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
TP73	7161	genome.wustl.edu	37	1	3646582	3646582	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005427.2	+1	reviewed	p.P405	0.002	27	0%	30	40%	19	47.3%	-	-	-	NULL
CEP104	9731	genome.wustl.edu	37	1	3754043	3754043	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014704.3	-1	validated	p.R311H	0.000	240	0%	221	45.7%	15	66.6%	benign(0.001)	tolerated(0.59)	neutral(0.004)	NULL
CAMTA1	23261	genome.wustl.edu	37	1	7724128	7724128	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015215.1	+1	validated	p.M507I	0.981	40	0%	37	45.9%	0	-	benign(0.006)	tolerated(0.08)	neutral(0.300)	NULL
H6PD	9563	genome.wustl.edu	37	1	9323719	9323719	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004285.3	+1	reviewed	p.A389	0.000	51	0%	55	45.5%	12	25%	-	-	-	superfamily_SSF55347
MFN2	9927	genome.wustl.edu	37	1	12067288	12067288	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127660.1	+1	reviewed	p.C684Y	1.000	55	0%	40	10%	42	2.3%	probably_damaging(0.994)	deleterious(0)	deleterious(0.897)	HMMPfam_Fzo_mitofusin
PLA2G2E	30814	genome.wustl.edu	37	1	20249129	20249129	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014589.1	-1	provisional	p.P54S	1.000	86	0%	75	41.3%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Phospholip_A2_1,HMMSmart_PA2c,superfamily_PhospholipaseA2
MUL1	79594	genome.wustl.edu	37	1	20827284	20827284	+	Missense_Mutation	SNP	C	C	T	rs189393223	by1000genomes	TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024544.2	-1	validated	p.V320I	0.985	97	0%	80	27.5%	34	35.2%	benign(0.029)	tolerated(0.19)	neutral(0.051)	HMMSmart_RING,superfamily_SSF57850
RUNX3	864	genome.wustl.edu	37	1	25256138	25256138	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031680.2	-1	reviewed	p.F88	1.000	37	0%	49	22.4%	6	33.3%	-	-	-	superfamily_p53-like transcription factors,HMMPfam_Runt
CATSPER4	378807	genome.wustl.edu	37	1	26524887	26524887	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198137.1	+1	validated	p.W263*	1.000	211	0%	173	45.7%	0	-	-	-	-	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
ZNF683	257101	genome.wustl.edu	37	1	26691429	26691429	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001114759.1	-1	validated	p.P203H	0.001	503	0%	470	37%	3	0%	unknown(0)	deleterious(0)	-	NULL
ARID1A	8289	genome.wustl.edu	37	1	27087503	27087503	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006015.4	+1	reviewed	p.R693*	1.000	224	0%	188	30.3%	21	28.5%	-	-	-	NULL
MAP3K6	9064	genome.wustl.edu	37	1	27685058	27685058	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000472410	-1	known	p.R600Q	0.017	56	0%	52	42.3%	24	50%	-	-	-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase
MACF1	23499	genome.wustl.edu	37	1	39818804	39818804	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000372925	+1	known	p.G847R	0.002	164	0%	168	35.1%	0	-	-	-	-	NULL
PTPRF	5792	genome.wustl.edu	37	1	44086177	44086179	+	In_Frame_Del	DEL	TTG	TTG	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	TTG	TTG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002840.3	+1	reviewed	p.V1766in_frame_del	1.000:0.994:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II
TESK2	10420	genome.wustl.edu	37	1	45811044	45811044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007170.2	-1	reviewed	p.R395H	0.001	54	0%	65	49.2%	5	20%	benign(0.001)	tolerated(0.8)	neutral(0.001)	NULL
TESK2	10420	genome.wustl.edu	37	1	45923415	45923415	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007170.2	-1	reviewed	p.R15C	1.000	313	0%	268	39.9%	3	33.3%	possibly_damaging(0.847)	tolerated(0.15)	deleterious(0.566)	NULL
PODN	127435	genome.wustl.edu	37	1	53546475	53546475	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153703.3	+1	validated	p.Q578*	1.000	113	0%	70	38.6%	1	0%	-	-	-	HMMPfam_LRR_1,superfamily_SSF52047
C8B	732	genome.wustl.edu	37	1	57411609	57411609	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000066.2	-1	reviewed	p.Y330	0.441	254	0.4%	199	33.2%	0	-	-	-	-	HMMPfam_MACPF,HMMSmart_SM00457
LRRC7	57554	genome.wustl.edu	37	1	70225913	70225913	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020794.2	+1	validated	p.G9D	1.000	87	0%	74	33.8%	0	-	possibly_damaging(0.944)	tolerated(0.06)	deleterious(0.711)	superfamily_L domain-like
PIGK	10026	genome.wustl.edu	37	1	77627342	77627342	+	Silent	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005482.2	-1	reviewed	p.E213	0.678	216	0%	146	47.3%	8	62.5%	-	-	-	HMMPfam_Peptidase_C13
DR1	1810	genome.wustl.edu	37	1	93826181	93826181	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001938.2	+1	reviewed	p.D172E	1.000	213	0%	196	41.8%	16	37.5%	unknown(0)	tolerated(0.31)	-	NULL
RHOC	389	genome.wustl.edu	37	1	113244200	113244200	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001042678.1	-1	reviewed	p.R182S	1.000	142	0%	147	42.9%	446	43%	benign(0.001)	tolerated(0.1)	neutral(0.286)	HMMSmart_SM00173,superfamily_P-loop containing nucleoside triphosphate hydrolases
TRIM33	51592	genome.wustl.edu	37	1	114964249	114964249	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015906.3	-1	reviewed	p.P624S	1.000	764	0%	675	37%	21	38%	probably_damaging(0.999)	tolerated(0.28)	deleterious(0.522)	NULL
CSDE1	7812	genome.wustl.edu	37	1	115262208	115262208	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130523.1	-1	validated	p.W751*	1.000	129	0%	128	44.5%	188	5.3%	-	-	-	HMMPfam_CSD,HMMSmart_SM00357,superfamily_Nucleic acid-binding proteins
CSDE1	7812	genome.wustl.edu	37	1	115280681	115280681	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130523.1	-1	validated	p.F117C	1.000	431	0%	408	39.5%	51	78.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_CSD,HMMSmart_SM00357,superfamily_Nucleic acid-binding proteins
TXNIP	10628	genome.wustl.edu	37	1	145440289	145440289	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006472.3	+1	validated	p.A199T	1.000	144	0%	232	14.2%	396	17.4%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	HMMPfam_Arrestin_C,superfamily_Ig_E-set
POLR3GL	84265	genome.wustl.edu	37	1	145457040	145457042	+	In_Frame_Del	DEL	TCT	TCT	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	TCT	TCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032305.1	-1	provisional	p.E174in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
S100A7A	338324	genome.wustl.edu	37	1	153391728	153391728	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_176823.3	+1	validated	p.A83	0.000	168	0%	188	21.8%	1	0%	-	-	-	superfamily_SSF47473
ETV3L	440695	genome.wustl.edu	37	1	157067666	157067666	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004341.2	-1	validated	p.V201I	0.000	110	0%	166	17.5%	0	-	benign(0)	tolerated(0.09)	neutral(0.296)	NULL
IGSF8	93185	genome.wustl.edu	37	1	160061683	160061683	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052868.2	-1	provisional	p.A591V	0.759	149	0%	244	20.1%	461	24%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
USP21	27005	genome.wustl.edu	37	1	161130777	161130777	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001014443.2	+1	reviewed	p.S116N	1.000	123	0%	215	21.4%	56	19.6%	possibly_damaging(0.873)	deleterious(0)	deleterious(0.784)	NULL
FCGR2C	9103	genome.wustl.edu	37	1	161561069	161561069	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_201563.4	+1	reviewed	p.R176H	0.000	564	0.4%	859	17.3%	2	0%	benign(0)	tolerated(1)	-	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin
PRRX1	5396	genome.wustl.edu	37	1	170695427	170695427	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022716.2	+1	reviewed	p.A162T	1.000	121	0%	172	16.9%	70	25.7%	probably_damaging(0.99)	tolerated(0.06)	deleterious(0.764)	superfamily_Homeodomain-like
KLHL20	27252	genome.wustl.edu	37	1	173703366	173703366	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014458.3	+1	reviewed	p.H180Y	1.000	168	0%	258	17.4%	4	25%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_BACK
CACNA1E	777	genome.wustl.edu	37	1	181765921	181765921	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000721.2	+1	reviewed	p.A2066V	0.846	109	0%	152	19.7%	0	-	possibly_damaging(0.821)	tolerated(0.31)	neutral(0.338)	NULL
GLT25D2	23127	genome.wustl.edu	37	1	183913408	183913408	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015101.2	-1	validated	p.R440H	1.000	281	0%	452	22.6%	4	25%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Glyco_transf_25
TRMT1L	81627	genome.wustl.edu	37	1	185089163	185089163	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030934.4	-1	reviewed	p.C730	0.876	172	0%	266	21.1%	18	33.3%	-	-	-	NULL
CFHR5	81494	genome.wustl.edu	37	1	196952157	196952157	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030787.3	+1	reviewed	p.W67*	0.335	304	0%	445	18.2%	0	-	-	-	-	HMMPfam_Sushi,HMMSmart_CCP,superfamily_Complement_control_module
PLEKHA6	22874	genome.wustl.edu	37	1	204217950	204217950	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014935.2	-1	validated	p.T608M	1.000	238	0%	358	24.6%	15	20%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PTPN14	5784	genome.wustl.edu	37	1	214638039	214638039	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005401.4	-1	reviewed	p.T36	0.018	197	0%	332	19.3%	8	37.5%	-	-	-	HMMPfam_FERM_N,HMMSmart_B41,superfamily_SSF54236
OBSCN	84033	genome.wustl.edu	37	1	228470802	228470802	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098623.1	+1	reviewed	p.R2852W	0.000	37	0%	70	12.9%	2	0%	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin
LYST	1130	genome.wustl.edu	37	1	235918789	235918789	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000081.2	-1	reviewed	p.G2406	1.000	174	0%	323	15.8%	2	50%	-	-	-	NULL
MTR	4548	genome.wustl.edu	37	1	237057694	237057694	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000254.2	+1	reviewed	p.C1081Y	1.000	289	0%	458	16.2%	31	16.1%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	superfamily_Methionine synthase activation domain-like
CHRM3	1131	genome.wustl.edu	37	1	240071263	240071263	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000740.2	+1	reviewed	p.T171M	1.000	194	0%	332	21.1%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_7tm_1,superfamily_SSF81321
ZNF672	79894	genome.wustl.edu	37	1	249142437	249142437	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024836.1	+1	provisional	p.D322N	0.112	25	0%	20	30%	101	20.7%	probably_damaging(0.987)	tolerated(0.21)	deleterious(0.480)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
PGBD2	267002	genome.wustl.edu	37	1	249211654	249211654	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_170725.2	+1	validated	p.R291*	0.000	181	0%	232	25.4%	11	27.2%	-	-	-	NULL
LOC100288793	100288793	genome.wustl.edu	37	2	1653106	1653106	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002342190.1	+1	model	p.W79*	1.000	105	0%	112	38.4%	6	0%	probably_damaging(0.987)	deleterious(0)	deleterious(0.881)	NULL
RNF144A	9781	genome.wustl.edu	37	2	7154616	7154618	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	AAG	AAG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014746.3	+1	reviewed	p.E57in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMSmart_RING
