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
PANK4	55229	genome.wustl.edu	37	1	2442174	2442174	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018216.1	-1	reviewed	p.I627M	1.000	13	0%	16	68.8%	10	30%	-	-	-	HMMPfam_DUF89,superfamily_Hypothetical protein At2g17340
SLC2A7	155184	genome.wustl.edu	37	1	9083117	9083117	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207420.2	-1	provisional	p.N57	0.017	140	0%	122	36.9%	1	0%	-	-	-	HMMPfam_Sugar_tr,superfamily_MFS_gen_substrate_transporter
PRAMEF4	400735	genome.wustl.edu	37	1	12943095	12943095	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001009611.2	-1	validated	p.L41	0.089	248	0%	206	42.7%	0	-	-	-	-	superfamily_SSF52047
DDI2	84301	genome.wustl.edu	37	1	15964878	15964878	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032341.3	+1	provisional	p.Y237H	1.000	200	0%	191	41.4%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_Acid proteases,HMMPfam_Asp_protease
TAS1R2	80834	genome.wustl.edu	37	1	19166927	19166927	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152232.2	-1	validated	p.H562	0.808	77	0%	76	46.1%	2	0%	-	-	-	NULL
MACF1	23499	genome.wustl.edu	37	1	39844153	39844153	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033044.2	+1	reviewed	p.G2852*	1.000	108	0%	72	38.9%	0	-	-	-	-	HMMPfam_Spectrin,HMMSmart_SPEC,superfamily_Spectrin
DMBX1	127343	genome.wustl.edu	37	1	46976764	46976764	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_147192.2	+1	reviewed	p.R169H	0.000	103	0%	72	40.3%	0	-	benign(0)	tolerated(0.57)	neutral(0.006)	NULL
ACOT11	26027	genome.wustl.edu	37	1	55065043	55065043	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015547.2	+1	reviewed	p.D280G	1.000	67	0%	61	42.6%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_4HBT,superfamily_Thioesterase/thiol ester dehydrase-isomerase
KANK4	163782	genome.wustl.edu	37	1	62703951	62703951	+	Nonstop_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181712.4	-1	validated	p.*996Q	0.562	34	0%	13	30.8%	30	66.6%	-	-	-	NULL
PGM1	5236	genome.wustl.edu	37	1	64102017	64102017	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002633.2	+1	reviewed	p.R329H	0.883	105	0%	95	46.3%	5	20%	possibly_damaging(0.771)	tolerated(0.13)	deleterious(0.539)	HMMPfam_PGM_PMM_III,superfamily_Phosphoglucomutase first 3 domains
DEPDC1	55635	genome.wustl.edu	37	1	68942697	68942697	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001114120.1	-1	validated	p.E785G	1.000	119	0%	112	36.6%	1	0%	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	NULL
DNAJB4	11080	genome.wustl.edu	37	1	78478980	78478980	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007034.3	+1	provisional	p.R153C	0.997	302	0%	284	43.7%	1	0%	benign(0.07)	deleterious(0.01)	neutral(0.411)	NULL
ALG14	199857	genome.wustl.edu	37	1	95448777	95448777	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144988.3	-1	validated	p.I169T	1.000	145	0%	113	23.9%	13	0%	benign(0.093)	deleterious(0.04)	neutral(0.356)	HMMPfam_Alg14,superfamily_UDP-Glycosyltransferase/glycogen phosphorylase
LOC126987	126987	genome.wustl.edu	37	1	106623729	106623729	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002342097.1	-1	model	p.S110	0.999	24	0%	18	33.3%	0	-	-	-	-	NULL
PHGDH	26227	genome.wustl.edu	37	1	120269521	120269521	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006623.3	+1	reviewed	p.R135Q	1.000	114	0%	99	35.4%	47	31.9%	probably_damaging(0.992)	deleterious(0.01)	deleterious(0.853)	HMMPfam_2-Hacid_dh,HMMPfam_2-Hacid_dh_C,superfamily_NAD(P)-binding Rossmann-fold domains
GJA5	2702	genome.wustl.edu	37	1	147231020	147231020	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005266.5	-1	reviewed	p.R109	0.769	127	0%	142	28.2%	0	-	-	-	-	HMMPfam_Connexin
OTUD7B	56957	genome.wustl.edu	37	1	149916838	149916838	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020205.2	-1	validated	p.R484W	0.980	226	0%	255	22%	6	50%	probably_damaging(0.986)	deleterious(0.02)	deleterious(0.818)	NULL
RPRD2	23248	genome.wustl.edu	37	1	150444477	150444477	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015203.3	+1	validated	p.R1018H	0.840	424	0%	518	17.4%	6	0%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
FLG	2312	genome.wustl.edu	37	1	152284305	152284305	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002016.1	-1	reviewed	p.A1019	0.000	427	0%	499	34.5%	0	-	-	-	-	NULL
UBAP2L	9898	genome.wustl.edu	37	1	154218817	154218817	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014847.3	+1	validated	p.P327H	1.000	154	0%	178	22.5%	5	40%	possibly_damaging(0.46)	deleterious(0.01)	deleterious(0.556)	NULL
MTX1	4580	genome.wustl.edu	37	1	155181921	155181921	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002455.3	+1	validated	p.Y228H	1.000	47	0%	63	36.5%	87	20.6%	probably_damaging(0.997)	tolerated(0.13)	deleterious(0.719)	HMMPfam_Tom37
CLK2	1196	genome.wustl.edu	37	1	155233190	155233190	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003993.2	-1	reviewed	p.R439Q	1.000	53	0%	47	23.4%	128	9.3%	possibly_damaging(0.445)	tolerated(0.56)	neutral(0.152)	HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase
CLK2	1196	genome.wustl.edu	37	1	155236573	155236573	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003993.2	-1	reviewed	p.Y261C	1.000	49	0%	73	38.4%	49	30.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase
OR10X1	128367	genome.wustl.edu	37	1	158549050	158549050	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004477.1	-1	provisional	p.I214V	0.000	188	0%	219	30.6%	0	-	benign(0.182)	tolerated(1)	neutral(0.017)	HMMPfam_7tm_1,superfamily_SSF81321
OR10J3	441911	genome.wustl.edu	37	1	159283745	159283745	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004467.1	-1	provisional	p.Q235H	0.545	282	0%	282	28%	0	-	possibly_damaging(0.565)	deleterious(0)	deleterious(0.637)	HMMPfam_7tm_1,superfamily_SSF81321
FCRL6	343413	genome.wustl.edu	37	1	159778152	159778152	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004310.2	+1	validated	p.G79	0.025	250	0%	207	30%	0	-	-	-	-	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin
LOC100287448	100287448	genome.wustl.edu	37	1	160012095	160012095	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002342164.1	+1	model	p.C109R	0.956	316	0.3%	351	30.8%	0	-	-	-	-	NULL
LY9	4063	genome.wustl.edu	37	1	160783653	160783653	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002348.2	+1	validated	p.V228I	0.640	296	0.3%	352	26.1%	0	-	probably_damaging(0.999)	tolerated(0.07)	deleterious(0.809)	superfamily_Immunoglobulin
