-1	known	NULL	0.000	250	0%	155	45.8%	0	-	-	-	-	-
NPAS3	64067	genome.wustl.edu	37	14	34243680	34243680	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173159.2	+1	reviewed	p.C317	1.000	172	0%	141	41.1%	0	-	-	-	-	HMMSmart_PAS,superfamily_SSF55785
CFL2	1073	genome.wustl.edu	37	14	35182459	35182459	+	Splice_Site	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021914.7	-1	reviewed	e2+1	1.000	89	0%	63	41.3%	0	-	-	-	-	-
PNN	5411	genome.wustl.edu	37	14	39649880	39649880	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002687.3	+1	validated	p.G323C	1.000	56	0%	88	43.2%	94	62.7%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	NULL
PRPF39	55015	genome.wustl.edu	37	14	45564489	45564489	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017922.3	+1	validated	p.S16N	1.000	279	0%	206	40.3%	14	57.1%	benign(0.001)	tolerated(0.6)	neutral(0.004)	NULL
NIN	51199	genome.wustl.edu	37	14	51238089	51238089	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020921.3	-1	reviewed	p.A360V	1.000	63	0%	67	47.8%	3	100%	unknown(0)	deleterious(0)	-	superfamily_EF-hand
GMFB	2764	genome.wustl.edu	37	14	54950424	54950424	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004124.2	-1	validated	p.R22H	1.000	99	0%	82	36.6%	6	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Cofilin_ADF,HMMSmart_SM00102,superfamily_Actin depolymerizing proteins
PPP2R5E	5529	genome.wustl.edu	37	14	64006378	64006380	+	In_Frame_Del	DEL	GGA	GGA	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	GGA	GGA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006246.2	-1	reviewed	p.P9in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
ZBTB25	7597	genome.wustl.edu	37	14	64954442	64954442	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006977.2	-1	validated	p.Q169	1.000	179	0%	200	44%	6	66.6%	-	-	-	NULL
SPTB	6710	genome.wustl.edu	37	14	65253879	65253879	+	Splice_Site	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001024858.2	-1	reviewed	e15-1	1.000	23	0%	26	57.7%	0	-	-	-	-	-
DCAF5	8816	genome.wustl.edu	37	14	69558513	69558513	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003861.2	-1	validated	p.R253*	1.000	122	0%	96	51%	11	36.3%	-	-	-	superfamily_WD40 repeat-like
SIPA1L1	26037	genome.wustl.edu	37	14	72056005	72056005	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015556.1	+1	provisional	p.L472F	1.000	213	0%	116	36.2%	3	66.6%	possibly_damaging(0.893)	tolerated(0.76)	neutral(0.353)	NULL
NEK9	91754	genome.wustl.edu	37	14	75562102	75562102	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033116.4	-1	validated	p.N736D	1.000	63	0%	54	42.6%	7	85.7%	benign(0.235)	deleterious(0)	neutral(0.468)	NULL
C14orf118	55668	genome.wustl.edu	37	14	76621125	76621125	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017926.2	+1	validated	p.A140V	1.000	79	0%	84	42.9%	4	25%	probably_damaging(0.955)	tolerated(0.66)	neutral(0.401)	NULL
C14orf133	63894	genome.wustl.edu	37	14	77919683	77919683	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022067.2	-1	provisional	p.D52G	0.962	327	0%	372	42.7%	6	50%	possibly_damaging(0.948)	tolerated(0.28)	neutral(0.422)	HMMPfam_Golgin_A5
CPSF2	53981	genome.wustl.edu	37	14	92627523	92627523	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017437.1	+1	validated	p.R730Q	1.000	299	0%	190	28.9%	46	54.3%	benign(0.242)	deleterious(0.03)	neutral(0.389)	NULL
RIN3	79890	genome.wustl.edu	37	14	93107605	93107605	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024832.3	+1	validated	p.R155W	0.945	57	0%	70	42.9%	1	100%	unknown(0)	deleterious(0)	-	superfamily_SH2 domain
GOLGA5	9950	genome.wustl.edu	37	14	93263849	93263849	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005113.2	+1	reviewed	p.A23T	1.000	94	0%	88	40.9%	21	47.6%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	NULL
ITPK1	3705	genome.wustl.edu	37	14	93460301	93460301	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142593.1	-1	validated	p.P96	0.808	35	0%	32	53.1%	75	37.3%	-	-	-	HMMPfam_Ins134_P3_kin,superfamily_Glutathione synthetase ATP-binding domain-like
ATG2B	55102	genome.wustl.edu	37	14	96784189	96784189	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018036.5	-1	validated	p.I961	1.000	236	0%	142	41.5%	1	100%	-	-	-	NULL
CYP46A1	10858	genome.wustl.edu	37	14	100188308	100188308	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006668.1	+1	reviewed	p.L361M	0.993	38	0%	36	33.3%	0	-	possibly_damaging(0.925)	deleterious(0)	deleterious(0.818)	HMMPfam_p450,superfamily_Cytochrome_P450
DYNC1H1	1778	genome.wustl.edu	37	14	102495903	102495903	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001376.4	+1	reviewed	p.G3166S	0.999	78	0%	67	47.8%	14	7.1%	benign(0.004)	tolerated(0.11)	neutral(0.272)	superfamily_SSF52540
PPP1R13B	23368	genome.wustl.edu	37	14	104206784	104206784	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015316.2	-1	reviewed	p.P657S	0.003	26	0%	22	50%	18	83.3%	benign(0)	tolerated(0.55)	neutral(0.007)	NULL
GPR132	29933	genome.wustl.edu	37	14	105521734	105521734	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013345.2	-1	reviewed	p.N8	0.013	110	0%	96	43.8%	9	22.2%	-	-	-	NULL
BRF1	2972	genome.wustl.edu	37	14	105685575	105685575	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000440513	-1	known	p.A17T	0.000	13	0%	29	55.2%	3	0%	benign(0.007)	tolerated(0.55)	neutral(0.007)	HMMPfam_BRF1
IGHG1	3500	genome.wustl.edu	37	14	106206433	106206433	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000390548	-1	known	p.S361	1.000	19	0%	24	20.8%	0	-	-	-	-	NULL
IGHV3-43	28426	genome.wustl.edu	37	14	106926401	106926401	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000434710	-1	known	p.T47	0.976	611	0%	552	46.4%	0	-	-	-	-	HMMSmart_IGv,HMMPfam_V-set,superfamily_SSF48726
NDN	4692	genome.wustl.edu	37	15	23931941	23931941	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002487.2	-1	reviewed	p.R142C	0.902	29	0%	12	75%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_MAGE
ATP10A	57194	genome.wustl.edu	37	15	25959252	25959252	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024490.3	-1	reviewed	p.G638D	0.299	38	0%	33	45.5%	0	-	possibly_damaging(0.893)	tolerated(0.41)	neutral(0.367)	superfamily_SSF56784
OCA2	4948	genome.wustl.edu	37	15	28228541	28228541	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000275.2	-1	reviewed	p.G485R	1.000	110	0%	109	50.5%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_CitMHS