SOS1	6654	genome.wustl.edu	37	2	39250044	39250044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005633.3	-1	reviewed	p.E509K	1.000	223	0%	184	42.4%	1	0%	probably_damaging(0.996)	deleterious(0.01)	deleterious(0.867)	HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like
MAP4K3	8491	genome.wustl.edu	37	2	39505605	39505605	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000437545	-1	known	p.R546*	0.187	146	0%	118	27.1%	5	40%	-	-	-	HMMPfam_CNH,HMMSmart_SM00036
TSPYL6	388951	genome.wustl.edu	37	2	54482503	54482503	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003937.2	-1	validated	p.L262	0.217	107	0%	63	46%	0	-	-	-	-	HMMPfam_NAP
PNPT1	87178	genome.wustl.edu	37	2	55874529	55874529	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033109.3	-1	validated	p.P519T	0.140	173	0%	194	41.8%	13	46.1%	benign(0.011)	tolerated(0.09)	neutral(0.297)	HMMPfam_RNase_PH_C,superfamily_3_ExoRNase
CCDC85A	114800	genome.wustl.edu	37	2	56420129	56420129	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080433.1	+1	provisional	p.C265Y	0.984	47	0%	53	37.7%	0	-	benign(0)	deleterious(0.04)	neutral(0.349)	NULL
USP34	9736	genome.wustl.edu	37	2	61441455	61441455	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014709.3	-1	validated	p.V2808F	1.000	104	0%	103	35.9%	19	63.1%	possibly_damaging(0.687)	-	-	NULL
WBP1	23559	genome.wustl.edu	37	2	74687092	74687092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012477.2	+1	reviewed	p.R89W	1.000	264	0.4%	226	45.1%	202	43%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
GPAT2	150763	genome.wustl.edu	37	2	96688770	96688770	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000335448	-1	known	p.V774I	0.699	100	0%	83	33.7%	23	30.4%	benign(0.014)	tolerated(0.2)	neutral(0.050)	NULL
TGFBRAP1	9392	genome.wustl.edu	37	2	105896918	105896918	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142621.1	-1	validated	p.D462N	1.000	151	0%	115	33.9%	15	40%	benign(0.308)	tolerated(0.27)	neutral(0.130)	HMMPfam_Vps39_1
SULT1C2	6819	genome.wustl.edu	37	2	108921145	108921145	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_176825.2	+1	reviewed	p.I175T	1.000	221	0%	176	47.2%	8	12.5%	possibly_damaging(0.484)	deleterious(0)	deleterious(0.605)	HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases
BCL2L11	10018	genome.wustl.edu	37	2	111881511	111881511	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138621.3	+1	reviewed	p.P63	0.974	116	0%	94	50%	9	44.4%	-	-	-	NULL
SMPD4	55627	genome.wustl.edu	37	2	130910890	130910890	+	Splice_Site	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017951.3	-1	validated	e18+2	1.000	101	0%	72	43.1%	2	100%	-	-	-	-
RIF1	55183	genome.wustl.edu	37	2	152320637	152320637	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018151.4	+1	reviewed	p.R1535W	1.000	106	0%	83	36.1%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_ARM repeat
SCN3A	6328	genome.wustl.edu	37	2	165947767	165947767	+	Silent	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006922.3	-1	reviewed	p.L1632	0.048	356	0%	290	37.6%	0	-	-	-	-	HMMPfam_Ion_trans,superfamily_SSF81324
G6PC2	57818	genome.wustl.edu	37	2	169758043	169758043	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021176.2	+1	reviewed	p.N68D	1.000	149	0%	140	45.7%	0	-	possibly_damaging(0.556)	deleterious(0)	deleterious(0.634)	HMMPfam_PAP2,HMMSmart_SM00014,superfamily_Acid phosphatase/Vanadium-dependent haloperoxidase
RBM45	129831	genome.wustl.edu	37	2	178985903	178985903	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000456670	+1	known	p.G226R	1.000	97	0%	80	25%	1	0%	-	-	-	NULL
TTN	7273	genome.wustl.edu	37	2	179587193	179587193	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000356127	-1	known	p.R6197*	0.996	83	0%	69	29%	0	-	-	-	-	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set
C2orf62	375307	genome.wustl.edu	37	2	219222777	219222777	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198559.1	+1	predicted	p.L113	0.003	108	0%	119	31.1%	14	28.5%	-	-	-	NULL
PSMD1	5707	genome.wustl.edu	37	2	231941836	231941836	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002807.2	+1	reviewed	p.R344Q	1.000	134	0%	105	34.3%	11	45.4%	possibly_damaging(0.921)	deleterious(0.05)	deleterious(0.716)	NULL
LINC00471	151477	genome.wustl.edu	37	2	232378884	232378885	+	RNA	DEL	AT	AT	-	rs10534780	byCluster;by1000genomes	TCGA-D1-A176-01	TCGA-D1-A176-01	AT	AT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_024079.1	-1	predicted	NULL	0.000:0.000	-	-	-	-	-	-	-	-	-	-
DIS3L2	129563	genome.wustl.edu	37	2	233201208	233201208	+	Silent	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000418143	+1	known	p.G123C	1.000	79	0%	77	36.4%	34	64.7%	-	-	-	NULL
PASK	23178	genome.wustl.edu	37	2	242080067	242080067	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015148.2	-1	validated	p.E100K	0.001	157	0%	104	38.5%	8	75%	benign(0)	deleterious(0.01)	neutral(0.406)	NULL
LOC401052	401052	genome.wustl.edu	37	3	10049185	10049187	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	TTC	TTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001008737.1	-1	predicted	p.K67in_frame_del	0.001:0.001:0.001	-	-	-	-	-	-	-	-	-	NULL
ATP2B2	491	genome.wustl.edu	37	3	10384561	10384561	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001331.2	-1	reviewed	p.T931M	0.997	123	0%	112	43.8%	1	0%	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMPfam_Cation_ATPase_C,superfamily_Calcium ATPase transmembrane domain M
GLB1	2720	genome.wustl.edu	37	3	33038787	33038787	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000404.2	-1	reviewed	p.R595L	0.014	86	0%	80	31.2%	326	37.4%	probably_damaging(0.96)	tolerated(0.31)	neutral(0.430)	NULL
ITGA9	3680	genome.wustl.edu	37	3	37555305	37555305	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002207.2	+1	reviewed	p.G317S	1.000	277	0%	250	36%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_FG-GAP,HMMSmart_Int_alpha,superfamily_SSF69318
TRAIP	10293	genome.wustl.edu	37	3	49885583	49885583	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005879.2	-1	reviewed	p.R50Q	1.000	220	0%	203	33.5%	2	0%	possibly_damaging(0.666)	deleterious(0.01)	deleterious(0.641)	superfamily_SSF57850
DNAH1	25981	genome.wustl.edu	37	3	52394428	52394428	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015512.4	+1	validated	p.P1558H	1.000	192	0%	162	41.4%	6	33.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_P-loop containing nucleoside triphosphate hydrolases
LRIG1	26018	genome.wustl.edu	37	3	66467647	66467647	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015541.2	-1	validated	p.A137T	0.209	217	0%	232	37.9%	109	39.4%	benign(0.002)	tolerated(0.57)	neutral(0.006)	superfamily_L domain-like
ARL6IP5	10550	genome.wustl.edu	37	3	69153644	69153644	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006407.3	+1	reviewed	p.R142W	1.000	100	0%	65	43.1%	171	39.7%	unknown(0)	-	-	HMMPfam_PRA1
KIAA1524	57650	genome.wustl.edu	37	3	108285486	108285486	+	Splice_Site	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020890.2	-1	validated	e11-1	1.000	278	0%	234	36.3%	0	-	-	-	-	-
CD96	10225	genome.wustl.edu	37	3	111356988	111356988	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198196.2	+1	reviewed	p.T500A	0.971	302	0%	274	34.7%	1	0%	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	NULL
BOC	91653	genome.wustl.edu	37	3	113003294	113003294	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033254.2	+1	validated	p.L922	0.829	118	0%	112	40.2%	10	60%	-	-	-	NULL
ADCY5	111	genome.wustl.edu	37	3	123021985	123021985	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_183357.1	-1	validated	p.V881M	0.996	83	0%	64	29.7%	11	18.1%	benign(0.011)	tolerated(0.09)	neutral(0.297)	NULL
KBTBD12	166348	genome.wustl.edu	37	3	127642005	127642005	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207335.2	+1	validated	p.V34A	0.985	203	0%	229	16.6%	0	-	probably_damaging(1)	deleterious(0.04)	deleterious(0.849)	HMMSmart_SM00225,superfamily_POZ domain,HMMPfam_BTB
ATP2C1	27032	genome.wustl.edu	37	3	130717235	130717235	+	Splice_Site	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001486.1	+1	reviewed	e25+2	1.000	319	0%	258	38%	3	100%	-	-	-	-
IGSF10	285313	genome.wustl.edu	37	3	151165062	151165062	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178822.4	-1	validated	p.F903L	0.000	202	0%	202	35.6%	0	-	benign(0.141)	deleterious(0.03)	neutral(0.377)	NULL
FNDC3B	64778	genome.wustl.edu	37	3	172025166	172025166	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135095.1	+1	validated	p.Y359H	1.000	243	0%	190	46.3%	33	42.4%	possibly_damaging(0.686)	tolerated(0.54)	neutral(0.253)	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
VWA5B2	90113	genome.wustl.edu	37	3	183958875	183958875	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138345.1	+1	provisional	p.P981H	0.016	156	0%	109	39.4%	12	66.6%	benign(0.163)	tolerated(0.13)	neutral(0.267)	NULL
KIAA0226	9711	genome.wustl.edu	37	3	197403805	197403805	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145642.2	-1	validated	p.R821Q	1.000	196	0%	166	44%	10	0%	benign(0.057)	tolerated(0.32)	neutral(0.028)	NULL
WHSC2	7469	genome.wustl.edu	37	4	1991522	1991522	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005663.3	-1	reviewed	p.A164T	0.998	198	0.5%	138	38.4%	46	50%	benign(0.108)	deleterious(0.02)	neutral(0.392)	NULL
TLR6	10333	genome.wustl.edu	37	4	38828822	38828822	+	Missense_Mutation	SNP	C	C	T	rs55963748		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006068.3	-1	validated	p.R758Q	0.366	312	0%	302	36.8%	2	100%	probably_damaging(0.955)	deleterious(0.02)	deleterious(0.782)	HMMPfam_TIR,HMMSmart_TIR,superfamily_TIR
NOA1	84273	genome.wustl.edu	37	4	57830572	57830572	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032313.2	-1	provisional	p.G629C	1.000	173	0%	149	46.3%	36	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
UGT2B11	10720	genome.wustl.edu	37	4	69874749	69874749	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000381096	-1	known	p.G379D	1.000	280	0%	236	35.6%	0	-	-	-	-	HMMPfam_UDPGT,PatternScan_UDPGT,superfamily_UDP-Glycosyltransferase/glycogen phosphorylase
USO1	8615	genome.wustl.edu	37	4	76722325	76722325	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000264904	+1	known	p.T581I	1.000	205	0%	139	24.5%	30	33.3%	benign(0.263)	tolerated(0.1)	neutral(0.314)	superfamily_ARM repeat
FGF5	2250	genome.wustl.edu	37	4	81207633	81207633	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004464.3	+1	reviewed	p.R205Q	0.928	128	0.8%	100	32%	0	-	probably_damaging(0.997)	deleterious(0.01)	deleterious(0.872)	HMMPfam_FGF,HMMSmart_SM00442,superfamily_Cytokine
HSD17B11	51170	genome.wustl.edu	37	4	88295861	88295861	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016245.3	-1	validated	p.A147V	1.000	172	0%	149	30.2%	10	30%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_adh_short,superfamily_NAD(P)-binding Rossmann-fold domains