TADA1	117143	genome.wustl.edu	37	1	166829473	166829473	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_053053.3	-1	validated	p.P214	0.286	128	0%	119	30.3%	0	-	-	-	-	NULL
PRRC2C	23215	genome.wustl.edu	37	1	171560884	171560884	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000412837	+1	known	p.K1887R	1.000	197	0%	243	33.7%	10	50%	-	-	-	NULL
CENPL	91687	genome.wustl.edu	37	1	173772291	173772291	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127181.2	-1	validated	p.P304Q	1.000	185	0%	195	29.7%	3	0%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
CENPL	91687	genome.wustl.edu	37	1	173780309	173780309	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127181.2	-1	validated	p.T43	0.618	601	0%	772	21.1%	0	-	-	-	-	NULL
DARS2	55157	genome.wustl.edu	37	1	173822697	173822697	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018122.4	+1	reviewed	p.P519S	1.000	139	0%	162	32.7%	3	66.6%	probably_damaging(0.999)	tolerated(0.48)	deleterious(0.501)	HMMPfam_tRNA-synt_2,superfamily_SSF55681
CEP350	9857	genome.wustl.edu	37	1	180034367	180034367	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014810.4	+1	reviewed	p.M1843V	1.000	66	0%	90	31.1%	0	-	possibly_damaging(0.916)	deleterious(0.03)	deleterious(0.732)	NULL
ZNF648	127665	genome.wustl.edu	37	1	182025893	182025893	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001009992.1	-1	provisional	p.R418Q	0.943	7	0.000	13	0.308	0	-	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	superfamily_SSF57667
TPR	7175	genome.wustl.edu	37	1	186301421	186301421	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003292.2	-1	reviewed	p.D1837G	1.000	115	0%	145	26.2%	14	14.2%	possibly_damaging(0.44)	tolerated(0.06)	neutral(0.466)	NULL
KCNT2	343450	genome.wustl.edu	37	1	196397396	196397396	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198503.2	-1	validated	p.E275K	1.000	97	0%	132	25.8%	0	-	probably_damaging(0.996)	deleterious(0.01)	deleterious(0.867)	HMMPfam_Ion_trans_2,superfamily_Voltage-gated potassium channels
CFH	3075	genome.wustl.edu	37	1	196712711	196712711	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000186.3	+1	reviewed	p.E1088G	0.616	492	0%	604	19.7%	11	9%	possibly_damaging(0.656)	tolerated(0.17)	neutral(0.290)	HMMPfam_Sushi,HMMSmart_SM00032,superfamily_Complement control module/SCR domain
KIF14	9928	genome.wustl.edu	37	1	200584666	200584666	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014875.2	-1	validated	p.T395M	0.996	158	0%	192	28.6%	0	-	benign(0.001)	tolerated(0.25)	neutral(0.037)	HMMPfam_Kinesin,HMMSmart_KISc,superfamily_SSF52540
CNTN2	6900	genome.wustl.edu	37	1	205036348	205036348	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005076.2	+1	reviewed	p.P699S	1.000	76	0%	77	28.6%	0	-	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	superfamily_FN_III-like
RASSF5	83593	genome.wustl.edu	37	1	206757805	206757805	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182663.2	+1	reviewed	p.Q259	0.995	152	0%	206	30.1%	0	-	-	-	-	NULL
IL10	3586	genome.wustl.edu	37	1	206945709	206945709	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000572.2	-1	reviewed	p.T24	0.027	71	0%	69	26.1%	0	-	-	-	-	HMMPfam_IL10
SYT14	255928	genome.wustl.edu	37	1	210273522	210273522	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153262.2	+1	validated	p.G294S	1.000	124	0%	172	25.6%	0	-	benign(0.037)	tolerated(0.07)	neutral(0.321)	HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)
EPRS	2058	genome.wustl.edu	37	1	220151974	220151974	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004446.2	-1	reviewed	p.R1333*	0.806	225	0%	252	31.3%	43	4.6%	-	-	-	HMMPfam_HGTP_anticodon,superfamily_Anticodon_bd
DUSP10	11221	genome.wustl.edu	37	1	221875854	221875854	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007207.3	-1	reviewed	p.N450T	1.000	311	0%	336	27.4%	12	16.6%	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	HMMPfam_DSPc,HMMSmart_SM00195,superfamily_(Phosphotyrosine protein) phosphatases II
OBSCN	84033	genome.wustl.edu	37	1	228506833	228506833	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098623.1	+1	reviewed	p.R4794C	0.864	22	0%	38	23.7%	3	100%	probably_damaging(1)	deleterious(0.03)	deleterious(0.865)	NULL
TAF5L	27097	genome.wustl.edu	37	1	229730315	229730315	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014409.3	-1	reviewed	p.G500V	1.000	72	0%	112	30.4%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40
TARBP1	6894	genome.wustl.edu	37	1	234556492	234556492	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005646.3	-1	reviewed	p.R1171*	1.000	315	0%	455	29.7%	0	-	-	-	-	superfamily_ARM-type_fold
GPR137B	7107	genome.wustl.edu	37	1	236343213	236343213	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003272.3	+1	validated	p.V241A	1.000	304	0%	338	27.5%	0	-	benign(0.001)	tolerated(0.68)	neutral(0.002)	NULL
FH	2271	genome.wustl.edu	37	1	241675321	241675321	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000143.2	-1	reviewed	p.G167	0.934	434	0%	497	20.1%	9	22.2%	-	-	-	HMMPfam_Lyase_1,superfamily_L-aspartase-like
AKT3	10000	genome.wustl.edu	37	1	243668575	243668575	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005465.3	-1	reviewed	p.S472	1.000	83	0%	77	18.2%	2	0%	-	-	-	HMMSmart_SM00133,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase_C
SMYD3	64754	genome.wustl.edu	37	1	246093225	246093226	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	AG	AG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022743.2	-1	validated	p.S123fs	0.876:0.987	-	-	-	-	-	-	-	-	-	HMMSmart_SET,superfamily_SSF82199
AHCTF1	25909	genome.wustl.edu	37	1	247025322	247025322	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015446.4	-1	validated	p.R1225Q	0.905	65	0%	88	35.2%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
NLRP3	114548	genome.wustl.edu	37	1	247588487	247588487	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001079821.2	+1	reviewed	p.F581S	1.000	137	0%	150	32%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
OR2W5	441932	genome.wustl.edu	37	1	247655060	247655060	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004698.2	+1	validated	p.A211T	0.005	209	0%	249	25.7%	0	-	-	-	-	HMMPfam_7tm_1
OR2G2	81470	genome.wustl.edu	37	1	247752299	247752299	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001915.1	+1	provisional	p.P213H	0.139	324	0%	357	25.5%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_7tm_1,superfamily_SSF81321
POMC	5443	genome.wustl.edu	37	2	25384359	25384359	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000939.2	-1	reviewed	p.P132L	0.087	5	0.000	7	0.714	15	73.3%	benign(0)	tolerated(0.14)	neutral(0.249)	NULL