ARHGAP11B	89839	genome.wustl.edu	37	15	30927692	30927692	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039841.1	+1	provisional	p.G221	0.999	690	0%	485	39.4%	2	50%	-	-	-	HMMSmart_RhoGAP,superfamily_Rho_GAP
SPTBN5	51332	genome.wustl.edu	37	15	42171576	42171576	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016642.2	-1	validated	p.Q987K	0.000	14	0%	10	40%	0	-	possibly_damaging(0.442)	tolerated(0.16)	neutral(0.204)	HMMSmart_SM00150
SORD	6652	genome.wustl.edu	37	15	45353270	45353270	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003104.4	+1	validated	p.R91C	1.000	90	0%	78	38.5%	59	49.1%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_GroES-like,HMMPfam_ADH_N
CEP152	22995	genome.wustl.edu	37	15	49048120	49048120	+	Missense_Mutation	SNP	C	C	T	rs115832709	byFrequency;by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014985.2	-1	provisional	p.A1109T	0.000	448	0%	294	40.8%	1	0%	benign(0)	tolerated(0.19)	neutral(0.050)	NULL
PIGB	9488	genome.wustl.edu	37	15	55612548	55612548	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004855.4	+1	reviewed	p.T80I	1.000	83	0%	39	43.6%	6	83.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Glyco_transf_22
MIR422A	494334	genome.wustl.edu	37	15	64163132	64163132	+	RNA	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000362286	-1	known	NULL	0.003	100	0%	98	52%	0	-	-	-	-	-
MIR1272	100302184	genome.wustl.edu	37	15	65054696	65054696	+	RNA	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000408106	-1	known	NULL	0.000	64	1.6%	39	46.2%	0	-	-	-	-	-
IQCH	64799	genome.wustl.edu	37	15	67692501	67692501	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031715.2	+1	validated	p.R652H	1.000	92	0%	72	34.7%	2	0%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
CYP11A1	1583	genome.wustl.edu	37	15	74635450	74635450	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000781.2	-1	reviewed	p.W286C	0.011	134	0%	103	38.8%	0	-	possibly_damaging(0.756)	deleterious(0)	deleterious(0.724)	HMMPfam_p450,superfamily_Cytochrome P450
MPI	4351	genome.wustl.edu	37	15	75182953	75182953	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002435.1	+1	reviewed	p.S34	1.000	35	0%	49	49%	35	54.2%	-	-	-	HMMPfam_PMI_typeI,superfamily_RmlC-like cupins
FANCI	55215	genome.wustl.edu	37	15	89843577	89843577	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001113378.1	+1	reviewed	p.S950	0.376	128	0%	31	41.9%	47	46.8%	-	-	-	NULL
SLCO3A1	28232	genome.wustl.edu	37	15	92459361	92459361	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013272.3	+1	validated	p.R107C	1.000	12	0%	17	58.8%	0	-	probably_damaging(0.999)	deleterious(0.03)	deleterious(0.855)	HMMPfam_OATP,superfamily_MFS general substrate transporter
LRRK1	79705	genome.wustl.edu	37	15	101605686	101605686	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024652.3	+1	validated	p.A1682T	0.199	176	0%	126	43.7%	11	45.4%	benign(0)	tolerated(0.38)	neutral(0.018)	NULL
AXIN1	8312	genome.wustl.edu	37	16	396589	396589	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003502.2	-1	reviewed	p.R146Q	0.996	40	0%	39	59%	18	38.8%	possibly_damaging(0.756)	deleterious(0.02)	deleterious(0.662)	HMMPfam_RGS,HMMSmart_SM00315,superfamily_Regulator of G-protein signaling RGS
HMOX2	3163	genome.wustl.edu	37	16	4557995	4557995	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127204.1	+1	reviewed	p.S162	0.001	56	0%	31	45.2%	83	54.2%	-	-	-	HMMPfam_Heme_oxygenase,superfamily_Heme oxygenase-like
TEKT5	146279	genome.wustl.edu	37	16	10721610	10721610	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144674.1	-1	provisional	p.K430E	0.252	38	0%	64	48.4%	0	-	benign(0.058)	tolerated(0.11)	neutral(0.275)	HMMPfam_Tektin
CIITA	4261	genome.wustl.edu	37	16	11001471	11001471	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000246.3	+1	reviewed	p.F708V	1.000	120	0%	83	53%	2	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
CLEC16A	23274	genome.wustl.edu	37	16	11272483	11272483	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015226.2	+1	validated	p.A1033G	0.000	21	0%	27	48.1%	5	20%	benign(0.004)	tolerated(0.2)	neutral(0.049)	NULL
CPPED1	55313	genome.wustl.edu	37	16	12758860	12758860	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018340.2	-1	validated	p.H276	0.498	37	0%	46	47.8%	35	77.1%	possibly_damaging(0.466)	deleterious(0.02)	deleterious(0.536)	superfamily_Metallo-dependent phosphatases
SYT17	51760	genome.wustl.edu	37	16	19195208	19195208	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016524.2	+1	validated	p.Y230	1.000	186	0%	280	44.6%	8	75%	-	-	-	HMMPfam_C2,HMMSmart_C2,superfamily_C2_CaLB
TMC5	79838	genome.wustl.edu	37	16	19475197	19475197	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001105248.1	+1	validated	p.V446I	1.000	349	0%	330	49.7%	8	62.5%	possibly_damaging(0.799)	tolerated(0.18)	neutral(0.357)	NULL
TNRC6A	27327	genome.wustl.edu	37	16	24835005	24835005	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000450465	+1	known	p.A813T	0.119	198	0%	245	45.7%	12	25%	-	-	-	NULL
ATXN2L	11273	genome.wustl.edu	37	16	28838193	28838193	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_148414.1	+1	reviewed	p.T209	0.996	61	0%	64	50%	45	40%	-	-	-	NULL
RRN3P2	653390	genome.wustl.edu	37	16	29110458	29110458	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000427965	+1	known	p.W375R	0.991	108	0.9%	95	22.1%	0	-	benign(0)	tolerated(1)	-	HMMPfam_RRN3
ZNF720	124411	genome.wustl.edu	37	16	31733952	31733952	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130913.1	+1	validated	p.L3	0.404	303	0%	165	35.8%	8	37.5%	unknown(0)	-	-	superfamily_KRAB domain (Kruppel-associated box Pfam 01352)
VPS35	55737	genome.wustl.edu	37	16	46706238	46706238	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018206.4	-1	reviewed	p.M436T	1.000	103	0%	71	11.3%	30	6.6%	benign(0.051)	deleterious(0.02)	neutral(0.386)	HMMPfam_Vps35
MMP2	4313	genome.wustl.edu	37	16	55522489	55522489	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004530.4	+1	reviewed	p.Q289	1.000	40	0%	56	48.2%	91	51.6%	-	-	-	HMMSmart_FN2,HMMPfam_Peptidase_M10,HMMSmart_ZnMc,superfamily_Kringle-like,superfamily_SSF55486
CDH1	999	genome.wustl.edu	37	16	68857362	68857362	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004360.3	+1	reviewed	p.N666S	0.038	150	0.7%	130	39.2%	146	49.3%	benign(0.362)	tolerated(0.39)	neutral(0.131)	HMMPfam_Cadherin,superfamily_Cadherin-like