MAML3	55534	genome.wustl.edu	37	4	140811081	140811081	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018717.4	-1	validated	p.Q503	1.000	60	0%	83	34.9%	0	-	-	-	-	NULL
DDX60L	91351	genome.wustl.edu	37	4	169341410	169341410	+	Splice_Site	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001012967.1	-1	validated	e17+2	0.949	49	0%	44	40.9%	0	-	-	-	-	-
FAT1	2195	genome.wustl.edu	37	4	187541661	187541661	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005245.3	-1	reviewed	p.R2027C	1.000	296	0%	244	34.8%	11	27.2%	probably_damaging(0.988)	deleterious(0.04)	deleterious(0.786)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Cadherin-like
SLC9A3	6550	genome.wustl.edu	37	5	488478	488478	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004174.2	-1	validated	p.F210L	1.000	54	0%	39	38.5%	1	0%	probably_damaging(0.996)	deleterious(0.01)	deleterious(0.867)	HMMPfam_Na_H_Exchanger
SLC6A3	6531	genome.wustl.edu	37	5	1411427	1411427	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001044.4	-1	reviewed	p.T400	0.438	85	0%	77	39%	0	-	-	-	-	HMMPfam_SNF
ADAMTS16	170690	genome.wustl.edu	37	5	5303837	5303838	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139056.2	+1	reviewed	p.P1049fs	1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
NSUN2	54888	genome.wustl.edu	37	5	6625761	6625761	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017755.4	-1	validated	p.W127*	1.000	258	0%	212	12.7%	12	8.3%	-	-	-	superfamily_SSF53335
MYO10	4651	genome.wustl.edu	37	5	16762723	16762723	+	Silent	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012334.2	-1	validated	p.I506	1.000	254	0%	210	31.9%	13	46.1%	-	-	-	HMMPfam_Myosin_head,HMMSmart_MYSc,superfamily_SSF52540
BASP1	10409	genome.wustl.edu	37	5	17275411	17275411	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006317.3	+1	reviewed	p.A29V	0.300	28	3.6%	27	44.4%	110	31.8%	unknown(0)	tolerated(0.15)	-	HMMPfam_BASP1
RXFP3	51289	genome.wustl.edu	37	5	33938124	33938124	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016568.3	+1	validated	p.E427*	1.000	35	0%	26	50%	0	-	-	-	-	superfamily_SSF81321
PIK3R1	5295	genome.wustl.edu	37	5	67589610	67589612	+	In_Frame_Del	DEL	AAA	AAA	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	AAA	AAA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181523.1	+1	reviewed	p.K459in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
ATG10	83734	genome.wustl.edu	37	5	81460231	81460231	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001131028.1	+1	validated	p.L77P	0.000	361	0%	252	39.7%	5	20%	benign(0)	tolerated(0.13)	neutral(0.253)	NULL
TTC37	9652	genome.wustl.edu	37	5	94803683	94803683	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014639.2	-1	provisional	p.R1503C	0.997	200	0%	180	43.3%	44	34%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
LNPEP	4012	genome.wustl.edu	37	5	96363454	96363454	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005575.2	+1	reviewed	p.Y961C	1.000	321	0%	254	36.2%	5	0%	probably_damaging(0.986)	tolerated(0.08)	deleterious(0.734)	NULL
GIN1	54826	genome.wustl.edu	37	5	102442584	102442584	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017676.2	-1	validated	p.R57G	1.000	93	0%	108	36.1%	0	-	possibly_damaging(0.843)	tolerated(0.05)	deleterious(0.668)	NULL
FBN2	2201	genome.wustl.edu	37	5	127611738	127611738	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001999.3	-1	reviewed	p.T2529I	0.995	413	0%	356	11.2%	7	42.8%	benign(0.003)	tolerated(0.08)	neutral(0.300)	HMMSmart_SM00179,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Growth factor receptor domain,PatternScan_EGF_2,HMMPfam_EGF_CA,superfamily_EGF/Laminin
PCDHGB7	56099	genome.wustl.edu	37	5	140799123	140799123	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018927.2	+1	reviewed	p.A566V	0.489	27	0%	30	40%	1	0%	benign(0.03)	tolerated(0.25)	neutral(0.038)	superfamily_Cadherin-like
RNF14	9604	genome.wustl.edu	37	5	141359765	141359765	+	Silent	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004290.3	+1	reviewed	p.A304	0.996	131	0%	120	44.2%	30	53.3%	-	-	-	HMMPfam_IBR,HMMSmart_SM00647,superfamily_RING/U-box
FBXO38	81545	genome.wustl.edu	37	5	147818023	147818023	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_205836.1	+1	validated	p.E996K	1.000	295	0%	283	36.4%	25	32%	possibly_damaging(0.891)	deleterious(0)	deleterious(0.795)	NULL
SYNPO	11346	genome.wustl.edu	37	5	150029778	150029778	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007286.5	+1	validated	p.P647	0.000	26	0%	25	48%	8	25%	-	-	-	NULL
DOCK2	1794	genome.wustl.edu	37	5	169461533	169461533	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004946.2	+1	validated	p.R1200C	1.000	165	0%	165	33.9%	2	0%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
HNRNPH1	3187	genome.wustl.edu	37	5	179042546	179042546	+	Splice_Site	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005520.2	-1	reviewed	e12+1	1.000	125	0%	103	29.1%	1	0%	-	-	-	-
SLC17A4	10050	genome.wustl.edu	37	6	25770690	25770690	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005495.2	+1	validated	p.A204T	0.458	175	0%	137	12.4%	0	-	benign(0.024)	tolerated(0.29)	neutral(0.030)	HMMPfam_MFS_1,superfamily_MFS general substrate transporter
NFKBIL1	4795	genome.wustl.edu	37	6	31525437	31525437	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005007.3	+1	reviewed	p.R123C	0.997	166	0%	172	46.5%	24	54.1%	probably_damaging(0.999)	deleterious(0.03)	deleterious(0.855)	HMMPfam_Ank,superfamily_Ankyrin repeat
ATF6B	1388	genome.wustl.edu	37	6	32087733	32087733	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004381.4	-1	reviewed	p.V278	0.999	112	0%	116	37.9%	155	35.4%	-	-	-	NULL
NOTCH4	4855	genome.wustl.edu	37	6	32165333	32165333	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004557.3	-1	reviewed	p.E1599*	1.000	143	0%	113	32.7%	1	0%	-	-	-	HMMPfam_Ank,superfamily_Ankyrin repeat
KIFC1	3833	genome.wustl.edu	37	6	33377450	33377450	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002263.3	+1	validated	p.Q669*	0.991	181	0%	177	36.7%	59	33.8%	-	-	-	HMMSmart_KISc
PHF1	5252	genome.wustl.edu	37	6	33381251	33381251	+	Silent	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024165.2	+1	reviewed	p.P168	0.973	210	0%	231	43.7%	29	20.6%	-	-	-	NULL
DST	667	genome.wustl.edu	37	6	56418138	56418138	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015548.4	-1	reviewed	p.N2528I	0.980	273	0%	213	28.2%	1	0%	possibly_damaging(0.917)	-	-	HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_Spectrin repeat
DST	667	genome.wustl.edu	37	6	56484743	56484745	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	TTC	TTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001723.5	-1	reviewed	p.E1363in_frame_del	0.004:0.240:0.054	-	-	-	-	-	-	-	-	-	NULL
PHF3	23469	genome.wustl.edu	37	6	64394234	64394234	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015153.2	+1	provisional	p.S204N	0.000	124	0%	111	41.4%	5	20%	benign(0.086)	deleterious(0.04)	neutral(0.355)	NULL
MDN1	23195	genome.wustl.edu	37	6	90368559	90368559	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014611.1	-1	provisional	p.D4931N	0.031	954	0%	872	34.4%	8	37.5%	unknown(0)	tolerated(0.55)	-	NULL
REV3L	5980	genome.wustl.edu	37	6	111650842	111650843	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	CT	CT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002912.3	-1	validated	p.R2711fs	1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_DNA_pol_B,HMMSmart_SM00486,superfamily_DNA/RNA polymerases
EPB41L2	2037	genome.wustl.edu	37	6	131211472	131211472	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001431.3	-1	validated	p.R541H	1.000	349	0.3%	304	38.2%	67	47.7%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_FA,superfamily_SSF50729
NOX3	50508	genome.wustl.edu	37	6	155750022	155750022	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015718.2	-1	reviewed	p.V351M	1.000	100	0%	77	45.5%	0	-	possibly_damaging(0.88)	deleterious(0)	deleterious(0.788)	HMMPfam_FAD_binding_8,superfamily_Riboflavin_synthase_like_b-brl
ZDHHC14	79683	genome.wustl.edu	37	6	157963706	157963706	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024630.2	+1	provisional	p.T112I	0.998	92	0%	60	40%	0	-	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	NULL
C6orf120	387263	genome.wustl.edu	37	6	170102682	170102682	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001029863.1	+1	predicted	p.H43Y	1.000	27	0%	20	25%	26	7.6%	possibly_damaging(0.447)	deleterious(0.03)	deleterious(0.510)	NULL
BRAT1	221927	genome.wustl.edu	37	7	2577948	2577948	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152743.2	-1	provisional	p.G741C	0.000	25	0%	18	44.4%	75	40%	possibly_damaging(0.758)	tolerated(0.17)	neutral(0.340)	NULL
TTYH3	80727	genome.wustl.edu	37	7	2697960	2697960	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025250.2	+1	reviewed	p.P431S	0.630	12	0%	18	33.3%	99	33.3%	benign(0)	tolerated(0.44)	neutral(0.013)	NULL
BZW2	28969	genome.wustl.edu	37	7	16722469	16722469	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014038.2	+1	validated	p.K135R	1.000	95	0%	90	40%	39	41%	benign(0.396)	deleterious(0.02)	deleterious(0.510)	NULL
CDCA7L	55536	genome.wustl.edu	37	7	21946056	21946056	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018719.4	-1	validated	p.R258W	0.995	130	0%	104	50%	5	20%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PDE1C	5137	genome.wustl.edu	37	7	31917638	31917638	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005020.1	-1	provisional	p.R146Q	1.000	256	0%	210	42.4%	0	-	probably_damaging(0.996)	deleterious(0.01)	deleterious(0.867)	NULL
KBTBD2	25948	genome.wustl.edu	37	7	32909547	32909547	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015483.2	-1	validated	p.H428N	1.000	165	0%	143	46.2%	28	50%	benign(0.291)	tolerated(0.24)	neutral(0.127)	HMMSmart_SM00612,superfamily_Galactose oxidase central domain
CDK13	8621	genome.wustl.edu	37	7	40127782	40127782	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003718.4	+1	reviewed	p.K1029	1.000	203	0%	166	39.8%	14	50%	-	-	-	superfamily_Protein kinase-like (PK-like)
LOC100289196	100289196	genome.wustl.edu	37	7	56671167	56671167	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002342722.1	+1	model	p.Y22C	0.950	22	0%	16	43.8%	0	-	-	-	-	NULL
WBSCR17	64409	genome.wustl.edu	37	7	71177023	71177023	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022479.1	+1	reviewed	p.G564fs	0.964	-	-	-	-	-	-	-	-	-	HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,superfamily_Ricin B-like lectins
BAZ1B	9031	genome.wustl.edu	37	7	72856582	72856582	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032408.3	-1	validated	p.G1466W	1.000	189	0%	153	39.9%	46	43.4%	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	NULL
BAZ1B	9031	genome.wustl.edu	37	7	72892038	72892038	+	Silent	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032408.3	-1	validated	p.L585	0.995	21	0%	25	52%	5	20%	-	-	-	NULL
PDAP1	11333	genome.wustl.edu	37	7	98995583	98995583	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014891.5	-1	validated	p.A130V	1.000	370	0.3%	380	34.7%	167	40.1%	benign(0.041)	deleterious(0.04)	neutral(0.351)	HMMPfam_PP28