ALK	238	genome.wustl.edu	37	2	29416281	29416281	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004304.3	-1	reviewed	p.E1558Q	1.000	429	0%	371	38.5%	0	-	benign(0.414)	deleterious(0)	deleterious(0.579)	NULL
STRN	6801	genome.wustl.edu	37	2	37105036	37105036	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003162.2	-1	validated	p.D441N	1.000	385	0%	334	39.5%	0	-	possibly_damaging(0.948)	deleterious(0)	deleterious(0.836)	NULL
HEATR5B	54497	genome.wustl.edu	37	2	37240994	37240994	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019024.1	-1	validated	p.A1425D	1.000	102	0%	99	49.5%	2	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PRKCE	5581	genome.wustl.edu	37	2	46207514	46207514	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005400.2	+1	reviewed	p.P229	0.008	93	0%	81	38.3%	0	-	-	-	-	NULL
TSPYL6	388951	genome.wustl.edu	37	2	54482384	54482384	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003937.2	-1	validated	p.P302H	0.957	215	0%	177	41.8%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_NAP
ATP6V1B1	525	genome.wustl.edu	37	2	71187160	71187160	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001692.3	+1	reviewed	p.R179	0.677	55	0%	49	38.8%	8	87.5%	-	-	-	HMMPfam_ATP-synt_ab,superfamily_SSF52540
ZNF638	27332	genome.wustl.edu	37	2	71650295	71650295	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001014972.1	+1	reviewed	p.I1217	0.009	167	0%	141	38.3%	7	57.1%	-	-	-	NULL
RETSAT	54884	genome.wustl.edu	37	2	85578850	85578850	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017750.3	-1	validated	p.G103V	1.000	50	0%	49	38.8%	2	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_FAD_binding_2,superfamily_FAD/NAD(P)-binding domain
GPAT2	150763	genome.wustl.edu	37	2	96688915	96688915	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207328.2	-1	validated	p.P696	0.015	23	0%	34	52.9%	27	37%	-	-	-	NULL
LIMS1	3987	genome.wustl.edu	37	2	109297179	109297179	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004987.3	+1	reviewed	p.C272	0.803	90	0%	83	27.7%	10	10%	-	-	-	HMMPfam_LIM,HMMSmart_LIM,superfamily_SSF57716
BIN1	274	genome.wustl.edu	37	2	127827579	127827579	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139343.1	-1	reviewed	p.D135N	1.000	20	0%	14	35.7%	15	40%	probably_damaging(0.993)	deleterious(0)	deleterious(0.895)	HMMPfam_BAR,HMMSmart_SM00721
LCT	3938	genome.wustl.edu	37	2	136566477	136566477	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002299.2	-1	reviewed	p.L1147P	0.999	92	0%	91	51.6%	0	-	probably_damaging(0.981)	deleterious(0.01)	deleterious(0.831)	HMMPfam_Glyco_hydro_1,superfamily_Glyco_hydro_cat
TTC21B	79809	genome.wustl.edu	37	2	166732697	166732697	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024753.3	-1	validated	p.D1284G	1.000	100	0%	71	33.8%	7	14.2%	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	HMMSmart_SM00028,superfamily_TPR-like
TTN	7273	genome.wustl.edu	37	2	179427308	179427308	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000356127	-1	known	p.P25281S	1.000	135	0%	98	33.7%	0	-	probably_damaging(1)	-	-	HMMPfam_fn3
SF3B1	23451	genome.wustl.edu	37	2	198257052	198257052	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012433.2	-1	reviewed	p.R1297H	1.000	69	0%	63	28.6%	410	38.2%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PLCL1	5334	genome.wustl.edu	37	2	198950755	198950755	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006226.3	+1	validated	p.H740	0.183	242	0%	185	47.6%	0	-	-	-	-	superfamily_C2_CaLB
KCTD18	130535	genome.wustl.edu	37	2	201371697	201371697	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152387.2	-1	validated	p.R15*	0.934	68	0%	55	47.3%	0	-	-	-	-	HMMPfam_K_tetra,superfamily_POZ domain
ERBB4	2066	genome.wustl.edu	37	2	212989562	212989562	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005235.2	-1	reviewed	p.R50H	1.000	75	0%	53	37.7%	0	-	probably_damaging(0.989)	tolerated(0.12)	deleterious(0.700)	superfamily_L domain-like
CNPPD1	27013	genome.wustl.edu	37	2	220040384	220040384	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015680.4	-1	validated	p.V63	1.000	81	0%	58	46.6%	2	0%	-	-	-	HMMPfam_Cyclin
SPEG	10290	genome.wustl.edu	37	2	220326644	220326644	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005876.4	+1	validated	p.D827	0.597	60	0%	63	46%	25	52%	-	-	-	NULL
NYAP2	57624	genome.wustl.edu	37	2	226447570	226447570	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020864.1	+1	validated	p.P479	0.000	54	0%	28	39.3%	0	-	-	-	-	NULL
SLC16A14	151473	genome.wustl.edu	37	2	230911371	230911371	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152527.4	-1	validated	p.R157	0.999	92	0%	81	39.5%	2	50%	-	-	-	HMMPfam_MFS_1,superfamily_MFS general substrate transporter
B3GNT7	93010	genome.wustl.edu	37	2	232262515	232262515	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145236.2	+1	validated	p.L29I	0.842	18	0%	20	25%	2	0%	benign(0.027)	tolerated(0.89)	neutral(0.002)	NULL
GIGYF2	26058	genome.wustl.edu	37	2	233656045	233656045	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001103147.1	+1	reviewed	p.A412P	0.940	316	0%	255	45.5%	0	-	benign(0)	tolerated(0.26)	neutral(0.034)	NULL
HDAC4	9759	genome.wustl.edu	37	2	239988532	239988532	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006037.3	-1	reviewed	p.K958N	1.000	25	0%	21	52.4%	0	-	possibly_damaging(0.799)	deleterious(0.04)	deleterious(0.650)	HMMPfam_Hist_deacetyl,superfamily_Arginase/deacetylase
FARP2	9855	genome.wustl.edu	37	2	242432832	242432832	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014808.2	+1	validated	p.R1007Q	1.000	35	0%	30	50%	13	46.1%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like
D2HGDH	728294	genome.wustl.edu	37	2	242690743	242690743	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000432449	+1	known	p.R114C	0.073	26	0%	27	44.4%	5	80%	-	-	-	HMMPfam_FAD-oxidase_C,superfamily_FAD-linked oxidases C-terminal domain
EDEM1	9695	genome.wustl.edu	37	3	5255168	5255168	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014674.2	+1	validated	p.P615	0.001	50	0%	29	51.7%	2	0%	-	-	-	NULL
PPARG	5468	genome.wustl.edu	37	3	12458437	12458437	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015869.4	+1	reviewed	p.E352K	1.000	166	0%	87	44.8%	20	55%	probably_damaging(0.993)	deleterious(0)	deleterious(0.895)	HMMPfam_Hormone_recep,HMMSmart_SM00430,superfamily_Nuclear receptor ligand-binding domain
ZFYVE20	64145	genome.wustl.edu	37	3	15116031	15116031	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022340.2	-1	validated	p.R538L	0.165	135	0%	131	45%	0	-	benign(0)	tolerated(1)	-	NULL