ENSG00000205152	0	genome.wustl.edu	37	16	70265334	70265334	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000378955	-1	known	p.N346D	1.000	75	0%	57	47.4%	0	-	-	-	-	NULL
ZFHX3	463	genome.wustl.edu	37	16	72830903	72830904	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	CT	CT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006885.3	-1	reviewed	p.R1893fs	0.999:0.991	-	-	-	-	-	-	-	-	-	NULL
ZFHX3	463	genome.wustl.edu	37	16	72923834	72923834	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006885.3	-1	reviewed	p.E1082K	1.000	90	0%	102	18.6%	4	25%	unknown(0)	-	-	NULL
CHST5	23563	genome.wustl.edu	37	16	75563170	75563170	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024533.3	-1	validated	p.C371	0.986	14	0%	22	54.5%	1	0%	-	-	-	HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases
ADAT1	23536	genome.wustl.edu	37	16	75654164	75654164	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012091.2	-1	reviewed	p.G80R	0.996	135	0%	116	56%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_A_deamin,HMMSmart_SM00552
ENSG00000232329	0	genome.wustl.edu	37	16	81142175	81142175	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000453104	-1	known	p.Y204H	0.046	30	0%	32	37.5%	0	-	-	-	-	NULL
KCNG4	93107	genome.wustl.edu	37	16	84256074	84256074	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_172347.1	-1	reviewed	p.S437G	1.000	48	0%	56	51.8%	0	-	probably_damaging(0.999)	tolerated(0.43)	deleterious(0.504)	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
FBXO31	79791	genome.wustl.edu	37	16	87367618	87367618	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024735.3	-1	validated	p.G424D	0.000	21	0%	18	44.4%	3	0%	possibly_damaging(0.648)	tolerated(0.13)	deleterious(0.480)	NULL
SCARF1	8578	genome.wustl.edu	37	17	1538710	1538710	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003693.2	-1	reviewed	p.P612L	0.978	31	0%	38	57.9%	2	0%	possibly_damaging(0.527)	deleterious(0)	deleterious(0.623)	NULL
OR1A2	26189	genome.wustl.edu	37	17	3101038	3101038	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012352.1	+1	provisional	p.V76I	0.523	460	0%	483	44.9%	0	-	probably_damaging(0.988)	tolerated(0.06)	deleterious(0.760)	HMMPfam_7tm_1,superfamily_SSF81321
OR1E2	8388	genome.wustl.edu	37	17	3336748	3336748	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003554.1	-1	provisional	p.M130L	0.971	167	0.6%	325	46.8%	0	-	unknown(0)	tolerated(0.5)	-	HMMPfam_7tm_1,superfamily_SSF81321
ZFP3	124961	genome.wustl.edu	37	17	4994995	4994996	+	Frame_Shift_Del	DEL	GA	GA	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	GA	GA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153018.2	+1	validated	p.D68fs	0.014:0.011	-	-	-	-	-	-	-	-	-	NULL
WSCD1	23302	genome.wustl.edu	37	17	6023654	6023654	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015253.1	+1	validated	p.Y467	0.523	169	0%	80	35%	6	16.6%	-	-	-	superfamily_SSF52540
CLEC10A	10462	genome.wustl.edu	37	17	6978707	6978707	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182906.2	-1	reviewed	p.D252N	1.000	108	0%	146	41.8%	1	0%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_C-type lectin-like
NEURL4	84461	genome.wustl.edu	37	17	7224913	7224913	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032442.2	-1	validated	p.R1022M	1.000	78	0%	29	34.5%	8	62.5%	probably_damaging(0.989)	deleterious(0.03)	deleterious(0.804)	HMMSmart_SM00588
CYB5D1	124637	genome.wustl.edu	37	17	7762002	7762002	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144607.4	+1	validated	p.Q106*	0.361	21	0%	22	45.5%	2	0%	-	-	-	superfamily_Cytochrome b5-like heme/steroid binding domain
ARHGEF15	22899	genome.wustl.edu	37	17	8222125	8222125	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173728.2	+1	reviewed	p.L644	0.984	67	0%	99	41.4%	1	0%	-	-	-	superfamily_SSF50729
PIK3R5	23533	genome.wustl.edu	37	17	8791556	8791556	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142633.1	-1	validated	p.T516	0.000	25	0%	19	47.4%	0	-	-	-	-	HMMPfam_PI3K_1B_p101
MYH1	4619	genome.wustl.edu	37	17	10404777	10404777	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005963.3	-1	reviewed	p.R1130W	1.000	183	0%	139	54%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Myosin_tail_1
NCOR1	9611	genome.wustl.edu	37	17	16001708	16001708	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006311.2	-1	reviewed	p.Q931	0.993	157	0.6%	77	40.3%	6	83.3%	-	-	-	NULL
PIGL	9487	genome.wustl.edu	37	17	16229178	16229178	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004278.3	+1	reviewed	p.R242Q	1.000	76	0%	69	46.4%	9	22.2%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_LmbE-like
SHMT1	6470	genome.wustl.edu	37	17	18251702	18251702	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004169.3	-1	reviewed	p.R99*	1.000	44	0%	90	48.9%	25	0%	-	-	-	HMMPfam_SHMT,superfamily_PLP-dependent transferases
KCNJ12	3768	genome.wustl.edu	37	17	21319341	21319341	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021012.4	+1	validated	p.R229	0.231	29	0%	43	16.3%	0	-	-	-	-	HMMPfam_IRK,superfamily_Ig_E-set
SSH2	85464	genome.wustl.edu	37	17	27959571	27959571	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033389.2	-1	reviewed	p.G854W	0.986	161	0%	220	48.2%	2	100%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	NULL
MYO19	80179	genome.wustl.edu	37	17	34862952	34862952	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000431794	-1	known	p.S498	0.996	21	0%	12	33.3%	25	36%	-	-	-	HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases
KRT33B	3884	genome.wustl.edu	37	17	39521059	39521059	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002279.3	-1	reviewed	p.R357	0.992	228	0%	229	38.9%	0	-	-	-	-	HMMPfam_Filament,PatternScan_IF
KRT35	3886	genome.wustl.edu	37	17	39636983	39636983	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002280.4	-1	reviewed	p.A123T	0.008	101	0%	78	46.2%	0	-	benign(0)	tolerated(0.14)	neutral(0.249)	HMMPfam_Filament
ENSG00000247918	0	genome.wustl.edu	37	17	40126023	40126026	+	RNA	DEL	TTTT	TTTT	-	rs34645700		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	TTTT	TTTT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000499234	-1	novel	NULL	0.001:0.001:0.000:0.003	-	-	-	-	-	-	-	-	-	-