SLC12A9	56996	genome.wustl.edu	37	7	100463482	100463482	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020246.2	+1	validated	p.P667H	1.000	33	0%	42	33.3%	22	54.5%	probably_damaging(0.998)	tolerated(0.53)	deleterious(0.482)	NULL
MET	4233	genome.wustl.edu	37	7	116423476	116423476	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127500.1	+1	reviewed	p.A1269T	1.000	235	0%	168	38.1%	16	31.2%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like
NAA38	51691	genome.wustl.edu	37	7	117825749	117825749	+	Splice_Site	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016200.4	+1	reviewed	e2+1	1.000	537	0%	426	29.1%	0	-	-	-	-	-
FLNC	2318	genome.wustl.edu	37	7	128487998	128487998	+	Splice_Site	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001458.4	+1	reviewed	e26-1	1.000	57	0%	55	43.6%	0	-	-	-	-	-
FLNC	2318	genome.wustl.edu	37	7	128488661	128488661	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001458.4	+1	reviewed	p.R1543W	1.000	137	0%	116	34.5%	3	0%	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	HMMSmart_SM00557,superfamily_E set domains,HMMPfam_Filamin
WDR91	29062	genome.wustl.edu	37	7	134889080	134889080	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014149.3	-1	validated	p.S277	0.000	185	0%	117	37.6%	12	25%	-	-	-	NULL
PARP12	64761	genome.wustl.edu	37	7	139724428	139724428	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022750.2	-1	provisional	p.S680T	0.008	269	0%	248	35.9%	77	37.6%	benign(0)	tolerated(0.27)	neutral(0.034)	superfamily_ADP-ribosylation
EPHB6	2051	genome.wustl.edu	37	7	142561883	142561883	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004445.3	+1	reviewed	p.F109L	1.000	37	0%	29	37.9%	0	-	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_Ephrin_lbd,HMMSmart_SM00615,superfamily_Galactose-binding domain-like
FAM115C	285966	genome.wustl.edu	37	7	143400425	143400425	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130025.1	+1	validated	p.A113V	0.868	124	0%	117	13.7%	0	-	benign(0.047)	tolerated(1)	neutral(0.003)	NULL
ARHGEF5	7984	genome.wustl.edu	37	7	144075893	144075893	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005435.3	+1	reviewed	p.R1524*	1.000	352	0%	315	39.4%	26	19.2%	-	-	-	HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_SH3_2
GIMAP4	55303	genome.wustl.edu	37	7	150269650	150269650	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018326.2	+1	reviewed	p.L164	0.000	112	0%	112	40.2%	7	0%	-	-	-	HMMPfam_AIG1,superfamily_SSF52540
KCNH2	3757	genome.wustl.edu	37	7	150648143	150648143	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000238.2	-1	reviewed	p.A671T	1.000	103	0%	82	37.8%	3	0%	benign(0.216)	tolerated(0.26)	neutral(0.055)	superfamily_cAMP-binding domain-like
KCNH2	3757	genome.wustl.edu	37	7	150649557	150649557	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000238.2	-1	reviewed	p.A505T	1.000	174	0%	165	37%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
KCNH2	3757	genome.wustl.edu	37	7	150654534	150654534	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000238.2	-1	reviewed	p.V325M	0.997	210	0%	164	40.9%	1	100%	benign(0.014)	tolerated(0.2)	neutral(0.050)	NULL
MLL3	58508	genome.wustl.edu	37	7	151860244	151860244	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_170606.2	-1	reviewed	p.P3473Q	1.000	324	0%	252	35.7%	7	71.4%	probably_damaging(1)	-	-	NULL
RP1L1	94137	genome.wustl.edu	37	8	10469900	10469900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178857.5	-1	validated	p.E570K	0.000	22	0%	22	45.5%	0	-	benign(0.001)	tolerated(0.57)	neutral(0.006)	NULL
RNF122	79845	genome.wustl.edu	37	8	33424237	33424237	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024787.2	-1	reviewed	p.H2R	0.997	53	0%	52	40.4%	16	43.7%	benign(0.261)	tolerated(0.07)	neutral(0.346)	NULL
ARMC1	55156	genome.wustl.edu	37	8	66525537	66525537	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018120.4	-1	validated	p.G136V	1.000	311	0%	282	36.2%	1	0%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
GRHL2	79977	genome.wustl.edu	37	8	102589723	102589723	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024915.3	+1	reviewed	p.A327P	1.000	177	0%	122	40.2%	32	31.2%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_CP2
FAM91A1	157769	genome.wustl.edu	37	8	124824792	124824792	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144963.2	+1	validated	p.P789S	1.000	335	0%	252	39.7%	5	20%	benign(0)	tolerated(0.72)	neutral(0.002)	NULL
KIAA0196	9897	genome.wustl.edu	37	8	126088714	126088714	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014846.3	-1	reviewed	p.R247H	1.000	173	0%	163	36.2%	11	0%	possibly_damaging(0.913)	deleterious(0.02)	deleterious(0.748)	HMMPfam_Strumpellin
OC90	729330	genome.wustl.edu	37	8	133044206	133044206	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080399.2	-1	validated	p.R318Q	0.535	186	0%	173	39.9%	0	-	possibly_damaging(0.925)	deleterious(0)	deleterious(0.818)	HMMPfam_Phospholip_A2_1,HMMSmart_SM00085,superfamily_Phospholipase A2 PLA2
ZFAT	57623	genome.wustl.edu	37	8	135613723	135613723	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020863.3	-1	reviewed	p.C747G	1.000	153	0%	134	41.8%	6	16.6%	possibly_damaging(0.907)	deleterious(0)	deleterious(0.805)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
FBXL6	26233	genome.wustl.edu	37	8	145580713	145580713	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012162.1	-1	reviewed	p.D236	0.000	41	0%	61	32.8%	60	33.3%	-	-	-	HMMSmart_SM00367,superfamily_RNI-like
CPSF1	29894	genome.wustl.edu	37	8	145619642	145619642	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013291.2	-1	validated	p.S1232	0.983	46	0%	58	36.2%	106	33.9%	-	-	-	HMMPfam_CPSF_A
RANBP6	26953	genome.wustl.edu	37	9	6015579	6015579	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012416.2	-1	validated	p.P10L	0.985	49	0%	45	48.9%	2	50%	unknown(0)	deleterious(0)	-	NULL
IFNA8	3445	genome.wustl.edu	37	9	21409403	21409403	+	Silent	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002170.3	+1	validated	p.A76	0.933	139	0.7%	114	35.1%	0	-	-	-	-	HMMPfam_Interferon,HMMSmart_SM00076,superfamily_4-helical cytokines
ENHO	375704	genome.wustl.edu	37	9	34521558	34521559	+	Frame_Shift_Ins	INS	-	-	AG	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198573.2	-1	validated	p.E45fs	0.605:0.053	-	-	-	-	-	-	-	-	-	NULL
RPP25L	138716	genome.wustl.edu	37	9	34611205	34611205	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_148178.1	-1	validated	p.V30A	1.000	177	0%	148	37.8%	53	45.2%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Alba,superfamily_SSF82704
POLR1E	64425	genome.wustl.edu	37	9	37486091	37486091	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022490.1	+1	provisional	p.A16V	0.989	173	0%	114	28.9%	10	50%	benign(0.011)	tolerated(0.81)	neutral(0.001)	NULL
PGM5	5239	genome.wustl.edu	37	9	71094364	71094364	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021965.3	+1	validated	p.L397P	1.000	340	0%	282	37.2%	7	28.5%	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	HMMPfam_PGM_PMM_III,superfamily_Phosphoglucomutase first 3 domains
TRPM3	80036	genome.wustl.edu	37	9	73233869	73233869	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001007471.2	-1	reviewed	p.D746N	1.000	124	0%	114	40.4%	0	-	benign(0.218)	tolerated(0.4)	neutral(0.037)	NULL
C9orf47	286223	genome.wustl.edu	37	9	91606832	91606832	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001938.3	+1	validated	p.L180	0.000	229	0%	127	32.3%	0	-	-	-	-	NULL
COL15A1	1306	genome.wustl.edu	37	9	101801007	101801007	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001855.3	+1	reviewed	p.G823W	0.957	313	0%	211	36.5%	4	0%	probably_damaging(1)	-	-	HMMPfam_Collagen
TGFBR1	7046	genome.wustl.edu	37	9	101891238	101891238	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004612.2	+1	reviewed	p.H67Y	1.000	189	0%	130	36.9%	3	0%	benign(0.002)	deleterious(0)	neutral(0.445)	HMMPfam_Activin_recp,superfamily_Snake toxin-like
TEX10	54881	genome.wustl.edu	37	9	103109439	103109439	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017746.3	-1	validated	p.H144N	1.000	237	0%	173	42.2%	5	0%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	superfamily_ARM-type_fold
FKBP15	23307	genome.wustl.edu	37	9	115932150	115932151	+	In_Frame_Ins	INS	-	-	TTC	rs113480096	byCluster;by1000genomes	TCGA-D1-A176-01	TCGA-D1-A176-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015258.1	-1	validated	p.946in_frame_insE	0.001:0.005	-	-	-	-	-	-	-	-	-	NULL
TTLL11	158135	genome.wustl.edu	37	9	124751605	124751605	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001139442.1	-1	validated	p.V470I	0.988	189	0%	185	38.9%	4	50%	benign(0.123)	tolerated(0.18)	neutral(0.066)	HMMPfam_TTL,superfamily_Glutathione synthetase ATP-binding domain-like
OR1Q1	158131	genome.wustl.edu	37	9	125377536	125377536	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012364.1	+1	provisional	p.I174F	0.389	315	0%	272	40.8%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_7tm_1,superfamily_SSF81321
ST6GALNAC6	30815	genome.wustl.edu	37	9	130653188	130653188	+	Silent	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013443.3	-1	provisional	p.S144	0.019	239	0%	217	41%	39	28.2%	-	-	-	HMMPfam_Glyco_transf_29
PIP5KL1	138429	genome.wustl.edu	37	9	130684308	130684308	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135219.1	-1	validated	p.L335M	0.731	66	0%	54	48.1%	3	0%	benign(0.332)	tolerated(0.23)	neutral(0.145)	HMMPfam_PIP5K,HMMSmart_SM00330,superfamily_SAICAR synthase-like
SPTAN1	6709	genome.wustl.edu	37	9	131394407	131394407	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130438.1	+1	validated	p.R2255H	1.000	14	0%	15	53.3%	144	36.1%	probably_damaging(0.988)	tolerated(0.09)	deleterious(0.734)	HMMPfam_Spectrin,HMMSmart_SPEC,superfamily_Spectrin
C9orf50	375759	genome.wustl.edu	37	9	132381903	132381903	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_199350.3	-1	validated	p.S204	0.000	243	0%	185	41.6%	0	-	-	-	-	NULL
NUP214	8021	genome.wustl.edu	37	9	134016082	134016082	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005085.2	+1	reviewed	p.Q427*	0.507	211	0%	196	38.8%	10	10%	-	-	-	NULL
NTNG2	84628	genome.wustl.edu	37	9	135073579	135073579	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032536.2	+1	validated	p.T147M	0.998	36	0%	39	59%	0	-	probably_damaging(0.997)	deleterious(0.02)	deleterious(0.849)	HMMPfam_Laminin_N,HMMSmart_SM00136
SETX	23064	genome.wustl.edu	37	9	135152522	135152522	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015046.5	-1	reviewed	p.R2287Q	0.970	193	0%	221	19.5%	14	42.8%	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	superfamily_P-loop containing nucleoside triphosphate hydrolases
LOC100289446	100289446	genome.wustl.edu	37	9	139265512	139265512	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002344209.1	+1	model	p.Q219*	0.970	91	0%	85	11.8%	5	0%	-	-	-	NULL