SCN10A	6336	genome.wustl.edu	37	3	38835250	38835250	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006514.2	-1	validated	p.P84	0.998	587	0%	579	38.5%	0	-	-	-	-	NULL
EXOSC7	23016	genome.wustl.edu	37	3	45046872	45046872	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015004.3	+1	validated	p.V194A	1.000	228	0%	202	39.1%	100	38%	benign(0.043)	tolerated(0.07)	neutral(0.322)	NULL
CLEC3B	7123	genome.wustl.edu	37	3	45077077	45077077	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003278.2	+1	validated	p.T90	1.000	36	0%	25	56%	14	0%	-	-	-	HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_C-type lectin-like
CSPG5	10675	genome.wustl.edu	37	3	47619182	47619182	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006574.3	-1	validated	p.T112A	0.307	8	0.000	9	0.556	6	0%	possibly_damaging(0.889)	deleterious(0)	deleterious(0.794)	HMMPfam_Chon_Sulph_att
CELSR3	1951	genome.wustl.edu	37	3	48686197	48686197	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001407.2	-1	reviewed	p.Q2244H	1.000	5	0.000	6	0.833	0	-	probably_damaging(0.998)	tolerated(0.16)	deleterious(0.534)	NULL
LAMB2	3913	genome.wustl.edu	37	3	49160758	49160758	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002292.3	-1	reviewed	p.E1344G	1.000	61	0%	57	47.4%	29	27.5%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
TRAIP	10293	genome.wustl.edu	37	3	49866910	49866910	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005879.2	-1	reviewed	p.R423Q	0.997	63	0%	49	36.7%	20	20%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
VPRBP	9730	genome.wustl.edu	37	3	51477907	51477907	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014703.2	-1	validated	p.E130K	1.000	114	0%	120	39.2%	0	-	benign(0.027)	tolerated(0.83)	neutral(0.002)	superfamily_ARM repeat
CACNA1D	776	genome.wustl.edu	37	3	53808638	53808638	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000720.2	+1	validated	p.D1399Y	1.000	79	0%	74	35.1%	0	-	probably_damaging(1)	tolerated(0.07)	deleterious(0.819)	HMMPfam_Ion_trans,superfamily_SSF81324
CCDC66	285331	genome.wustl.edu	37	3	56655847	56655851	+	RNA	DEL	AAAAA	AAAAA	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	AAAAA	AAAAA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_024460.1	+1	validated	NULL	0.000:0.000:0.007:0.115:0.134	-	-	-	-	-	-	-	-	-	-
FLNB	2317	genome.wustl.edu	37	3	58132691	58132691	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001457.3	+1	reviewed	p.P1900H	1.000	70	0%	52	46.2%	8	25%	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMSmart_IG_FLMN,superfamily_Ig_E-set,HMMPfam_Filamin
OR5H6	79295	genome.wustl.edu	37	3	97983879	97983879	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005479.1	+1	provisional	p.R251*	0.000	184	0%	139	40.3%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
RG9MTD1	54931	genome.wustl.edu	37	3	101283742	101283742	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017819.2	+1	provisional	p.Y39	0.001	327	0%	297	46.5%	5	20%	-	-	-	NULL
TPRA1	131601	genome.wustl.edu	37	3	127292461	127292461	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016372.2	-1	validated	p.G342D	0.996	21	0%	19	26.3%	112	42.8%	benign(0.045)	deleterious(0.01)	neutral(0.408)	NULL
ESYT3	83850	genome.wustl.edu	37	3	138191381	138191381	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031913.3	+1	validated	p.D639	0.000	199	0%	186	43.5%	1	100%	-	-	-	NULL
MED12L	116931	genome.wustl.edu	37	3	151078369	151078369	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_053002.4	+1	reviewed	p.R943I	1.000	377	0%	311	47.6%	0	-	possibly_damaging(0.95)	deleterious(0)	deleterious(0.838)	NULL
PIK3CA	5290	genome.wustl.edu	37	3	178916726	178916726	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.R38H	1.000	167	0%	168	47%	0	-	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B
PIK3CA	5290	genome.wustl.edu	37	3	178916936	178916936	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.R108H	1.000	210	0%	171	50.3%	0	-	possibly_damaging(0.945)	tolerated(0.06)	deleterious(0.712)	HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B,superfamily_SSF54236
TP63	8626	genome.wustl.edu	37	3	189586389	189586389	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003722.4	+1	reviewed	p.R338H	0.999	182	0%	136	50.7%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_p53-like transcription factors,HMMPfam_P53
LEPREL1	55214	genome.wustl.edu	37	3	189692408	189692408	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018192.3	-1	validated	p.R464Q	1.000	117	0%	117	38.5%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00702
HTT	3064	genome.wustl.edu	37	4	3237461	3237461	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002111.6	+1	reviewed	p.R2914L	1.000	28	0%	16	37.5%	16	25%	probably_damaging(1)	tolerated(1)	deleterious(0.500)	NULL
EVC	2121	genome.wustl.edu	37	4	5735137	5735137	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153717.2	+1	reviewed	p.T226M	0.007	426	0%	335	39.4%	0	-	unknown(0)	deleterious(0.05)	-	NULL
GRPEL1	80273	genome.wustl.edu	37	4	7065881	7065881	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025196.2	-1	provisional	p.M44I	0.000	40	0%	40	42.5%	17	41.1%	benign(0)	tolerated(0.19)	neutral(0.050)	NULL
SORCS2	57537	genome.wustl.edu	37	4	7716003	7716003	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020777.2	+1	reviewed	p.R676W	1.000	19	0%	13	53.8%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMSmart_SM00602
KLF3	51274	genome.wustl.edu	37	4	38690413	38690413	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016531.5	+1	validated	p.R89	0.974	153	0%	108	50.9%	1	0%	-	-	-	NULL
TLR6	10333	genome.wustl.edu	37	4	38828786	38828786	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006068.3	-1	validated	p.R770H	0.812	161	0%	133	42.9%	0	-	possibly_damaging(0.485)	tolerated(1)	neutral(0.161)	HMMPfam_TIR,HMMSmart_TIR,superfamily_TIR
CHRNA9	55584	genome.wustl.edu	37	4	40351319	40351319	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017581.2	+1	reviewed	p.P262	0.985	753	0.1%	631	39.6%	0	-	-	-	-	HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore
PHOX2B	8929	genome.wustl.edu	37	4	41749373	41749373	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003924.3	-1	reviewed	p.R141Q	1.000	7	0.000	17	0.647	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like,PatternScan_HOMEOBOX_1
DCAF4L1	285429	genome.wustl.edu	37	4	41984296	41984296	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001029955.3	+1	validated	p.R163W	0.933	184	0%	125	44%	0	-	benign(0.322)	deleterious(0)	deleterious(0.545)	superfamily_WD40 repeat-like