SLC4A1	6521	genome.wustl.edu	37	17	42331904	42331904	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000342.3	-1	reviewed	p.L673	1.000	18	0%	23	30.4%	0	-	-	-	-	HMMPfam_HCO3_cotransp
PLCD3	113026	genome.wustl.edu	37	17	43190566	43190566	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_133373.3	-1	reviewed	p.T685I	1.000	18	0%	19	36.8%	18	55.5%	-	-	-	NULL
KAT7	11143	genome.wustl.edu	37	17	47904070	47904070	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007067.3	+1	provisional	p.T548M	1.000	176	0%	140	42.1%	14	21.4%	probably_damaging(0.999)	tolerated(0.06)	deleterious(0.813)	HMMPfam_MOZ_SAS,superfamily_Acyl-CoA N-acyltransferases (Nat)
MYCBPAP	84073	genome.wustl.edu	37	17	48594768	48594768	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032133.4	+1	validated	p.R150C	0.768	140	0%	93	48.4%	1	100%	probably_damaging(0.992)	deleterious(0)	deleterious(0.892)	NULL
EPX	8288	genome.wustl.edu	37	17	56280666	56280666	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000502.4	+1	reviewed	p.R645	0.539	84	0%	66	37.9%	2	100%	-	-	-	HMMPfam_An_peroxidase,superfamily_Peroxidase_super
RNF43	54894	genome.wustl.edu	37	17	56492875	56492875	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017763.4	-1	validated	p.Q22*	1.000	52	0%	80	52.5%	3	33.3%	-	-	-	NULL
TEX14	56155	genome.wustl.edu	37	17	56665301	56665301	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198393.2	-1	reviewed	p.R886	0.000	85	0%	64	46.9%	0	-	-	-	-	NULL
KCNH6	81033	genome.wustl.edu	37	17	61622450	61622450	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030779.2	+1	reviewed	p.R839H	0.984	32	0%	36	55.6%	0	-	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	NULL
FTSJ3	117246	genome.wustl.edu	37	17	61899116	61899116	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017647.3	-1	reviewed	p.L521	0.808	559	0.2%	585	50.6%	41	56%	-	-	-	NULL
SCN4A	6329	genome.wustl.edu	37	17	62034671	62034671	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000334.4	-1	reviewed	p.H743Y	1.000	66	0%	59	44.1%	0	-	benign(0.014)	deleterious(0.02)	neutral(0.384)	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
ERN1	2081	genome.wustl.edu	37	17	62133221	62133223	+	In_Frame_Del	DEL	GCT	GCT	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	GCT	GCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001433.3	-1	reviewed	p.Q495in_frame_del	0.999:0.998:0.998	-	-	-	-	-	-	-	-	-	NULL
ENSG00000214176	0	genome.wustl.edu	37	17	62820964	62820964	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000397718	-1	known	p.S25	0.989	71	0%	77	36.4%	5	20%	-	-	-	NULL
TNRC6C	57690	genome.wustl.edu	37	17	76060930	76060930	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142640.1	+1	validated	p.G838	0.183	37	0%	29	31%	1	0%	-	-	-	HMMPfam_Ago_hook
ENPP7	339221	genome.wustl.edu	37	17	77709122	77709122	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178543.3	+1	validated	p.R227Q	0.560	21	0%	24	54.2%	0	-	probably_damaging(0.999)	deleterious(0.04)	deleterious(0.839)	HMMPfam_Phosphodiest,superfamily_Alkaline_phosphatase_core
TBC1D16	125058	genome.wustl.edu	37	17	77921611	77921611	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019020.2	-1	provisional	p.A521T	1.000	16	0%	22	31.8%	33	36.3%	benign(0.336)	tolerated(0.07)	neutral(0.425)	HMMPfam_TBC,HMMSmart_SM00164,superfamily_Ypt/Rab-GAP domain of gyp1p
SLC38A10	124565	genome.wustl.edu	37	17	79249914	79249914	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001037984.1	-1	validated	p.T256M	0.908	10	0%	10	50%	97	52.5%	probably_damaging(0.999)	tolerated(0.19)	deleterious(0.540)	HMMPfam_Aa_trans
SIRT7	51547	genome.wustl.edu	37	17	79872370	79872370	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016538.1	-1	reviewed	p.R206W	0.996	14	0.000	7	0.571	34	67.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_SIR2,superfamily_DHS-like NAD/FAD-binding domain
CCDC57	284001	genome.wustl.edu	37	17	80153187	80153187	+	Silent	SNP	A	A	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198082.2	-1	validated	p.R190	0.000	17	0%	11	36.4%	11	18.1%	-	-	-	NULL
TWSG1	57045	genome.wustl.edu	37	18	9399351	9399351	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020648.5	+1	validated	p.M166I	1.000	91	0%	50	34%	15	66.6%	benign(0.024)	tolerated(0.33)	neutral(0.025)	HMMPfam_Tsg
LOC729602	729602	genome.wustl.edu	37	18	11621122	11621122	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002344140.1	-1	model	p.V206I	0.057	247	0%	241	41.1%	0	-	-	-	-	HMMPfam_NPIP
GATA6	2627	genome.wustl.edu	37	18	19780733	19780733	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005257.3	+1	validated	p.E579K	0.998	65	0%	72	38.9%	0	-	unknown(0)	tolerated(0.16)	-	NULL
LAMA3	3909	genome.wustl.edu	37	18	21437853	21437853	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198129.1	+1	reviewed	p.S1394	0.087	119	0%	90	37.8%	2	100%	-	-	-	HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMSmart_SM00181,superfamily_EGF/Laminin
TTC39C	125488	genome.wustl.edu	37	18	21703899	21703899	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135993.1	+1	validated	p.V430M	0.993	77	0%	41	39%	13	69.2%	benign(0.013)	tolerated(0.27)	neutral(0.034)	HMMPfam_Deme6,superfamily_TPR-like
SLC39A6	25800	genome.wustl.edu	37	18	33696636	33696636	+	Splice_Site	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012319.3	-1	validated	e5+1	1.000	58	0%	40	45%	1	100%	-	-	-	-
ZBTB7C	201501	genome.wustl.edu	37	18	45567179	45567179	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039360.1	-1	validated	p.T100	0.350	58	0%	45	44.4%	7	14.2%	-	-	-	HMMSmart_SM00225,superfamily_POZ domain,HMMPfam_BTB
TCF4	6925	genome.wustl.edu	37	18	52896159	52896159	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001083962.1	-1	reviewed	p.K600E	1.000	92	0%	65	41.5%	0	-	probably_damaging(0.974)	deleterious(0)	deleterious(0.861)	HMMPfam_HLH,HMMSmart_HLH,superfamily_HLH_basic
TCF4	6925	genome.wustl.edu	37	18	53018187	53018187	+	Silent	SNP	A	A	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001083962.1	-1	reviewed	p.L139	1.000	250	0%	169	49.1%	0	-	-	-	-	NULL
WDR7	23335	genome.wustl.edu	37	18	54547241	54547241	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015285.2	+1	reviewed	p.A1124V	1.000	174	0%	148	43.2%	2	0%	probably_damaging(0.954)	tolerated(0.08)	deleterious(0.698)	NULL
CDH7	1005	genome.wustl.edu	37	18	63477133	63477133	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004361.2	+1	reviewed	p.P135L	1.000	192	0%	146	38.4%	0	-	probably_damaging(0.997)	deleterious(0.02)	deleterious(0.849)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