NOTCH1	4851	genome.wustl.edu	37	9	139397677	139397677	+	Silent	SNP	C	C	T	rs35980907	byCluster;byFrequency;by1000genomes	TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017617.3	-1	reviewed	p.S1708	0.644	94	0%	59	33.9%	22	54.5%	-	-	-	HMMPfam_NODP
C9orf86	55684	genome.wustl.edu	37	9	139734632	139734633	+	In_Frame_Ins	INS	-	-	AGA	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024718.4	+1	validated	p.657in_frame_insK	0.999:1.000	-	-	-	-	-	-	-	-	-	NULL
ANAPC2	29882	genome.wustl.edu	37	9	140076140	140076140	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013366.3	-1	reviewed	p.A487	0.107	74	0%	53	28.3%	57	42.1%	-	-	-	HMMPfam_Cullin,superfamily_Cullin homology domain
CUBN	8029	genome.wustl.edu	37	10	17152969	17152969	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001081.3	-1	reviewed	p.V322I	0.996	148	0%	119	31.9%	0	-	probably_damaging(0.998)	tolerated(0.07)	deleterious(0.793)	HMMSmart_SM00179,HMMSmart_SM00181,HMMPfam_EGF_CA,superfamily_EGF/Laminin
ARHGAP21	57584	genome.wustl.edu	37	10	24880575	24880575	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020824.3	-1	validated	p.P1347H	1.000	151	0%	99	32.3%	5	40%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
LOC646360	646360	genome.wustl.edu	37	10	37626843	37626843	+	RNA	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_078419.1	+1	model	NULL	1.000	154	0%	102	35.3%	0	-	-	-	-	-
ZWINT	11130	genome.wustl.edu	37	10	58119527	58119527	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007057.3	-1	reviewed	p.T115I	0.000	187	0%	150	36%	54	37%	possibly_damaging(0.815)	deleterious(0.01)	deleterious(0.713)	NULL
SUPV3L1	6832	genome.wustl.edu	37	10	70947427	70947427	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003171.3	+1	provisional	p.L163V	1.000	243	0%	204	31.4%	15	20%	benign(0.3)	tolerated(0.16)	neutral(0.152)	superfamily_SSF52540
AGAP5	729092	genome.wustl.edu	37	10	75434712	75434712	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001144000.1	-1	validated	p.S569F	1.000	389	0%	302	11.3%	11	0%	probably_damaging(0.97)	deleterious(0.04)	deleterious(0.761)	HMMPfam_ArfGap,HMMSmart_SM00105,superfamily_Pyk2-associated protein beta ARF-GAP domain,superfamily_Ankyrin repeat
PTEN	5728	genome.wustl.edu	37	10	89692902	89692902	+	Missense_Mutation	SNP	G	G	T	rs121909218		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.G129V	1.000	335	0.6%	265	86.8%	5	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II
DNTT	1791	genome.wustl.edu	37	10	98087331	98087331	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004088.3	+1	reviewed	p.F327	0.120	349	0%	288	38.5%	0	-	-	-	-	HMMSmart_SM00483,HMMPfam_NTP_transf_2,superfamily_Nucleotidyltransferase
LOXL4	84171	genome.wustl.edu	37	10	100017543	100017543	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032211.6	-1	reviewed	p.L375P	1.000	108	0%	92	37%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_SRCR,HMMSmart_SM00202,superfamily_SRCR-like
NKX2-3	159296	genome.wustl.edu	37	10	101293016	101293016	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145285.2	+1	reviewed	p.A43V	0.982	104	0%	120	46.7%	1	0%	possibly_damaging(0.497)	tolerated(0.1)	neutral(0.453)	NULL
CWF19L1	55280	genome.wustl.edu	37	10	102006559	102006559	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018294.4	-1	validated	p.A281V	0.045	185	0%	153	26.1%	10	50%	benign(0.045)	tolerated(0.29)	neutral(0.032)	NULL
PSD	5662	genome.wustl.edu	37	10	104165166	104165166	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002779.3	-1	provisional	p.A755T	0.283	34	0%	32	31.2%	7	28.5%	possibly_damaging(0.824)	deleterious(0.05)	deleterious(0.657)	superfamily_PH domain-like
PKP3	11187	genome.wustl.edu	37	11	396974	396974	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007183.2	+1	reviewed	p.P158H	0.102	20	0%	14	50%	36	41.6%	probably_damaging(0.986)	deleterious(0)	deleterious(0.879)	NULL
INSC	387755	genome.wustl.edu	37	11	15134110	15134110	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031853.3	+1	provisional	p.A32V	0.917	217	0%	176	35.2%	0	-	benign(0)	tolerated(1)	-	PatternScan_PA2_HIS
DEPDC7	91614	genome.wustl.edu	37	11	33054458	33054458	+	Silent	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001077242.1	+1	validated	p.I429	1.000	270	0%	224	37.1%	1	0%	-	-	-	NULL
PACSIN3	29763	genome.wustl.edu	37	11	47200814	47200814	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016223.4	-1	reviewed	p.R266C	0.960	98	0%	101	36.6%	78	38.4%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
OR4A5	81318	genome.wustl.edu	37	11	51411605	51411605	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005272.3	-1	validated	p.T264S	0.013	90	0%	75	42.7%	0	-	benign(0)	tolerated(0.12)	neutral(0.261)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
OR5T2	219464	genome.wustl.edu	37	11	56000556	56000556	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004746.1	-1	provisional	p.F36L	0.001	79	0%	64	29.7%	0	-	benign(0)	deleterious(0.01)	neutral(0.406)	superfamily_SSF81321
MS4A10	341116	genome.wustl.edu	37	11	60561576	60561576	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_206893.3	+1	validated	p.T164	0.016	241	0%	163	43.6%	0	-	-	-	-	HMMPfam_CD20
PTGDR2	11251	genome.wustl.edu	37	11	60620716	60620716	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004778.2	-1	reviewed	p.V160	0.549	55	0%	32	31.2%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
SCYL1	57410	genome.wustl.edu	37	11	65304600	65304601	+	Splice_Site	DEL	GT	GT	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	GT	GT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020680.3	+1	reviewed	e14+1	1.000:0.981	-	-	-	-	-	-	-	-	-	-
C11orf24	53838	genome.wustl.edu	37	11	68030295	68030295	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022338.3	-1	validated	p.T56	0.000	121	0%	83	37.3%	38	47.3%	-	-	-	NULL
ANO1	55107	genome.wustl.edu	37	11	70017046	70017046	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018043.5	+1	validated	p.L751M	0.997	288	0%	298	33.9%	144	50%	probably_damaging(0.988)	deleterious(0.04)	deleterious(0.786)	HMMPfam_DUF590
OR7E87P	8586	genome.wustl.edu	37	11	71304933	71304935	+	In_Frame_Del	DEL	TCG	TCG	-	rs36047994		TCGA-D1-A176-01	TCGA-D1-A176-01	TCG	TCG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000329336	+1	known	p.V170in_frame_del	0.023:0.028:0.021	-	-	-	-	-	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
NUMA1	4926	genome.wustl.edu	37	11	71724081	71724081	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006185.2	-1	validated	p.R1490C	0.108	180	0%	149	49%	179	39.6%	probably_damaging(0.999)	deleterious(0.04)	deleterious(0.839)	NULL
ODZ4	26011	genome.wustl.edu	37	11	78467851	78467851	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098816.2	-1	validated	p.G919W	1.000	165	0%	152	41.4%	0	-	probably_damaging(0.977)	deleterious(0)	deleterious(0.863)	NULL
FAT3	120114	genome.wustl.edu	37	11	92086576	92086576	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001008781.2	+1	validated	p.R433Q	0.065	133	0.8%	119	38.7%	0	-	benign(0.001)	tolerated(0.61)	neutral(0.004)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
CWF19L2	143884	genome.wustl.edu	37	11	107313684	107313684	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152434.2	-1	validated	p.D144V	0.065	403	0%	286	31.5%	3	33.3%	benign(0.014)	tolerated(0.11)	neutral(0.272)	NULL
HEPACAM	220296	genome.wustl.edu	37	11	124794933	124794933	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152722.4	-1	validated	p.V40M	0.046	102	0%	86	44.2%	0	-	possibly_damaging(0.678)	tolerated(0.06)	deleterious(0.564)	HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin
KCNJ5	3762	genome.wustl.edu	37	11	128781631	128781631	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000890.3	+1	reviewed	p.R155*	1.000	194	0.5%	162	40.1%	0	-	-	-	-	HMMPfam_IRK,superfamily_SSF81324
ST14	6768	genome.wustl.edu	37	11	130060578	130060578	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021978.3	+1	reviewed	p.H288	0.000	26	0%	28	28.6%	336	40.7%	-	-	-	HMMPfam_CUB,HMMSmart_CUB,superfamily_CUB
KCNA5	3741	genome.wustl.edu	37	12	5154642	5154642	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002234.2	+1	reviewed	p.I443	0.892	339	0%	237	36.3%	0	-	-	-	-	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
VWF	7450	genome.wustl.edu	37	12	6127546	6127546	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000552.3	-1	reviewed	p.L1680I	0.124	42	0%	34	35.3%	8	0%	possibly_damaging(0.675)	deleterious(0.02)	deleterious(0.623)	NULL
CHD4	1108	genome.wustl.edu	37	12	6711582	6711582	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001273.2	-1	reviewed	p.R61Q	0.978	554	0%	530	25.3%	15	20%	possibly_damaging(0.666)	deleterious(0.03)	deleterious(0.601)	NULL
ACSM4	341392	genome.wustl.edu	37	12	7469832	7469832	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080454.1	+1	provisional	p.Q240	1.000	233	0%	210	40.5%	0	-	-	-	-	HMMPfam_AMP-binding,superfamily_SSF56801
SLC2A14	144195	genome.wustl.edu	37	12	7984225	7984225	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153449.2	-1	provisional	p.G106R	1.000	159	0%	172	41.3%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Sugar_tr,superfamily_MFS general substrate transporter
DDX11	1663	genome.wustl.edu	37	12	31254802	31254802	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152438.1	+1	reviewed	p.C696	0.896	772	0%	535	33.1%	13	53.8%	-	-	-	NULL
PRPF40B	25766	genome.wustl.edu	37	12	50028324	50028324	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031698.1	+1	provisional	p.V292I	1.000	153	0%	118	33.1%	25	36%	possibly_damaging(0.512)	tolerated(0.26)	neutral(0.206)	HMMPfam_FF,HMMSmart_SM00441,superfamily_FF domain
KRT78	196374	genome.wustl.edu	37	12	53238401	53238401	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173352.2	-1	reviewed	p.R288Q	0.975	160	0%	123	26.8%	0	-	probably_damaging(0.999)	tolerated(1)	deleterious(0.490)	HMMPfam_Filament
DPY19L2	283417	genome.wustl.edu	37	12	63987907	63987907	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173812.4	-1	validated	p.R514C	0.934	87	0%	76	38.2%	1	0%	probably_damaging(0.996)	deleterious(0.04)	deleterious(0.810)	HMMPfam_DUF2211
HCFC2	29915	genome.wustl.edu	37	12	104487281	104487281	+	Silent	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013320.2	+1	reviewed	p.L468	0.209	188	0%	198	34.3%	4	25%	-	-	-	HMMSmart_SM00060,superfamily_Fibronectin type III
TPCN1	53373	genome.wustl.edu	37	12	113698217	113698217	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001143819.1	+1	validated	p.S125G	0.017	137	0%	127	34.6%	10	20%	benign(0)	tolerated(0.42)	neutral(0.014)	NULL
HIP1R	9026	genome.wustl.edu	37	12	123343633	123343633	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003959.1	+1	validated	p.C728	0.819	28	0%	30	30%	21	42.8%	-	-	-	NULL
NCOR2	9612	genome.wustl.edu	37	12	124817009	124817009	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006312.3	-1	validated	p.M2261V	0.998	380	0%	271	40.6%	97	30.9%	possibly_damaging(0.916)	tolerated(0.08)	deleterious(0.667)	NULL