NOA1	84273	genome.wustl.edu	37	4	57842757	57842757	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032313.2	-1	provisional	p.Q332R	1.000	54	0%	56	35.7%	2	100%	possibly_damaging(0.516)	tolerated(0.44)	neutral(0.186)	superfamily_SSF52540
YTHDC1	91746	genome.wustl.edu	37	4	69202890	69202890	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001031732.2	-1	validated	p.E246	0.643	254	0%	198	49.5%	2	100%	-	-	-	NULL
SHROOM3	57619	genome.wustl.edu	37	4	77676129	77676129	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020859.3	+1	validated	p.P1498L	0.189	98	0%	83	43.4%	0	-	benign(0.023)	deleterious(0)	neutral(0.446)	NULL
CCNG2	901	genome.wustl.edu	37	4	78085442	78085444	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	TTC	TTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004354.2	+1	reviewed	p.F242in_frame_del	0.998:1.000:0.991	-	-	-	-	-	-	-	-	-	NULL
FRAS1	80144	genome.wustl.edu	37	4	79173607	79173607	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_025074.6	+1	reviewed	p.R124Q	0.027	158	0%	154	45.5%	0	-	benign(0.082)	tolerated(0.37)	neutral(0.025)	HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1
NKX6-1	4825	genome.wustl.edu	37	4	85416882	85416882	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006168.2	-1	validated	p.A262	0.952	70	0%	60	48.3%	0	-	-	-	-	HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like
DSPP	1834	genome.wustl.edu	37	4	88533938	88533938	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014208.3	+1	reviewed	p.I200	0.000	173	0%	131	45%	0	-	-	-	-	NULL
EMCN	51705	genome.wustl.edu	37	4	101337095	101337095	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016242.3	-1	validated	p.S237	1.000	91	0%	78	46.2%	0	-	-	-	-	HMMPfam_Endomucin
TBCK	93627	genome.wustl.edu	37	4	107154782	107154782	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033115.3	-1	validated	p.A429V	1.000	66	0%	74	40.5%	1	100%	benign(0.256)	tolerated(0.27)	neutral(0.060)	HMMPfam_TBC,HMMSmart_TBC,superfamily_RabGAP_TBC
EGF	1950	genome.wustl.edu	37	4	110862109	110862109	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001963.4	+1	reviewed	p.A45	0.154	245	0%	252	10.3%	0	-	-	-	-	superfamily_SSF63825
ENPEP	2028	genome.wustl.edu	37	4	111397618	111397618	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001977.3	+1	validated	p.T16	0.000	193	0%	168	37.5%	0	-	-	-	-	NULL
KIAA1109	84162	genome.wustl.edu	37	4	123113394	123113394	+	Silent	SNP	G	G	A	rs143187683	by1000genomes	TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000424425	+1	known	p.G137R	1.000	90	0%	75	48%	0	-	-	-	-	NULL
ARFIP1	27236	genome.wustl.edu	37	4	153809337	153809337	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001025595.1	+1	validated	p.R282C	1.000	132	0%	94	39.4%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Arfaptin
DCHS2	54798	genome.wustl.edu	37	4	155219700	155219700	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017639.3	-1	validated	p.R1467	0.000	300	0%	272	42.6%	0	-	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like
ANP32C	23520	genome.wustl.edu	37	4	165118507	165118507	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012403.1	-1	reviewed	p.C119	1.000	236	0%	186	41.4%	1	0%	-	-	-	superfamily_L domain-like
DDX60	55601	genome.wustl.edu	37	4	169145442	169145442	+	Silent	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000511317	-1	known	p.C85S	0.845	189	0%	168	37.5%	4	50%	-	-	-	NULL
DCTD	1635	genome.wustl.edu	37	4	183815750	183815750	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001012732.1	-1	reviewed	p.A96T	0.998	179	0%	112	32.1%	13	53.8%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_dCMP_cyt_deam_1,PatternScan_CYT_DCMP_DEAMINASES,superfamily_Cytidine_deaminase-like
LOC391722	391722	genome.wustl.edu	37	4	185220396	185220396	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_373042.2	-1	model	p.T340	1.000	204	0%	132	12.1%	0	-	-	-	-	superfamily_EF-hand
HELT	391723	genome.wustl.edu	37	4	185941564	185941564	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001029887.1	+1	provisional	p.Q208*	1.000	69	0%	67	11.9%	0	-	-	-	-	HMMPfam_Hairy_orange
CLPTM1L	81037	genome.wustl.edu	37	5	1341804	1341804	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030782.3	-1	provisional	p.T145	0.004	33	0%	24	33.3%	3	100%	-	-	-	HMMPfam_CLPTM1
CDH9	1007	genome.wustl.edu	37	5	26906080	26906080	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016279.3	-1	reviewed	p.R267*	0.998	215	0%	167	44.3%	0	-	-	-	-	superfamily_Cadherin
PARP8	79668	genome.wustl.edu	37	5	50090895	50090895	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024615.3	+1	validated	p.K358Q	1.000	176	0%	147	43.5%	2	100%	benign(0)	tolerated(0.36)	neutral(0.020)	NULL
MAP3K1	4214	genome.wustl.edu	37	5	56177968	56177968	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005921.1	+1	validated	p.P981A	1.000	249	0%	160	33.8%	0	-	probably_damaging(0.99)	deleterious(0.02)	deleterious(0.825)	NULL
IQGAP2	10788	genome.wustl.edu	37	5	75871583	75871583	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006633.2	+1	validated	p.I149	1.000	126	0%	128	40.6%	0	-	-	-	-	HMMPfam_CH,HMMSmart_SM00033,superfamily_Calponin-homology domain CH-domain
DMXL1	1657	genome.wustl.edu	37	5	118485469	118485469	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005509.4	+1	validated	p.H1316R	1.000	191	0%	152	32.9%	3	100%	benign(0.089)	tolerated(1)	neutral(0.006)	NULL
MEGF10	84466	genome.wustl.edu	37	5	126734453	126734453	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032446.2	+1	validated	p.V249I	1.000	152	0%	113	40.7%	0	-	benign(0.002)	tolerated(0.46)	neutral(0.012)	HMMSmart_SM00181,superfamily_EGF/Laminin
FBN2	2201	genome.wustl.edu	37	5	127622436	127622436	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001999.3	-1	reviewed	p.R2329Q	0.971	92	0%	80	37.5%	0	-	benign(0.141)	tolerated(0.42)	neutral(0.026)	HMMSmart_SM00179,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_EGF_CA,superfamily_EGF/Laminin
PHF15	23338	genome.wustl.edu	37	5	133898036	133898036	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015288.4	+1	provisional	p.S277R	1.000	30	0%	44	47.7%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PITX1	5307	genome.wustl.edu	37	5	134364919	134364919	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002653.4	-1	reviewed	p.S165	1.000	29	0%	29	48.3%	1	0%	-	-	-	NULL
KLHL3	26249	genome.wustl.edu	37	5	137056158	137056158	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017415.2	-1	validated	p.R44W	1.000	323	0%	226	44.7%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_POZ domain,HMMPfam_BTB