FSD1	79187	genome.wustl.edu	37	19	4307924	4307924	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024333.2	+1	reviewed	p.L97F	1.000	5	0.000	9	0.667	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMSmart_BBC
PLIN4	729359	genome.wustl.edu	37	19	4511071	4511071	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080400.1	-1	provisional	p.G953	0.000	58	1.7%	60	68.3%	1	0%	-	-	-	NULL
TNFAIP8L1	126282	genome.wustl.edu	37	19	4651884	4651884	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152362.2	+1	validated	p.M1I	1.000	20	0%	20	50%	5	40%	possibly_damaging(0.473)	deleterious(0)	deleterious(0.601)	HMMPfam_DUF758
SAFB	6294	genome.wustl.edu	37	19	5653199	5653199	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002967.2	+1	reviewed	p.T456I	0.997	59	0%	62	40.3%	106	44.3%	possibly_damaging(0.952)	deleterious(0)	deleterious(0.840)	HMMPfam_RRM_1,HMMSmart_RRM,superfamily_SSF54928
MLLT1	4298	genome.wustl.edu	37	19	6270618	6270618	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005934.3	-1	validated	p.L55	1.000	35	0%	46	37%	24	45.8%	-	-	-	HMMPfam_YEATS
SLC25A23	79085	genome.wustl.edu	37	19	6454634	6454634	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024103.2	-1	validated	p.A193V	0.988	38	0%	39	35.9%	19	42.1%	possibly_damaging(0.761)	deleterious(0)	deleterious(0.726)	superfamily_Mitochondrial carrier,HMMPfam_Mito_carr
VAV1	7409	genome.wustl.edu	37	19	6848059	6848059	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005428.2	+1	reviewed	p.R688H	0.987	137	0%	110	40.9%	2	0%	possibly_damaging(0.895)	tolerated(0.24)	neutral(0.390)	HMMPfam_SH2,HMMSmart_SH2,superfamily_SH3,superfamily_SSF55550
ZNF557	79230	genome.wustl.edu	37	19	7075116	7075116	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001044387.1	+1	validated	p.A11S	0.058	31	0%	39	46.2%	2	0%	possibly_damaging(0.791)	tolerated(0.12)	deleterious(0.557)	NULL
INSR	3643	genome.wustl.edu	37	19	7267491	7267491	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000208.2	-1	reviewed	p.V173M	0.971	163	0%	203	37.9%	0	-	benign(0.023)	tolerated(0.07)	neutral(0.320)	superfamily_L domain-like
MUC16	94025	genome.wustl.edu	37	19	9090009	9090009	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024690.2	-1	validated	p.Q602	0.005	219	0%	220	52.3%	0	-	-	-	-	NULL
ICAM3	3385	genome.wustl.edu	37	19	10445855	10445855	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002162.3	-1	reviewed	p.T275M	0.000	16	0%	24	50%	11	45.4%	possibly_damaging(0.679)	tolerated(0.12)	deleterious(0.502)	superfamily_SSF48726
TYK2	7297	genome.wustl.edu	37	19	10461823	10461823	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003331.4	-1	reviewed	p.I1112V	1.000	36	0%	39	56.4%	71	63.3%	possibly_damaging(0.647)	tolerated(0.1)	deleterious(0.513)	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like
TYK2	7297	genome.wustl.edu	37	19	10475409	10475409	+	Silent	SNP	G	G	A	rs138350396	by1000genomes	TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003331.4	-1	reviewed	p.F416	0.921	21	0%	41	53.7%	39	58.9%	-	-	-	NULL
SMARCA4	6597	genome.wustl.edu	37	19	11123752	11123752	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001128849.1	+1	reviewed	p.R801H	1.000	57	0%	58	41.4%	117	52.1%	probably_damaging(0.993)	deleterious(0.02)	deleterious(0.833)	HMMPfam_SNF2_N,HMMSmart_DEXDc,superfamily_SSF52540
TNPO2	30000	genome.wustl.edu	37	19	12822220	12822220	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001136196.1	-1	validated	p.R336H	0.997	98	0%	82	30.5%	27	62.9%	possibly_damaging(0.697)	deleterious(0.01)	deleterious(0.655)	superfamily_ARM repeat
MAST1	22983	genome.wustl.edu	37	19	12969367	12969367	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014975.2	+1	validated	p.R394C	0.852	49	0%	64	43.8%	0	-	possibly_damaging(0.888)	deleterious(0)	deleterious(0.792)	HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase
MAST1	22983	genome.wustl.edu	37	19	12979907	12979907	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014975.2	+1	validated	p.A934V	1.000	68	0%	65	40%	3	100%	benign(0.001)	tolerated(0.05)	neutral(0.345)	NULL
DDX39A	10212	genome.wustl.edu	37	19	14523391	14523391	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005804.2	-1	reviewed	p.L103Q	1.000	12	0%	17	64.7%	167	52.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DEAD,HMMSmart_DEXDc,superfamily_SSF52540
SYDE1	85360	genome.wustl.edu	37	19	15224565	15224565	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033025.4	+1	provisional	p.R667W	1.000	62	0%	33	48.5%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
UPF1	5976	genome.wustl.edu	37	19	18966854	18966854	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002911.3	+1	reviewed	p.P555	0.003	32	0%	14	42.9%	38	60.5%	-	-	-	superfamily_SSF52540
ZNF93	81931	genome.wustl.edu	37	19	20044492	20044492	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031218.3	+1	validated	p.T243N	0.000	434	0%	267	40.1%	8	25%	benign(0.004)	tolerated(1)	-	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
ZNF431	170959	genome.wustl.edu	37	19	21350428	21350428	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_133473.2	+1	validated	p.P93H	0.150	346	0.3%	247	40.9%	2	50%	probably_damaging(0.993)	deleterious(0.02)	deleterious(0.833)	HMMSmart_SM00349
ENSG00000213974	0	genome.wustl.edu	37	19	22785451	22785451	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000397112	+1	known	p.R103Q	0.942	74	0%	71	43.7%	0	-	-	-	-	NULL
LOC440518	440518	genome.wustl.edu	37	19	22785822	22785822	+	RNA	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_041921.2	+1	model	NULL	0.952	10	0%	18	38.9%	0	-	-	-	-	-
ZNF675	171392	genome.wustl.edu	37	19	23836179	23836179	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138330.2	-1	validated	p.R519Q	0.000	255	0%	182	41.8%	12	41.6%	benign(0.019)	tolerated(0.78)	neutral(0.002)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
ANKRD27	84079	genome.wustl.edu	37	19	33130328	33130328	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032139.2	-1	validated	p.Y350	1.000	87	0%	94	38.3%	4	25%	-	-	-	HMMPfam_VPS9,HMMSmart_VPS9,superfamily_SSF109993
GPATCH1	55094	genome.wustl.edu	37	19	33586690	33586690	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018025.2	+1	provisional	p.G192	1.000	224	0%	163	46.6%	5	40%	-	-	-	HMMPfam_G-patch