TMEM132B	114795	genome.wustl.edu	37	12	125900193	125900193	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052907.2	+1	provisional	p.C354Y	1.000	108	0%	73	35.6%	0	-	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	NULL
TMEM132C	92293	genome.wustl.edu	37	12	128899822	128899822	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001136103.2	+1	provisional	p.G99C	0.000	70	0%	66	42.4%	0	-	benign(0.001)	tolerated(0.08)	neutral(0.300)	NULL
GOLGA3	2802	genome.wustl.edu	37	12	133351849	133351849	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005895.3	-1	reviewed	p.M1341V	0.000	233	0%	180	25.6%	31	51.6%	benign(0)	tolerated(0.36)	neutral(0.020)	NULL
TUBA3C	7278	genome.wustl.edu	37	13	19748295	19748295	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006001.1	-1	reviewed	p.G354D	1.000	98	0%	94	27.7%	0	-	probably_damaging(0.971)	deleterious(0)	deleterious(0.857)	superfamily_Tubulin C-terminal domain-like,HMMPfam_Tubulin_C
PARP4	143	genome.wustl.edu	37	13	25034183	25034183	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006437.3	-1	reviewed	p.T742N	0.002	223	0%	200	34.5%	21	47.6%	benign(0.013)	tolerated(0.45)	neutral(0.013)	NULL
MTUS2	23281	genome.wustl.edu	37	13	29599666	29599666	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001033602.2	+1	validated	p.S287	0.000	89	0%	92	47.8%	0	-	-	-	-	NULL
CDADC1	81602	genome.wustl.edu	37	13	49841858	49841858	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030911.2	+1	validated	p.P221	0.506	86	0%	84	35.7%	8	37.5%	-	-	-	NULL
GUCY1B2	2974	genome.wustl.edu	37	13	51590372	51590372	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000389600	-1	known	p.G363E	1.000	306	0%	240	40.4%	0	-	-	-	-	HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase
PCDH9	5101	genome.wustl.edu	37	13	67205541	67205541	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_203487.2	-1	reviewed	p.S1047	1.000	123	0%	102	12.7%	0	-	-	-	-	NULL
FBXL3	26224	genome.wustl.edu	37	13	77581534	77581534	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012158.2	-1	reviewed	p.R345W	1.000	281	0%	227	34.4%	20	45%	probably_damaging(0.992)	deleterious(0.03)	deleterious(0.812)	superfamily_SSF52047
POU4F1	5457	genome.wustl.edu	37	13	79175965	79175965	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006237.3	-1	validated	p.L282P	1.000	34	0%	20	30%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Pou,HMMSmart_SM00352,PatternScan_POU_1,superfamily_lambda repressor-like DNA-binding domains
TMTC4	84899	genome.wustl.edu	37	13	101288809	101288809	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032813.2	-1	validated	p.C393	1.000	194	0%	154	40.3%	16	25%	-	-	-	NULL
ERCC5	2073	genome.wustl.edu	37	13	103514757	103514757	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000123.2	+1	reviewed	p.R420S	0.001	185	0%	160	35.6%	17	52.9%	benign(0)	tolerated(0.29)	neutral(0.029)	superfamily_PIN domain-like
MYO16	23026	genome.wustl.edu	37	13	109379842	109379842	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015011.1	+1	validated	p.N118D	1.000	348	0%	287	40.1%	2	0%	probably_damaging(0.982)	deleterious(0)	deleterious(0.871)	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat
ARHGEF7	8874	genome.wustl.edu	37	13	111870106	111870106	+	Silent	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001113511.1	+1	reviewed	p.S204	0.740	237	0%	176	44.9%	15	53.3%	-	-	-	HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain
ABHD4	63874	genome.wustl.edu	37	14	23072483	23072483	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022060.2	+1	validated	p.D101N	1.000	100	0%	104	43.3%	45	24.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Abhydrolase_1,superfamily_SSF53474
REC8	9985	genome.wustl.edu	37	14	24648851	24648851	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001048205.1	+1	reviewed	p.P456L	0.977	233	0%	160	25.6%	79	17.7%	probably_damaging(0.996)	deleterious(0.02)	deleterious(0.845)	NULL
SPTB	6710	genome.wustl.edu	37	14	65239488	65239488	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001024858.2	-1	reviewed	p.T1788M	1.000	49	0%	38	26.3%	2	50%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Spectrin,HMMSmart_SPEC,superfamily_Spectrin
RAB15	376267	genome.wustl.edu	37	14	65415221	65415221	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198686.2	-1	validated	p.V208fs	0.998	-	-	-	-	-	-	-	-	-	NULL
TMEM63C	57156	genome.wustl.edu	37	14	77715147	77715147	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020431.2	+1	validated	p.A601V	1.000	413	0%	312	43.9%	0	-	probably_damaging(0.995)	deleterious(0)	deleterious(0.902)	HMMPfam_DUF221
ALKBH1	8846	genome.wustl.edu	37	14	78146249	78146249	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006020.2	-1	reviewed	p.G174C	1.000	130	0%	102	40.2%	4	25%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PSMC1	5700	genome.wustl.edu	37	14	90730172	90730172	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002802.2	+1	reviewed	p.S149L	1.000	103	0%	101	36.6%	51	41.1%	benign(0.011)	tolerated(0.14)	neutral(0.250)	NULL
JAG2	3714	genome.wustl.edu	37	14	105615413	105615413	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002226.3	-1	reviewed	p.C589	0.963	10	0%	13	46.2%	18	38.8%	-	-	-	HMMSmart_SM00179,HMMSmart_SM00181
C15orf2	23742	genome.wustl.edu	37	15	24922024	24922024	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018958.2	+1	reviewed	p.P337L	0.000	66	0%	43	48.8%	0	-	probably_damaging(0.995)	deleterious(0.04)	deleterious(0.806)	NULL
HERC2	8924	genome.wustl.edu	37	15	28422597	28422597	+	Silent	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004667.4	-1	reviewed	p.G3074	0.991	175	0%	142	24.6%	13	38.4%	-	-	-	HMMPfam_RCC1,superfamily_RCC1/BLIP-II
AQR	9716	genome.wustl.edu	37	15	35210541	35210541	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014691.2	-1	validated	p.Q420	0.992	192	0%	172	36%	5	60%	-	-	-	NULL
ZNF609	23060	genome.wustl.edu	37	15	64966167	64966167	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015042.1	+1	provisional	p.G372C	1.000	88	0%	66	39.4%	6	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PIAS1	8554	genome.wustl.edu	37	15	68434293	68434293	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016166.1	+1	reviewed	p.N160S	1.000	179	0%	160	35.6%	9	66.6%	benign(0.002)	tolerated(0.81)	neutral(0.001)	NULL
PARP6	56965	genome.wustl.edu	37	15	72558250	72558250	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020214.2	-1	provisional	p.S55C	1.000	240	0%	226	37.6%	37	56.7%	possibly_damaging(0.862)	deleterious(0)	deleterious(0.778)	NULL
AGBL1	123624	genome.wustl.edu	37	15	86813208	86813208	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152336.2	+1	validated	p.F587L	1.000	243	0%	152	22.4%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
NTRK3	4916	genome.wustl.edu	37	15	88522671	88522671	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001007156.1	-1	reviewed	p.P582A	1.000	185	0%	137	38%	0	-	possibly_damaging(0.543)	-	-	NULL
C15orf42	90381	genome.wustl.edu	37	15	90162953	90162953	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152259.3	+1	validated	p.R1012*	1.000	198	1.5%	169	31.4%	3	0%	-	-	-	NULL
ZNF774	342132	genome.wustl.edu	37	15	90904468	90904468	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004309.2	+1	validated	p.R469C	0.734	109	0%	93	35.5%	1	0%	possibly_damaging(0.492)	tolerated(0.12)	neutral(0.424)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
ANKS3	124401	genome.wustl.edu	37	16	4764173	4764173	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_133450.2	-1	provisional	p.D196	0.658	201	0%	177	41.2%	12	33.3%	-	-	-	HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK
ABCC1	4363	genome.wustl.edu	37	16	16232347	16232347	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004996.3	+1	reviewed	p.R1473	0.911	106	0%	116	32.8%	79	24%	-	-	-	HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases
TNRC6A	27327	genome.wustl.edu	37	16	24800899	24800899	+	Silent	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014494.2	+1	reviewed	p.P312	0.062	163	0%	134	34.3%	5	60%	-	-	-	NULL
APOBR	55911	genome.wustl.edu	37	16	28507472	28507472	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018690.2	+1	reviewed	p.D361	0.000	63	0%	62	27.4%	2	50%	-	-	-	NULL
RABEP2	79874	genome.wustl.edu	37	16	28922240	28922240	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024816.2	-1	validated	p.S353N	1.000	62	0%	62	41.9%	38	42.1%	possibly_damaging(0.737)	tolerated(0.06)	deleterious(0.592)	HMMPfam_Rab5-bind
ORC6	23594	genome.wustl.edu	37	16	46726293	46726293	+	Splice_Site	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014321.2	+1	reviewed	e3-1	0.998	199	0.5%	152	42.8%	0	-	-	-	-	-
PAPD5	64282	genome.wustl.edu	37	16	50251523	50251523	+	Silent	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001040284.2	+1	validated	p.F105	1.000	93	0%	110	13.6%	1	0%	-	-	-	HMMPfam_NTP_transf_2,superfamily_Nucleotidyltransferase
ZFHX3	463	genome.wustl.edu	37	16	72830903	72830904	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	CT	CT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006885.3	-1	reviewed	p.R1893fs	0.999:0.991	-	-	-	-	-	-	-	-	-	NULL
LDHD	197257	genome.wustl.edu	37	16	75147502	75147502	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153486.2	-1	reviewed	p.E362	0.917	34	0%	30	63.3%	43	48.8%	-	-	-	HMMPfam_FAD-oxidase_C,superfamily_FAD-linked oxidases C-terminal domain
KLHL36	79786	genome.wustl.edu	37	16	84695491	84695491	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024731.2	+1	provisional	p.A535T	1.000	42	2.4%	40	50%	45	31.1%	benign(0.001)	tolerated(0.15)	neutral(0.241)	HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain
JPH3	57338	genome.wustl.edu	37	16	87723471	87723471	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020655.2	+1	reviewed	p.S502L	0.893	15	0%	14	57.1%	0	-	benign(0.002)	tolerated(1)	-	NULL
SPG7	6687	genome.wustl.edu	37	16	89598338	89598338	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003119.2	+1	reviewed	p.G338	0.074	113	0%	121	35.5%	41	43.9%	-	-	-	superfamily_P-loop containing nucleoside triphosphate hydrolases
TCF25	22980	genome.wustl.edu	37	16	89977619	89977619	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000263347	+1	known	p.R473C	0.887	49	0%	32	46.9%	165	41.8%	unknown(0)	-	-	NULL
CAMTA2	23125	genome.wustl.edu	37	17	4883018	4883018	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015099.3	-1	validated	p.S533	0.036	155	0%	115	32.2%	17	47%	-	-	-	HMMPfam_TIG,superfamily_E set domains
SENP3	26168	genome.wustl.edu	37	17	7467982	7467982	+	Silent	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000321337	+1	known	p.Q252	0.996	195	0%	197	47.7%	35	34.2%	-	-	-	NULL
MYH3	4621	genome.wustl.edu	37	17	10551917	10551917	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002470.2	-1	reviewed	p.F231S	0.997	268	0%	242	39.7%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Myosin_head,HMMSmart_MYSc,superfamily_SSF52540
DNAH9	1770	genome.wustl.edu	37	17	11772537	11772537	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001372.3	+1	reviewed	p.V3340	0.086	141	0%	121	36.4%	5	40%	-	-	-	NULL