FAM13B	51306	genome.wustl.edu	37	5	137289931	137289931	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016603.2	-1	validated	p.D526Y	1.000	187	0%	129	39.5%	0	-	probably_damaging(0.998)	deleterious(0.04)	deleterious(0.823)	NULL
PCDHA3	56145	genome.wustl.edu	37	5	140182900	140182900	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018906.2	+1	reviewed	p.A706	0.070	96	0%	75	46.7%	0	-	-	-	-	NULL
WWC1	23286	genome.wustl.edu	37	5	167858266	167858266	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015238.2	+1	reviewed	p.R699	0.117	141	0%	149	48.3%	5	60%	-	-	-	superfamily_C2 domain (Calcium/lipid-binding domain CaLB)
PANK3	79646	genome.wustl.edu	37	5	167984623	167984623	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024594.2	-1	reviewed	p.Y356N	0.998	155	0%	158	39.9%	2	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Fumble,superfamily_SSF53067
CPEB4	80315	genome.wustl.edu	37	5	173316738	173316738	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030627.2	+1	validated	p.M1T	1.000	329	0%	256	45.3%	0	-	probably_damaging(0.959)	deleterious(0)	deleterious(0.847)	NULL
CPEB4	80315	genome.wustl.edu	37	5	173372021	173372021	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030627.2	+1	validated	p.G445V	1.000	186	0.5%	154	38.3%	0	-	benign(0)	deleterious(0.05)	neutral(0.345)	NULL
LMAN2	10960	genome.wustl.edu	37	5	176765529	176765529	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006816.2	-1	reviewed	p.D131	0.857	79	0%	65	36.9%	226	50.8%	-	-	-	HMMPfam_Lectin_leg-like,superfamily_ConA_like_lec_gl
BTNL3	10917	genome.wustl.edu	37	5	180432616	180432616	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_197975.1	+1	validated	p.L382P	0.009	221	0%	184	44.6%	0	-	probably_damaging(0.964)	deleterious(0.03)	deleterious(0.771)	HMMPfam_SPRY,HMMSmart_SPRY
TRIM7	81786	genome.wustl.edu	37	5	180626991	180626991	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_203293.1	-1	reviewed	p.R237S	0.961	90	0%	65	52.3%	1	0%	possibly_damaging(0.925)	deleterious(0)	deleterious(0.818)	NULL
TUBB2B	347733	genome.wustl.edu	37	6	3225881	3225881	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178012.4	-1	reviewed	p.G148S	1.000	74	0%	74	21.6%	182	53.2%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Tubulin,superfamily_Tubulin nucleotide-binding domain-like
SLC22A23	63027	genome.wustl.edu	37	6	3273421	3273421	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015482.1	-1	validated	p.P643	0.379	31	0%	43	39.5%	14	78.5%	-	-	-	NULL
RREB1	6239	genome.wustl.edu	37	6	7248912	7248912	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003699.3	+1	reviewed	p.S1647N	0.998	38	0%	25	48%	2	50%	possibly_damaging(0.746)	deleterious(0.01)	deleterious(0.679)	NULL
BMP6	654	genome.wustl.edu	37	6	7880555	7880555	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001718.4	+1	reviewed	p.V507	0.333	178	0%	140	42.9%	0	-	-	-	-	HMMPfam_TGF_beta,HMMSmart_TGFB,superfamily_SSF57501
FAM65B	9750	genome.wustl.edu	37	6	24873112	24873112	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014722.2	-1	validated	p.R111	1.000	73	0%	53	35.8%	0	-	-	-	-	NULL
SCGN	10590	genome.wustl.edu	37	6	25670234	25670234	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006998.3	+1	reviewed	p.L134H	1.000	330	0%	344	39%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00054,HMMPfam_efhand,superfamily_EF-hand
BTN3A1	11119	genome.wustl.edu	37	6	26406353	26406353	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007048.5	+1	validated	p.R101Q	0.000	192	0%	144	25%	1	0%	probably_damaging(0.997)	tolerated(0.22)	deleterious(0.508)	HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin
ZNF184	7738	genome.wustl.edu	37	6	27425100	27425100	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007149.2	-1	validated	p.D55V	0.989	314	0%	306	40.8%	0	-	probably_damaging(0.991)	deleterious(0)	deleterious(0.889)	HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352)
GABBR1	2550	genome.wustl.edu	37	6	29599213	29599213	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001470.2	-1	reviewed	p.A83	1.000	90	0%	79	48.1%	0	-	-	-	-	HMMSmart_SM00032,superfamily_Complement control module/SCR domain
LY6G6F	259215	genome.wustl.edu	37	6	31675860	31675860	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003693.1	+1	provisional	p.I199F	0.112	114	0%	101	37.6%	0	-	possibly_damaging(0.918)	tolerated(0.14)	deleterious(0.618)	NULL
RDBP	7936	genome.wustl.edu	37	6	31922644	31922644	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002904.5	-1	reviewed	p.R144*	1.000	131	0%	122	45.1%	74	12.1%	-	-	-	NULL
VPS52	6293	genome.wustl.edu	37	6	33218722	33218722	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022553.4	-1	reviewed	p.R690W	1.000	102	0%	81	38.3%	96	41.6%	probably_damaging(0.991)	deleterious(0)	deleterious(0.889)	NULL
MLIP	90523	genome.wustl.edu	37	6	53989307	53989307	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138569.2	+1	validated	p.S86G	0.007	186	0%	141	39.7%	0	-	benign(0.027)	tolerated(0.06)	neutral(0.324)	NULL
DST	667	genome.wustl.edu	37	6	56335937	56335937	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015548.4	-1	reviewed	p.R4807W	0.998	44	0%	34	44.1%	0	-	probably_damaging(1)	-	-	HMMSmart_SM00054,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_EF-hand
COL12A1	1303	genome.wustl.edu	37	6	75890693	75890693	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004370.5	-1	reviewed	p.F709S	1.000	295	0%	279	36.9%	0	-	benign(0.085)	-	-	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
NR2E1	7101	genome.wustl.edu	37	6	108501573	108501573	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003269.3	+1	validated	p.I230T	1.000	108	0%	114	43.9%	0	-	benign(0.271)	tolerated(0.21)	neutral(0.073)	HMMPfam_Hormone_recep,HMMSmart_SM00430,superfamily_Nuclear receptor ligand-binding domain
LOC100287430	100287430	genome.wustl.edu	37	6	116579937	116579937	+	RNA	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_078343.1	-1	model	NULL	0.995	126	0%	67	46.3%	230	0.4%	possibly_damaging(0.737)	-	-	-
ROS1	6098	genome.wustl.edu	37	6	117706926	117706926	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002944.2	-1	reviewed	p.L742I	0.865	181	0%	125	24%	0	-	benign(0)	tolerated(0.84)	neutral(0.001)	HMMSmart_LY,superfamily_SSF63825
THEMIS	387357	genome.wustl.edu	37	6	128134089	128134089	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001010923.2	-1	reviewed	p.T566I	0.000	268	0%	263	47.1%	0	-	benign(0)	tolerated(0.42)	neutral(0.014)	NULL