KIAA0355	9710	genome.wustl.edu	37	19	34842430	34842430	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014686.3	+1	validated	p.S946N	1.000	60	0%	32	18.8%	11	9%	possibly_damaging(0.456)	deleterious(0.03)	deleterious(0.514)	NULL
CD22	933	genome.wustl.edu	37	19	35829328	35829328	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001771.3	+1	validated	p.V415I	0.298	140	0%	228	35.5%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMSmart_SM00409,superfamily_Immunoglobulin
C19orf55	148137	genome.wustl.edu	37	19	36252950	36252950	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039887.1	+1	predicted	p.P114	0.994	33	0%	15	46.7%	8	50%	unknown(0)	-	-	NULL
ARHGAP33	115703	genome.wustl.edu	37	19	36276147	36276147	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052948.3	+1	reviewed	p.T593M	1.000	84	0%	52	40.4%	8	37.5%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
COX7A1	1346	genome.wustl.edu	37	19	36642409	36642409	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001864.2	-1	reviewed	p.V48I	0.000	80	0%	21	23.8%	8	0%	benign(0.004)	tolerated(0.35)	neutral(0.021)	HMMPfam_COX7a,superfamily_Mitochondrial cytochrome c oxidase subunit VIIa
ZNF461	92283	genome.wustl.edu	37	19	37130376	37130376	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153257.2	-1	validated	p.H291D	0.998	157	0%	114	42.1%	4	50%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
ZNF585B	92285	genome.wustl.edu	37	19	37677370	37677370	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152279.3	-1	validated	p.T357S	0.024	454	0%	400	46%	0	-	benign(0.004)	tolerated(0.52)	neutral(0.009)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667
GGN	199720	genome.wustl.edu	37	19	38876172	38876172	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152657.3	-1	reviewed	p.T577I	0.000	28	0%	19	31.6%	0	-	probably_damaging(0.962)	tolerated(0.12)	deleterious(0.665)	NULL
PLEKHG2	64857	genome.wustl.edu	37	19	39914682	39914682	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000205135	+1	known	p.Q838*	0.058	151	0%	221	41.6%	5	20%	possibly_damaging(0.911)	deleterious(0)	deleterious(0.807)	NULL
CYP2F1	1572	genome.wustl.edu	37	19	41622225	41622225	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000774.3	+1	reviewed	p.L44	0.975	705	0.1%	724	47.5%	0	-	-	-	-	HMMPfam_p450,superfamily_Cytochrome P450
HNRNPUL1	11100	genome.wustl.edu	37	19	41798387	41798387	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007040.3	+1	reviewed	p.V413I	0.006	130	0.8%	99	46.5%	207	50.2%	benign(0.008)	tolerated(0.24)	neutral(0.037)	NULL
MEGF8	1954	genome.wustl.edu	37	19	42839244	42839244	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001410.2	+1	validated	p.L206M	1.000	27	0%	46	39.1%	0	-	probably_damaging(0.999)	tolerated(0.12)	deleterious(0.751)	superfamily_Gal_oxid_central
ZNF283	284349	genome.wustl.edu	37	19	44351863	44351863	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181845.1	+1	validated	p.T370	0.990	254	0%	219	38.8%	1	100%	-	-	-	superfamily_C2H2 and C2HC zinc fingers
LIG1	3978	genome.wustl.edu	37	19	48619155	48619155	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000234.1	-1	reviewed	p.P884L	0.983	37	0%	27	37%	157	54.7%	probably_damaging(0.983)	deleterious(0.01)	deleterious(0.835)	NULL
SIGLEC5	8778	genome.wustl.edu	37	19	52131127	52131127	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003830.2	-1	validated	p.P319	0.000	62	0%	88	46.6%	0	-	-	-	-	HMMSmart_IGc2,superfamily_SSF48726
HAS1	3036	genome.wustl.edu	37	19	52217292	52217292	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000376738	-1	known	p.A205T	1.000	39	0%	36	33.3%	0	-	unknown(0)	deleterious(0.03)	-	NULL
ZNF841	284371	genome.wustl.edu	37	19	52570447	52570447	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001136499.1	-1	validated	p.V230I	0.000	18	0%	14	42.9%	0	-	possibly_damaging(0.792)	deleterious(0.05)	deleterious(0.642)	NULL
DEFB126	81623	genome.wustl.edu	37	20	126191	126191	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030931.2	+1	reviewed	p.R65H	0.000	293	0%	247	44.9%	3	66.6%	probably_damaging(0.994)	deleterious(0.03)	deleterious(0.817)	NULL
TMC2	117532	genome.wustl.edu	37	20	2591104	2591104	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080751.2	+1	validated	p.P485S	0.998	172	0%	108	40.7%	0	-	possibly_damaging(0.945)	tolerated(0.54)	neutral(0.397)	NULL
CPXM1	56265	genome.wustl.edu	37	20	2776337	2776337	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019609.4	-1	reviewed	p.M543T	1.000	26	0%	34	41.2%	12	8.3%	benign(0.023)	deleterious(0)	neutral(0.446)	HMMPfam_Peptidase_M14,HMMSmart_SM00631,superfamily_Zn-dependent exopeptidases
BTBD3	22903	genome.wustl.edu	37	20	11903546	11903546	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014962.2	+1	validated	p.Q267	1.000	143	0%	149	44.3%	7	42.8%	-	-	-	NULL
BTBD3	22903	genome.wustl.edu	37	20	11903891	11903891	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014962.2	+1	validated	p.A382	1.000	100	0%	113	46%	9	33.3%	-	-	-	HMMPfam_PHR
C20orf7	79133	genome.wustl.edu	37	20	13789531	13789531	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024120.4	+1	reviewed	p.L254S	1.000	77	0%	41	36.6%	35	45.7%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	superfamily_S-adenosyl-L-methionine-dependent methyltransferases
E2F1	1869	genome.wustl.edu	37	20	32265093	32265093	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005225.2	-1	reviewed	p.V295D	1.000	38	0%	10	50%	32	43.7%	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	NULL
GSS	2937	genome.wustl.edu	37	20	33533805	33533805	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000178.2	-1	reviewed	p.V76M	1.000	118	0%	146	46.6%	132	45.4%	possibly_damaging(0.903)	tolerated(0.38)	neutral(0.376)	HMMPfam_GSH_synth_ATP,superfamily_SSF56059
MYH7B	57644	genome.wustl.edu	37	20	33584523	33584523	+	Silent	SNP	T	T	G	rs11392289		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020884.3	+1	reviewed	p.A1118	0.037	10	0%	15	73.3%	2	0%	-	-	-	HMMPfam_Myosin_tail_1
PPP1R16B	26051	genome.wustl.edu	37	20	37546827	37546827	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000438192	+1	known	p.Y308*	1.000	141	0%	119	44.5%	0	-	benign(0.273)	tolerated(0.39)	neutral(0.045)	NULL