PMP22	5376	genome.wustl.edu	37	17	15142916	15142916	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000304.2	-1	reviewed	p.S64Y	1.000	102	0%	88	37.5%	17	17.6%	possibly_damaging(0.835)	deleterious(0)	deleterious(0.763)	HMMPfam_PMP22_Claudin
FLCN	201163	genome.wustl.edu	37	17	17127309	17127309	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144997.5	-1	reviewed	p.L182P	1.000	64	0%	46	41.3%	30	40%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
UTP6	55813	genome.wustl.edu	37	17	30216345	30216345	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018428.2	-1	validated	p.A168T	1.000	234	0%	189	48.7%	11	63.6%	probably_damaging(0.999)	deleterious(0.02)	deleterious(0.873)	HMMSmart_HAT,superfamily_SSF48452
KRTAP1-4	728255	genome.wustl.edu	37	17	39186038	39186038	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000377747	-1	known	p.C98Y	1.000	88	0%	45	35.6%	0	-	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_Keratin_B2
HAP1	9001	genome.wustl.edu	37	17	39881156	39881156	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_177977.2	-1	reviewed	p.M553V	0.000	326	0%	261	44.1%	0	-	benign(0.032)	deleterious(0.01)	neutral(0.407)	NULL
MAP3K14	9020	genome.wustl.edu	37	17	43364209	43364209	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003954.2	-1	reviewed	p.T247M	0.003	43	0%	41	53.7%	6	33.3%	-	-	-	NULL
TEX14	56155	genome.wustl.edu	37	17	56676693	56676693	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198393.2	-1	reviewed	p.A671	0.000	341	0%	310	33.5%	0	-	-	-	-	NULL
DDX5	1655	genome.wustl.edu	37	17	62496744	62496744	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004396.3	-1	validated	p.D455G	1.000	355	0%	276	36.6%	351	41.8%	benign(0.045)	deleterious(0.04)	neutral(0.351)	superfamily_P-loop containing nucleoside triphosphate hydrolases
BPTF	2186	genome.wustl.edu	37	17	65850651	65850651	+	Silent	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182641.3	+1	reviewed	p.L403	0.943	514	0%	489	10.8%	2	0%	-	-	-	HMMSmart_PHD,superfamily_FYVE_PHD_ZnF,PatternScan_ZF_PHD_1,HMMPfam_PHD
DNAH17	8632	genome.wustl.edu	37	17	76457792	76457792	+	Splice_Site	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000389840	-1	known	e57-2	0.998	64	0%	62	48.4%	0	-	-	-	-	-
RNF213	57674	genome.wustl.edu	37	17	78357598	78357598	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000508628	+1	known	p.R4731Q	0.000	263	0%	230	44.3%	19	31.5%	benign(0.001)	tolerated(0.44)	neutral(0.013)	NULL
SLC38A10	124565	genome.wustl.edu	37	17	79225390	79225390	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001037984.1	-1	validated	p.A656	0.000	23	0%	24	37.5%	168	47%	-	-	-	NULL
TYMS	7298	genome.wustl.edu	37	18	670816	670816	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001071.2	+1	reviewed	p.I227	0.787	184	0%	161	38.5%	92	33.6%	-	-	-	HMMPfam_Thymidylat_synt,superfamily_Thymidylate synthase/dCMP hydroxymethylase
DLGAP1	9229	genome.wustl.edu	37	18	3879376	3879376	+	Silent	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004746.2	-1	provisional	p.S231	0.916	81	0%	60	43.3%	0	-	-	-	-	NULL
APCDD1	147495	genome.wustl.edu	37	18	10485748	10485748	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153000.4	+1	validated	p.R355M	0.991	70	0%	83	36.1%	72	9.7%	possibly_damaging(0.492)	deleterious(0.01)	deleterious(0.570)	NULL
LAMA3	3909	genome.wustl.edu	37	18	21413807	21413807	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198129.1	+1	reviewed	p.R947W	0.047	243	0%	189	36.5%	0	-	benign(0.001)	deleterious(0.02)	neutral(0.383)	NULL
DSG3	1830	genome.wustl.edu	37	18	29041274	29041274	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001944.2	+1	reviewed	p.N300D	1.000	176	0%	124	37.1%	0	-	probably_damaging(0.99)	deleterious(0)	deleterious(0.886)	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
PIK3C3	5289	genome.wustl.edu	37	18	39575940	39575940	+	Silent	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002647.2	+1	validated	p.A291	0.997	132	0%	113	38.1%	4	0%	-	-	-	HMMPfam_PI3Ka,HMMSmart_PI3Ka,superfamily_ARM-type_fold
C19orf6	91304	genome.wustl.edu	37	19	1014260	1014260	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001033026.1	-1	validated	p.S146	0.000	84	0%	73	35.6%	104	47.1%	-	-	-	HMMPfam_Membralin
STK11	6794	genome.wustl.edu	37	19	1223071	1223072	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	TG	TG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000455.4	+1	reviewed	p.V337fs	0.323:1.000	-	-	-	-	-	-	-	-	-	NULL
TMPRSS9	360200	genome.wustl.edu	37	19	2416648	2416648	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182973.1	+1	provisional	p.P586T	0.383	75	0%	50	26%	0	-	probably_damaging(0.999)	tolerated(0.65)	deleterious(0.493)	HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases
LMNB2	84823	genome.wustl.edu	37	19	2432450	2432450	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032737.2	-1	reviewed	p.T498	0.749	304	0%	199	38.7%	34	32.3%	-	-	-	HMMPfam_IF_tail,superfamily_SSF74853
TJP3	27134	genome.wustl.edu	37	19	3736178	3736178	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014428.1	+1	provisional	p.T414	0.000	79	0%	64	31.2%	95	43.1%	-	-	-	superfamily_PDZ domain-like
CD70	970	genome.wustl.edu	37	19	6586324	6586324	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001252.3	-1	reviewed	p.R97C	0.178	153	0%	119	35.3%	0	-	probably_damaging(0.988)	deleterious(0)	deleterious(0.882)	HMMPfam_TNF,HMMSmart_SM00207,PatternScan_TNF_1,superfamily_TNF-like
MUC16	94025	genome.wustl.edu	37	19	9061630	9061630	+	Missense_Mutation	SNP	G	G	T	rs113691287		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024690.2	-1	validated	p.R8606S	0.000	383	0%	339	44.5%	3	66.6%	unknown(0)	-	-	NULL
MUC16	94025	genome.wustl.edu	37	19	9065164	9065164	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024690.2	-1	validated	p.P7428S	0.000	358	0%	292	32.5%	2	100%	unknown(0)	-	-	NULL
FBXL12	54850	genome.wustl.edu	37	19	9922067	9922067	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017703.1	-1	provisional	p.P162	0.086	38	0%	44	34.1%	29	41.3%	-	-	-	superfamily_RNI-like
DOCK6	57572	genome.wustl.edu	37	19	11348967	11348967	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020812.2	-1	validated	p.V553M	1.000	51	0%	36	36.1%	4	0%	probably_damaging(0.994)	deleterious(0)	deleterious(0.897)	NULL
RGL3	57139	genome.wustl.edu	37	19	11515998	11515998	+	Splice_Site	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001035223.2	-1	validated	e8+1	1.000	102	0%	100	50%	2	0%	-	-	-	-
TMEM38A	79041	genome.wustl.edu	37	19	16791335	16791335	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024074.1	+1	provisional	p.A137T	1.000	165	0%	162	32.1%	7	28.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DUF714
KIAA1683	80726	genome.wustl.edu	37	19	18378027	18378027	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145304.1	-1	validated	p.T108M	0.974	86	0%	106	36.8%	1	100%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_IQ,HMMSmart_SM00015,superfamily_P-loop containing nucleoside triphosphate hydrolases
MAU2	23383	genome.wustl.edu	37	19	19449687	19449687	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015329.3	+1	validated	p.A164T	1.000	229	0%	197	39.6%	13	46.1%	probably_damaging(0.997)	deleterious(0.01)	deleterious(0.872)	HMMPfam_Cohesin_load,superfamily_TPR-like
FFAR3	2865	genome.wustl.edu	37	19	35849967	35849967	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005304.3	+1	validated	p.A59T	0.000	464	0%	381	15.5%	0	-	benign(0)	tolerated(0.13)	neutral(0.253)	HMMPfam_7tm_1,superfamily_SSF81321
MLL4	9757	genome.wustl.edu	37	19	36224759	36224759	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014727.1	+1	reviewed	p.W2382*	1.000	197	0%	161	42.9%	27	51.8%	-	-	-	NULL
MLL4	9757	genome.wustl.edu	37	19	36229410	36229410	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014727.1	+1	reviewed	p.K2700N	1.000	96	0%	73	32.9%	77	58.4%	probably_damaging(0.989)	-	-	HMMSmart_SM00508,superfamily_SET domain
LOC644189	644189	genome.wustl.edu	37	19	36912850	36912850	+	RNA	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_016949.3	+1	model	NULL	1.000	11	0.000	9	0.444	0	-	-	-	-	-
ACTN4	81	genome.wustl.edu	37	19	39200922	39200922	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004924.3	+1	reviewed	p.D253	1.000	116	0%	110	33.6%	152	33.5%	-	-	-	HMMPfam_CH,HMMSmart_CH,superfamily_Calponin-homology
PAF1	54623	genome.wustl.edu	37	19	39877205	39877205	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019088.2	-1	provisional	p.R367Q	1.000	386	0%	411	43.3%	53	45.2%	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	HMMPfam_Paf1
FCGBP	8857	genome.wustl.edu	37	19	40384077	40384077	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003890.2	-1	validated	p.A3178V	0.000	314	0%	296	19.3%	17	5.8%	unknown(0)	tolerated(0.18)	-	superfamily_Cysrich_TIL,HMMPfam_TIL
FCGBP	8857	genome.wustl.edu	37	19	40392058	40392058	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003890.2	-1	validated	p.N2776	0.990	189	0%	197	14.7%	18	11.1%	-	-	-	superfamily_Cysrich_TIL,HMMPfam_TIL
HIPK4	147746	genome.wustl.edu	37	19	40889771	40889771	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144685.3	-1	provisional	p.H247Q	1.000	264	0%	275	28%	0	-	benign(0.027)	tolerated(0.14)	neutral(0.251)	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase
SPTBN4	57731	genome.wustl.edu	37	19	40998912	40998912	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020971.2	+1	reviewed	p.R180C	0.921	141	0%	96	39.6%	2	50%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	superfamily_Calponin-homology domain CH-domain
ADCK4	79934	genome.wustl.edu	37	19	41220449	41220449	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024876.3	-1	validated	p.G30V	0.871	99	0%	79	44.3%	9	22.2%	possibly_damaging(0.837)	tolerated(0.12)	deleterious(0.580)	NULL
CIC	23152	genome.wustl.edu	37	19	42798999	42798999	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015125.3	+1	validated	p.A1495T	1.000	140	0%	145	33.1%	65	38.4%	benign(0.181)	tolerated(0.21)	neutral(0.060)	NULL
SNRNP70	6625	genome.wustl.edu	37	19	49611304	49611304	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003089.4	+1	validated	p.K306N	1.000	10	0%	11	45.5%	253	36.3%	unknown(0)	tolerated(0.06)	-	NULL
GPR32	2854	genome.wustl.edu	37	19	51274182	51274182	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001506.1	+1	provisional	p.L109F	0.039	389	0%	353	44.2%	0	-	benign(0.002)	tolerated(1)	-	HMMPfam_7tm_1,superfamily_SSF81321
CEACAM18	729767	genome.wustl.edu	37	19	51983758	51983758	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080405.1	+1	provisional	p.S136N	0.607	210	0%	202	45%	0	-	probably_damaging(0.999)	tolerated(0.07)	deleterious(0.809)	HMMSmart_SM00409,superfamily_Immunoglobulin
NCR1	9437	genome.wustl.edu	37	19	55424388	55424388	+	RNA	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_027041.1	+1	validated	NULL	0.000	25	0%	35	48.6%	0	-	-	-	-	-
ZNF416	55659	genome.wustl.edu	37	19	58085013	58085015	+	In_Frame_Del	DEL	CTT	CTT	-	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	CTT	CTT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017879.1	-1	provisional	p.E86in_frame_del	0.002:0.040:0.054	-	-	-	-	-	-	-	-	-	NULL