PTPRK	5796	genome.wustl.edu	37	6	128294910	128294910	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135648.1	-1	validated	p.E1350D	1.000	168	0%	147	38.8%	4	0%	benign(0)	tolerated(0.85)	neutral(0.001)	HMMPfam_Y_phosphatase,HMMSmart_PTPc,superfamily_SSF52799
LAMA2	3908	genome.wustl.edu	37	6	129807618	129807618	+	Splice_Site	DEL	G	G	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000426.3	+1	reviewed	e56-1	1.000	-	-	-	-	-	-	-	-	-	-
TMEM200A	114801	genome.wustl.edu	37	6	130762335	130762335	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052913.2	+1	provisional	p.G256	0.998	347	0%	267	40.1%	0	-	-	-	-	NULL
UTRN	7402	genome.wustl.edu	37	6	144812179	144812179	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007124.2	+1	reviewed	p.V1460I	0.227	147	0%	104	50%	0	-	probably_damaging(0.969)	tolerated(0.06)	deleterious(0.734)	HMMSmart_SPEC,superfamily_Spectrin
SASH1	23328	genome.wustl.edu	37	6	148865741	148865741	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015278.3	+1	validated	p.S1045	0.000	53	0%	41	41.5%	0	-	-	-	-	NULL
LATS1	9113	genome.wustl.edu	37	6	150005070	150005070	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004690.2	-1	reviewed	p.S385	1.000	394	0%	293	41.6%	2	0%	-	-	-	NULL
SYNE1	23345	genome.wustl.edu	37	6	152510430	152510430	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182961.2	-1	reviewed	p.R7753H	1.000	152	0%	153	37.9%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_Spectrin repeat
TAGAP	117289	genome.wustl.edu	37	6	159457224	159457224	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_054114.3	-1	reviewed	p.E611K	0.000	73	0%	62	41.9%	0	-	benign(0)	tolerated(0.91)	-	NULL
PAPOLB	56903	genome.wustl.edu	37	7	4900631	4900631	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020144.4	-1	validated	p.R271W	0.144	494	0%	349	41%	0	-	probably_damaging(0.964)	deleterious(0)	deleterious(0.851)	HMMPfam_PAP_central,superfamily_SSF81631
RBAK	57786	genome.wustl.edu	37	7	5104522	5104522	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021163.3	+1	reviewed	p.H479Y	1.000	247	0%	221	38.9%	0	-	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
DAGLB	221955	genome.wustl.edu	37	7	6474420	6474420	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139179.3	-1	validated	p.T217	0.998	197	0%	184	38%	1	0%	-	-	-	NULL
THSD7A	221981	genome.wustl.edu	37	7	11446664	11446664	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015204.2	-1	validated	p.R1312Q	1.000	50	0%	46	52.2%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat
DNAH11	8701	genome.wustl.edu	37	7	21913069	21913069	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003777.3	+1	reviewed	p.P4056T	1.000	111	0.9%	74	25.7%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Dynein_heavy
OSBPL3	26031	genome.wustl.edu	37	7	24874067	24874067	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000409452	-1	known	p.R595Q	0.000	116	0%	97	46.4%	0	-	unknown(0)	-	-	NULL
C7orf31	136895	genome.wustl.edu	37	7	25176293	25176293	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138811.3	-1	validated	p.P357	0.876	279	0%	216	49.5%	2	0%	-	-	-	NULL
SCRN1	9805	genome.wustl.edu	37	7	29966215	29966215	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145514.1	-1	reviewed	p.D333	0.918	48	0%	47	42.6%	9	66.6%	-	-	-	NULL
FAM188B	84182	genome.wustl.edu	37	7	30821663	30821663	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032222.2	+1	validated	p.T85M	0.003	205	0%	183	36.1%	0	-	possibly_damaging(0.93)	tolerated(0.23)	neutral(0.418)	NULL
ANLN	54443	genome.wustl.edu	37	7	36435887	36435887	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018685.2	+1	validated	p.R11*	1.000	162	0%	132	44.7%	1	100%	-	-	-	NULL
GLI3	2737	genome.wustl.edu	37	7	42004594	42004594	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000168.5	-1	reviewed	p.G1359	1.000	65	0%	60	38.3%	0	-	-	-	-	NULL
ABCA13	154664	genome.wustl.edu	37	7	48318114	48318114	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152701.3	+1	reviewed	p.L2441	0.000	153	0%	138	42.8%	0	-	-	-	-	NULL
COBL	23242	genome.wustl.edu	37	7	51258564	51258564	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015198.3	-1	validated	p.A223E	0.996	41	0%	31	29%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Cobl
AKAP9	10142	genome.wustl.edu	37	7	91671438	91671438	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005751.4	+1	reviewed	p.L1666M	0.999	127	0%	96	53.1%	0	-	probably_damaging(0.999)	tolerated(0.16)	deleterious(0.550)	NULL
COL1A2	1278	genome.wustl.edu	37	7	94029554	94029554	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000089.3	+1	reviewed	p.G60V	1.000	100	0%	87	40.2%	3	0%	unknown(0)	deleterious(0.01)	-	HMMPfam_Collagen
PPP1R9A	55607	genome.wustl.edu	37	7	94540658	94540658	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017650.2	+1	validated	p.N411K	0.939	86	0%	72	37.5%	0	-	unknown(0)	deleterious(0.03)	-	NULL
ZNF3	7551	genome.wustl.edu	37	7	99668798	99668798	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032924.3	-1	validated	p.T437A	0.307	167	0%	107	33.6%	6	16.6%	benign(0.002)	tolerated(0.34)	neutral(0.023)	NULL
MUC17	140453	genome.wustl.edu	37	7	100676145	100676145	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001040105.1	+1	provisional	p.V483A	0.000	1015	0.1%	721	41.6%	0	-	unknown(0)	-	-	NULL
SERPINE1	5054	genome.wustl.edu	37	7	100778853	100778853	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000602.3	+1	reviewed	p.Q326H	0.013	293	0.3%	236	32.6%	4	0%	benign(0.01)	tolerated(0.09)	neutral(0.297)	HMMPfam_Serpin,HMMSmart_SERPIN,superfamily_Prot_inh_serpin
SLC13A1	6561	genome.wustl.edu	37	7	122768954	122768954	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022444.3	-1	validated	p.L360	0.974	132	0%	111	42.3%	0	-	-	-	-	HMMPfam_Na_sulph_symp
GRM8	2918	genome.wustl.edu	37	7	126173080	126173080	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000845.2	-1	reviewed	p.T786A	1.000	117	0%	91	35.2%	0	-	probably_damaging(0.99)	deleterious(0)	deleterious(0.886)	HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_3
CPA1	1357	genome.wustl.edu	37	7	130027804	130027804	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001868.2	+1	reviewed	p.W404*	1.000	399	0%	279	40.1%	0	-	-	-	-	HMMPfam_Peptidase_M14,superfamily_SSF53187
AGK	55750	genome.wustl.edu	37	7	141296429	141296429	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018238.3	+1	validated	p.A70V	1.000	228	0%	134	47%	2	0%	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	HMMPfam_DAGK_cat,HMMSmart_SM00046
ABCB8	11194	genome.wustl.edu	37	7	150733045	150733045	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007188.3	+1	reviewed	p.R335Q	0.969	25	0%	30	33.3%	9	44.4%	benign(0.112)	tolerated(0.21)	neutral(0.053)	HMMPfam_ABC_membrane,superfamily_ABC_TM_1