ZSWIM3	140831	genome.wustl.edu	37	20	44506264	44506264	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080752.2	+1	validated	p.A356V	0.014	121	0%	126	41.3%	3	33.3%	benign(0)	tolerated(0.61)	neutral(0.004)	NULL
ZNF335	63925	genome.wustl.edu	37	20	44580951	44580951	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022095.3	-1	reviewed	p.P1008	0.001	17	0%	15	60%	15	46.6%	-	-	-	NULL
ARFGEF2	10564	genome.wustl.edu	37	20	47626792	47626792	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006420.2	+1	reviewed	p.A1203V	1.000	126	0.8%	152	36.8%	1	100%	benign(0)	tolerated(1)	-	HMMPfam_DUF1981,superfamily_ARM-type_fold
DDX27	55661	genome.wustl.edu	37	20	47845263	47845263	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017895.7	+1	reviewed	p.A271T	1.000	102	0%	124	41.1%	18	77.7%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DEAD,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases
FAM65C	140876	genome.wustl.edu	37	20	49221198	49221198	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080829.2	-1	predicted	p.R353Q	1.000	30	0%	28	28.6%	3	0%	probably_damaging(0.979)	tolerated(0.26)	neutral(0.456)	NULL
GNAS	2778	genome.wustl.edu	37	20	57415727	57415727	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016592.2	+1	reviewed	p.R189M	0.014	10	0%	10	40%	0	-	possibly_damaging(0.922)	deleterious(0.02)	deleterious(0.754)	HMMPfam_NESP55
CDH26	60437	genome.wustl.edu	37	20	58560066	58560066	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_177980.2	+1	reviewed	p.Q240R	0.000	80	0%	69	44.9%	0	-	benign(0.008)	tolerated(0.24)	neutral(0.037)	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
NRIP1	8204	genome.wustl.edu	37	21	16338588	16338588	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003489.3	-1	reviewed	p.M643fs	0.000	-	-	-	-	-	-	-	-	-	NULL
MRPL39	54148	genome.wustl.edu	37	21	26978959	26978959	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080794.3	-1	reviewed	p.A28T	0.167	89	0%	71	43.7%	32	43.7%	benign(0.004)	tolerated(0.14)	neutral(0.249)	NULL
TIAM1	7074	genome.wustl.edu	37	21	32638961	32638961	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003253.2	-1	validated	p.P110T	1.000	76	0%	91	31.9%	0	-	benign(0.049)	deleterious(0)	neutral(0.448)	NULL
SYNJ1	8867	genome.wustl.edu	37	21	34015756	34015756	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003895.3	-1	validated	p.P1148S	1.000	359	0%	171	40.9%	0	-	benign(0.323)	tolerated(0.52)	neutral(0.110)	NULL
DONSON	29980	genome.wustl.edu	37	21	34953768	34953768	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017613.2	-1	reviewed	p.P397H	1.000	123	0%	93	38.7%	34	61.7%	probably_damaging(1)	deleterious(0.04)	deleterious(0.849)	NULL
DSCR3	10311	genome.wustl.edu	37	21	38600086	38600086	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000309117	-1	known	p.R227H	0.997	20	0%	22	45.5%	17	64.7%	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	HMMPfam_Vps26
COL18A1	80781	genome.wustl.edu	37	21	46888523	46888523	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_130444.2	+1	reviewed	p.F573	0.000	25	0%	30	53.3%	13	76.9%	-	-	-	HMMSmart_SM00210,superfamily_Concanavalin A-like lectins/glucanases
CDC45	8318	genome.wustl.edu	37	22	19495353	19495353	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003504.3	+1	reviewed	p.R341W	0.998	113	0%	87	39.1%	60	53.3%	probably_damaging(0.99)	tolerated(0.13)	deleterious(0.694)	HMMPfam_CDC45
MED15	51586	genome.wustl.edu	37	22	20939198	20939198	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003891.1	+1	reviewed	p.P620	0.262	28	0%	24	37.5%	97	47.4%	-	-	-	NULL
TCN2	6948	genome.wustl.edu	37	22	31011718	31011718	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000355.3	+1	reviewed	p.V295A	0.053	78	0%	69	33.3%	4	75%	probably_damaging(0.959)	tolerated(0.66)	neutral(0.405)	HMMPfam_Cobalamin_bind
LIMK2	3985	genome.wustl.edu	37	22	31661933	31661933	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031801.1	+1	reviewed	p.R265C	1.000	89	0%	48	52.1%	12	58.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
SLC5A4	6527	genome.wustl.edu	37	22	32616924	32616924	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014227.2	-1	validated	p.D584V	0.001	335	0%	298	39.3%	0	-	benign(0.008)	tolerated(0.08)	neutral(0.300)	NULL
CSF2RB	1439	genome.wustl.edu	37	22	37318319	37318319	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000395.2	+1	reviewed	p.A24T	0.000	8	0.000	10	0.400	0	-	possibly_damaging(0.833)	deleterious(0.05)	deleterious(0.663)	NULL
KDELR3	11015	genome.wustl.edu	37	22	38875737	38875738	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	AC	AC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016657.1	+1	reviewed	p.Y111fs	1.000:0.996	-	-	-	-	-	-	-	-	-	HMMPfam_ER_lumen_recept
APOBEC3B	9582	genome.wustl.edu	37	22	39388407	39388407	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000402182	+1	known	p.C463R	0.002	190	1.1%	196	44.4%	1	100%	benign(0.014)	-	-	NULL
CERK	64781	genome.wustl.edu	37	22	47116899	47116900	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	CA	CA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022766.5	-1	validated	p.V52fs	0.818:0.822	-	-	-	-	-	-	-	-	-	HMMSmart_PH
KIR2DL5B	553128	genome.wustl.edu	37	GL000209.1	35881	35881	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000344867	+1	known	p.I330	NULL	299	0%	264	6.1%	0	-	-	-	-	NULL
ENSG00000211459	0	genome.wustl.edu	37	MT	727	727	+	RNA	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000389680	+1	known	NULL	NULL	19	0%	16	100%	1676	89.6%	-	-	-	-
STS	412	genome.wustl.edu	37	X	7268151	7268151	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000351.4	+1	reviewed	p.A534V	0.000	140	0%	90	41.1%	2	100%	benign(0.001)	tolerated(1)	-	superfamily_Alkaline_phosphatase_core
SHROOM2	357	genome.wustl.edu	37	X	9912913	9912913	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001649.2	+1	reviewed	p.A1515V	1.000	41	0%	22	50%	5	0%	probably_damaging(0.999)	tolerated(0.21)	deleterious(0.534)	HMMPfam_ASD2
CLCN4	1183	genome.wustl.edu	37	X	10188720	10188720	+	Silent	SNP	G	G	A	rs2238892		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001830.3	+1	reviewed	p.Q665	1.000	200	0%	153	44.4%	2	0%	-	-	-	HMMPfam_CBS
SH3KBP1	30011	genome.wustl.edu	37	X	19606544	19606544	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000379697	-1	known	p.A549	0.000	15	0%	41	34.1%	0	-	-	-	-	NULL