C20orf96	140680	genome.wustl.edu	37	20	259881	259881	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153269.1	-1	predicted	p.I133V	0.835	97	0%	88	39.8%	44	40.9%	probably_damaging(0.971)	deleterious(0)	deleterious(0.857)	NULL
ATRN	8455	genome.wustl.edu	37	20	3564713	3564713	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139321.2	+1	reviewed	p.T978M	1.000	124	0%	115	46.1%	35	48.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_PSI,HMMSmart_SM00423
MAVS	57506	genome.wustl.edu	37	20	3846537	3846537	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020746.3	+1	validated	p.E456*	0.963	63	0%	81	33.3%	16	31.2%	-	-	-	NULL
TMX4	56255	genome.wustl.edu	37	20	7963108	7963108	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021156.2	-1	provisional	p.E280	0.581	515	0%	470	39.1%	93	39.7%	-	-	-	NULL
PCSK2	5126	genome.wustl.edu	37	20	17208058	17208058	+	Silent	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002594.2	+1	reviewed	p.V36	1.000	364	0%	322	14%	0	-	-	-	-	superfamily_Protease propeptides/inhibitors
FOXA2	3170	genome.wustl.edu	37	20	22562757	22562758	+	Frame_Shift_Ins	INS	-	-	GT	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021784.4	-1	reviewed	p.H374fs	1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
SSTR4	6754	genome.wustl.edu	37	20	23016633	23016633	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001052.2	+1	validated	p.W171*	1.000	52	0%	47	14.9%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
NDRG3	57446	genome.wustl.edu	37	20	35317081	35317081	+	Splice_Site	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032013.2	-1	validated	e3+1	1.000	196	0%	195	37.9%	0	-	-	-	-	-
MYBL2	4605	genome.wustl.edu	37	20	42331157	42331157	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002466.2	+1	reviewed	p.K327E	0.993	219	0%	195	41%	58	62%	benign(0.054)	tolerated(0.23)	neutral(0.045)	NULL
ZNF335	63925	genome.wustl.edu	37	20	44590818	44590818	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022095.3	-1	reviewed	p.H513Y	1.000	129	0%	103	41.7%	15	60%	possibly_damaging(0.95)	deleterious(0)	deleterious(0.838)	HMMPfam_zf-C2H2,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
EYA2	2139	genome.wustl.edu	37	20	45801464	45801464	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005244.4	+1	reviewed	p.R383C	1.000	176	0%	240	21.7%	385	23.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Hydrolase
ENSG00000245952	0	genome.wustl.edu	37	20	47275808	47275809	+	RNA	DEL	GA	GA	-	rs141388612	by1000genomes	TCGA-D1-A176-01	TCGA-D1-A176-01	GA	GA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000456747	+1	known	NULL	0.002:0.000	-	-	-	-	-	-	-	-	-	-
CDH4	1002	genome.wustl.edu	37	20	60498692	60498692	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001794.2	+1	reviewed	p.V520M	0.425	101	0%	83	42.2%	0	-	possibly_damaging(0.894)	tolerated(0.06)	deleterious(0.674)	HMMPfam_Cadherin,superfamily_Cadherin
DIDO1	11083	genome.wustl.edu	37	20	61512169	61512169	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033081.1	-1	reviewed	p.S1713	0.000	76	0%	63	28.6%	16	50%	-	-	-	NULL
RTEL1	51750	genome.wustl.edu	37	20	62309535	62309535	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032957.3	+1	reviewed	p.K319N	1.000	230	0.4%	261	42.1%	5	20%	possibly_damaging(0.945)	deleterious(0)	deleterious(0.834)	NULL
TCEA2	6919	genome.wustl.edu	37	20	62694737	62694737	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003195.4	+1	reviewed	p.A24	1.000	47	0%	28	25%	48	14.5%	-	-	-	HMMSmart_SM00509,HMMPfam_TFIIS,superfamily_Conserved domain common to transcription factors TFIIS elongin A CRSP70
SIK1	150094	genome.wustl.edu	37	21	44836856	44836856	+	Silent	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173354.3	-1	validated	p.L706	0.962	14	0%	13	38.5%	25	44%	-	-	-	NULL
ADARB1	104	genome.wustl.edu	37	21	46596384	46596384	+	Silent	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015833.3	+1	validated	p.G256	0.998	272	0.4%	218	40.8%	2	50%	-	-	-	HMMPfam_dsrm,HMMSmart_SM00358,superfamily_dsRNA-binding domain-like
COL6A1	1291	genome.wustl.edu	37	21	47421967	47421967	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001848.2	+1	reviewed	p.N683	0.001	27	0%	19	42.1%	308	41.5%	-	-	-	HMMPfam_VWA,HMMSmart_VWA,superfamily_SSF53300
C21orf58	54058	genome.wustl.edu	37	21	47722414	47722414	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_058180.3	-1	validated	p.C266Y	1.000	92	0%	77	20.8%	23	13%	-	-	-	NULL
IL17RA	23765	genome.wustl.edu	37	22	17589697	17589697	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014339.4	+1	reviewed	p.E530K	0.999	39	0%	20	25%	11	36.3%	probably_damaging(0.999)	deleterious(0.04)	deleterious(0.839)	HMMPfam_SEFIR
IGLV2-23	28813	genome.wustl.edu	37	22	23040825	23040825	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000390306	+1	known	p.T91	0.002	244	0%	205	36.6%	32	0%	-	-	-	HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin
SGSM1	129049	genome.wustl.edu	37	22	25270413	25270413	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039948.2	+1	validated	p.S441	0.000	264	0%	216	44.9%	0	-	-	-	-	NULL
MGAT3	4248	genome.wustl.edu	37	22	39884264	39884264	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098270.1	+1	reviewed	p.L304	1.000	20	0%	26	38.5%	4	0%	-	-	-	HMMPfam_Glyco_transf_17
TCF20	6942	genome.wustl.edu	37	22	42564700	42564700	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005650.1	-1	reviewed	p.A1948T	1.000	152	0%	177	37.3%	17	41.1%	benign(0)	tolerated(0.37)	neutral(0.019)	NULL
SAMM50	25813	genome.wustl.edu	37	22	44373840	44373840	+	Splice_Site	SNP	T	T	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015380.4	+1	validated	e10+2	1.000	141	0%	158	44.3%	10	100%	-	-	-	-
PRR5	55615	genome.wustl.edu	37	22	45133113	45133113	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181333.2	+1	reviewed	p.Q385*	1.000	59	0%	51	45.1%	38	55.2%	-	-	-	NULL
TUBGCP6	85378	genome.wustl.edu	37	22	50659504	50659504	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020461.3	-1	reviewed	p.S1095L	0.996	132	0%	106	29.2%	9	55.5%	possibly_damaging(0.887)	deleterious(0.02)	deleterious(0.730)	HMMPfam_Spc97_Spc98
HDAC10	83933	genome.wustl.edu	37	22	50687179	50687179	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032019.5	-1	validated	p.G273E	1.000	76	0%	83	41%	56	46.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Hist_deacetyl,superfamily_Arginase/deacetylase
BMX	660	genome.wustl.edu	37	X	15540478	15540478	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001721.6	+1	reviewed	p.P174S	0.998	235	0%	170	40.6%	11	27.2%	benign(0.047)	tolerated(0.58)	neutral(0.008)	NULL
MAP3K15	389840	genome.wustl.edu	37	X	19389182	19389182	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001671.3	-1	validated	p.V574L	1.000	35	0%	23	47.8%	0	-	possibly_damaging(0.501)	deleterious(0.01)	deleterious(0.573)	NULL
ZNF645	158506	genome.wustl.edu	37	X	22291875	22291875	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152577.2	+1	provisional	p.P256H	0.000	52	0%	52	36.5%	0	-	probably_damaging(0.991)	deleterious(0)	deleterious(0.889)	NULL
SLC38A5	92745	genome.wustl.edu	37	X	48319079	48319079	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033518.2	-1	validated	p.V342M	0.998	95	0%	118	50%	1	0%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	HMMPfam_Aa_trans
PRICKLE3	4007	genome.wustl.edu	37	X	49032132	49032132	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006150.3	-1	reviewed	p.A580S	0.058	115	0%	128	42.2%	34	0%	probably_damaging(0.996)	deleterious(0.02)	deleterious(0.845)	NULL
MED12	9968	genome.wustl.edu	37	X	70354254	70354254	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005120.2	+1	reviewed	p.T1555	0.081	122	0%	124	45.2%	54	83.3%	-	-	-	NULL
NHSL2	340527	genome.wustl.edu	37	X	71358882	71358882	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001013627.2	+1	provisional	p.R129Q	1.000	20	0%	25	28%	0	-	probably_damaging(0.994)	deleterious(0.04)	deleterious(0.801)	NULL
SLC16A2	6567	genome.wustl.edu	37	X	73641340	73641340	+	Silent	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006517.3	+1	reviewed	p.G30	0.987	40	0%	35	22.9%	0	-	-	-	-	NULL
TAF9B	51616	genome.wustl.edu	37	X	77393464	77393464	+	Silent	SNP	T	T	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015975.4	-1	reviewed	p.R89	1.000	340	0%	310	39.7%	12	0%	-	-	-	HMMPfam_TFIID-31kDa
XKRX	402415	genome.wustl.edu	37	X	100182967	100182967	+	Silent	SNP	A	A	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_212559.2	-1	reviewed	p.P122	0.995	70	0%	59	37.3%	1	0%	-	-	-	NULL
TCEAL3	85012	genome.wustl.edu	37	X	102864096	102864096	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001006933.1	+1	reviewed	p.K35R	0.000	902	0%	804	39.7%	57	91.2%	probably_damaging(0.995)	deleterious(0.04)	deleterious(0.806)	HMMPfam_TFA
NRK	203447	genome.wustl.edu	37	X	105153427	105153427	+	Silent	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198465.2	+1	validated	p.V598	0.994	261	0%	203	32%	0	-	-	-	-	NULL
NRK	203447	genome.wustl.edu	37	X	105190347	105190347	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198465.2	+1	validated	p.L1415P	0.999	252	0%	182	35.7%	0	-	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_CNH,HMMSmart_SM00036
TEX13B	56156	genome.wustl.edu	37	X	107225309	107225309	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031273.2	-1	reviewed	p.V17M	0.007	225	0%	167	41.3%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
MIR1277	100302214	genome.wustl.edu	37	X	117520365	117520366	+	RNA	INS	-	-	AT	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000408536	+1	known	NULL	1.000:0.986	-	-	-	-	-	-	-	-	-	-
WDR44	54521	genome.wustl.edu	37	X	117540870	117540870	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019045.4	+1	reviewed	p.S472G	1.000	388	0%	341	38.7%	4	100%	possibly_damaging(0.944)	tolerated(0.33)	neutral(0.413)	superfamily_WD40 repeat-like
ZBTB33	10009	genome.wustl.edu	37	X	119387392	119387392	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006777.3	+1	reviewed	p.R41Q	1.000	169	0.6%	133	36.1%	4	0%	probably_damaging(0.996)	tolerated(0.13)	deleterious(0.714)	HMMSmart_SM00225,superfamily_POZ domain,HMMPfam_BTB
ATP1B4	23439	genome.wustl.edu	37	X	119496050	119496050	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142447.2	+1	reviewed	p.R9S	1.000	246	0%	249	40.2%	0	-	benign(0.31)	deleterious(0)	deleterious(0.541)	NULL
GPR50	9248	genome.wustl.edu	37	X	150348839	150348839	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004224.3	+1	reviewed	p.V262I	0.985	224	0%	206	43.2%	0	-	benign(0.057)	tolerated(0.3)	neutral(0.032)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
ABCD1	215	genome.wustl.edu	37	X	152991298	152991298	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A176-01	TCGA-D1-A176-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000033.3	+1	reviewed	p.P193T	1.000	78	0%	73	43.8%	5	0%	possibly_damaging(0.808)	tolerated(0.06)	deleterious(0.627)	HMMPfam_ABC_membrane_2