DDX53	168400	genome.wustl.edu	37	X	23019918	23019918	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182699.2	+1	validated	p.L582M	0.717	295	0%	214	43.9%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_SSF52540
IL1RAPL1	11141	genome.wustl.edu	37	X	29973827	29973827	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014271.3	+1	reviewed	p.R661W	1.000	72	0%	62	46.8%	0	-	probably_damaging(0.998)	deleterious(0.03)	deleterious(0.839)	NULL
CXorf27	25763	genome.wustl.edu	37	X	37850192	37850192	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012274.1	+1	validated	p.R34C	0.000	152	0%	98	43.9%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	superfamily_Histone-fold
BCOR	54880	genome.wustl.edu	37	X	39922961	39922961	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001123385.1	-1	reviewed	p.G1249	0.994	190	0%	147	46.9%	23	78.2%	-	-	-	NULL
CDK16	5127	genome.wustl.edu	37	X	47085410	47085410	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033018.3	+1	reviewed	p.N265S	1.000	44	0%	40	40%	296	44.9%	benign(0)	tolerated(0.65)	neutral(0.003)	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase
SSX3	10214	genome.wustl.edu	37	X	48206940	48206940	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021014.2	-1	reviewed	p.*189	0.002	775	0%	705	29.8%	0	-	-	-	-	NULL
RBM3	5935	genome.wustl.edu	37	X	48435516	48435516	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000354480	+1	known	p.A145V	0.000	75	0%	63	25.4%	7	0%	unknown(0)	-	-	NULL
PQBP1	10084	genome.wustl.edu	37	X	48759668	48759669	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	AG	AG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001032381.1	+1	reviewed	p.E154fs	0.483:0.996	-	-	-	-	-	-	-	-	-	NULL
CLCN5	1184	genome.wustl.edu	37	X	49851169	49851169	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127898.1	+1	reviewed	p.G400D	1.000	156	0%	153	47.1%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Voltage_CLC,superfamily_Clc chloride channel
SMC1A	8243	genome.wustl.edu	37	X	53439001	53439001	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006306.2	-1	reviewed	p.R353W	1.000	83	0%	123	44.7%	32	40.6%	probably_damaging(0.994)	deleterious(0.01)	deleterious(0.858)	HMMPfam_SMC_N,superfamily_SSF52540
ITIH6	347365	genome.wustl.edu	37	X	54815006	54815006	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198510.2	-1	reviewed	p.L231	0.028	95	0%	118	12.7%	0	-	-	-	-	NULL
FAM104B	90736	genome.wustl.edu	37	X	55172586	55172586	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000489298	-1	known	p.S92	0.008	218	0.5%	159	38.4%	88	0%	-	-	-	NULL
ZXDA	7789	genome.wustl.edu	37	X	57935316	57935316	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007156.4	-1	reviewed	p.P513	0.385	159	0.6%	103	65%	2	100%	-	-	-	PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2
TEX11	56159	genome.wustl.edu	37	X	69773239	69773239	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003811.1	-1	reviewed	p.H787Q	0.524	110	0%	60	31.7%	0	-	possibly_damaging(0.907)	tolerated(0.07)	deleterious(0.679)	NULL
IL2RG	3561	genome.wustl.edu	37	X	70327598	70327598	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000206.2	-1	reviewed	p.K366	0.423	86	0%	77	35.1%	25	0%	-	-	-	NULL
ZMYM3	9203	genome.wustl.edu	37	X	70464252	70464252	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005096.3	-1	reviewed	p.T1060	0.284	108	0%	97	44.3%	13	100%	-	-	-	NULL
TAF1	6872	genome.wustl.edu	37	X	70613215	70613215	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004606.3	+1	reviewed	p.R1059P	1.000	265	0%	176	43.8%	2	100%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
ATRX	546	genome.wustl.edu	37	X	76907772	76907772	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000489.3	-1	reviewed	p.E1463	0.963	827	0.1%	649	46.5%	5	100%	-	-	-	superfamily_P-loop containing nucleoside triphosphate hydrolases
POU3F4	5456	genome.wustl.edu	37	X	82764246	82764246	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000307.3	+1	reviewed	p.A305V	1.000	65	0%	103	42.7%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Homeobox,HMMSmart_HOX,superfamily_Homeodomain_like
BEX2	84707	genome.wustl.edu	37	X	102564786	102564786	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032621.3	-1	reviewed	p.P40H	0.001	281	0%	298	43.3%	1	0%	benign(0.03)	tolerated(0.22)	neutral(0.044)	HMMPfam_BEX
RAB40A	142684	genome.wustl.edu	37	X	102754919	102754920	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080879.2	-1	reviewed	p.V255fs	0.969:0.968	-	-	-	-	-	-	-	-	-	NULL
IL1RAPL2	26280	genome.wustl.edu	37	X	104512141	104512143	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	AAG	AAG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017416.1	+1	reviewed	p.E207in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin
LOC642357	642357	genome.wustl.edu	37	X	114937592	114937592	+	RNA	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_016681.3	+1	model	NULL	0.994	67	0%	93	38.7%	1	100%	-	-	-	-
KIAA1210	57481	genome.wustl.edu	37	X	118223601	118223601	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020721.1	-1	validated	p.A531V	0.000	625	0%	461	43.8%	0	-	possibly_damaging(0.515)	-	-	NULL
RHOXF2	84528	genome.wustl.edu	37	X	119293294	119293294	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032498.1	+1	provisional	p.R151	0.000	47	0%	40	27.5%	0	-	-	-	-	HMMPfam_Homeobox,HMMSmart_HOX,superfamily_Homeodomain_like
THOC2	57187	genome.wustl.edu	37	X	122765552	122765552	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001081550.1	-1	validated	p.A823V	1.000	539	0.2%	393	44.3%	5	100%	possibly_damaging(0.469)	tolerated(0.1)	neutral(0.441)	NULL
THOC2	57187	genome.wustl.edu	37	X	122866864	122866864	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001081550.1	-1	validated	p.A3	1.000	87	0%	24	33.3%	1	0%	-	-	-	NULL
ODZ1	10178	genome.wustl.edu	37	X	123654620	123654620	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014253.3	-1	reviewed	p.E1016	1.000	151	0%	154	42.9%	0	-	-	-	-	NULL
PASD1	139135	genome.wustl.edu	37	X	150844532	150844532	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173493.2	+1	reviewed	p.A747T	0.000	288	0.3%	168	49.4%	0	-	possibly_damaging(0.873)	tolerated(0.06)	deleterious(0.661)	NULL
L1CAM	3897	genome.wustl.edu	37	X	153133822	153133822	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LT-01	TCGA-AP-A0LT-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000455590	-1	known	p.P4H	0.975	95	0%	86	47.7%	0	-	-	-	-	NULL