MLL3	58508	genome.wustl.edu	37	7	152012314	152012314	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_170606.2	-1	reviewed	p.P167A	0.610	308	0%	209	39.2%	1	0%	benign(0.391)	-	-	NULL
RBM33	155435	genome.wustl.edu	37	7	155538249	155538249	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_053043.2	+1	validated	p.G978R	1.000	34	0%	30	43.3%	3	33.3%	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	NULL
DLGAP2	9228	genome.wustl.edu	37	8	1626512	1626512	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004745.3	+1	reviewed	p.S727	0.110	47	0%	41	56.1%	0	-	-	-	-	HMMPfam_GKAP
DOCK5	80005	genome.wustl.edu	37	8	25258506	25258506	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024940.6	+1	validated	p.P1617L	1.000	418	0%	413	54.2%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PTK2B	2185	genome.wustl.edu	37	8	27308288	27308288	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004103.3	+1	reviewed	p.S788N	1.000	38	0%	58	53.4%	1	0%	benign(0.02)	tolerated(0.54)	neutral(0.009)	NULL
EPHX2	2053	genome.wustl.edu	37	8	27396187	27396187	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001979.4	+1	reviewed	p.S418	0.000	152	0%	168	28%	2	0%	-	-	-	HMMPfam_Abhydrolase_1,superfamily_SSF53474
CLVS1	157807	genome.wustl.edu	37	8	62289226	62289226	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173519.2	+1	validated	p.P173L	0.995	106	0%	146	52.7%	0	-	benign(0.016)	tolerated(0.07)	neutral(0.320)	HMMPfam_CRAL_TRIO,HMMSmart_SM00516,superfamily_CRAL/TRIO domain
SGK3	23678	genome.wustl.edu	37	8	67752322	67752322	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001033578.1	+1	reviewed	p.Y276H	1.000	252	0%	274	49.3%	0	-	probably_damaging(1)	tolerated(0.19)	deleterious(0.549)	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase
JPH1	56704	genome.wustl.edu	37	8	75157400	75157400	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020647.2	-1	reviewed	p.Y423	0.294	159	0%	179	31.8%	0	-	-	-	-	NULL
DCAF4L2	138009	genome.wustl.edu	37	8	88885717	88885717	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152418.3	-1	validated	p.A161	0.223	185	0%	152	40.8%	0	-	-	-	-	superfamily_WD40_like
CCNE2	9134	genome.wustl.edu	37	8	95895030	95895030	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_057749.1	-1	reviewed	p.E308K	0.999	91	0%	127	55.9%	1	100%	possibly_damaging(0.577)	deleterious(0.01)	deleterious(0.604)	HMMPfam_Cyclin_C
EFR3A	23167	genome.wustl.edu	37	8	132991259	132991259	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015137.3	+1	validated	p.G498W	0.957	271	0%	230	31.3%	3	66.6%	possibly_damaging(0.861)	tolerated(0.07)	deleterious(0.652)	NULL
FAM135B	51059	genome.wustl.edu	37	8	139144953	139144953	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015912.3	-1	validated	p.H1368	0.996	200	0%	194	35.6%	0	-	-	-	-	NULL
PLEC	5339	genome.wustl.edu	37	8	144995815	144995815	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_201380.2	-1	reviewed	p.T2862K	1.000	22	0%	18	33.3%	4	75%	probably_damaging(1)	-	-	HMMPfam_Plectin,HMMSmart_SM00250,superfamily_Plakin repeat
FRMPD1	22844	genome.wustl.edu	37	9	37745886	37745886	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014907.2	+1	validated	p.S1286I	0.845	153	0%	135	57%	0	-	benign(0.001)	tolerated(0.06)	neutral(0.323)	NULL
CNTNAP3	79937	genome.wustl.edu	37	9	39078395	39078396	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	AG	AG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033655.3	-1	reviewed	p.S1244fs	0.992:1.000	-	-	-	-	-	-	-	-	-	NULL
PCSK5	5125	genome.wustl.edu	37	9	78853912	78853912	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000376754	+1	known	p.E671	0.991	11	0%	21	33.3%	0	-	-	-	-	HMMSmart_SM00261,superfamily_Growth factor receptor domain
TGFBR1	7046	genome.wustl.edu	37	9	101910027	101910027	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004612.2	+1	reviewed	p.K449N	1.000	161	0%	101	39.6%	4	0%	probably_damaging(0.994)	tolerated(0.29)	deleterious(0.481)	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase
ERP44	23071	genome.wustl.edu	37	9	102768897	102768897	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015051.1	-1	validated	p.K303*	1.000	92	0%	115	46.1%	106	1.8%	-	-	-	NULL
INVS	27130	genome.wustl.edu	37	9	103055198	103055198	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014425.2	+1	reviewed	p.Q887*	1.000	152	0%	93	31.2%	5	40%	-	-	-	NULL
ACTL7A	10881	genome.wustl.edu	37	9	111625546	111625546	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006687.2	+1	reviewed	p.R315Q	0.999	142	0%	95	47.4%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Actin,HMMSmart_SM00268,superfamily_Actin-like ATPase domain
RGS3	5998	genome.wustl.edu	37	9	116346503	116346503	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144488.4	+1	reviewed	p.L937	1.000	40	0%	33	60.6%	12	75%	-	-	-	NULL
AKNA	80709	genome.wustl.edu	37	9	117138988	117138988	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030767.4	-1	validated	p.R367W	0.893	51	0%	34	26.5%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PAPPA	5069	genome.wustl.edu	37	9	118997754	118997754	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002581.3	+1	reviewed	p.T857M	1.000	100	0%	84	47.6%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_SSF55486
OR1B1	347169	genome.wustl.edu	37	9	125391448	125391448	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004450.1	-1	provisional	p.D123N	1.000	251	0.4%	202	38.1%	0	-	probably_damaging(0.996)	deleterious(0.01)	deleterious(0.867)	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321
GARNL3	84253	genome.wustl.edu	37	9	130151331	130151331	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032293.4	+1	validated	p.T892	0.454	114	0%	78	41%	5	20%	-	-	-	NULL
LRRC8A	56262	genome.wustl.edu	37	9	131670440	131670440	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127244.1	+1	reviewed	p.G333S	1.000	76	0%	54	51.9%	1	0%	probably_damaging(1)	tolerated(0.1)	deleterious(0.786)	NULL
RXRA	6256	genome.wustl.edu	37	9	137326047	137326047	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002957.4	+1	reviewed	p.P412Q	0.993	15	0.000	9	0.444	26	30.7%	probably_damaging(0.998)	tolerated(0.23)	deleterious(0.516)	HMMPfam_Hormone_recep,HMMSmart_SM00430,superfamily_Nuclear receptor ligand-binding domain
LOC100131193	100131193	genome.wustl.edu	37	9	139699111	139699111	+	RNA	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_024580.1	-1	predicted	NULL	0.003	22	0%	22	36.4%	1	100%	-	-	-	-
ABCA2	20	genome.wustl.edu	37	9	139912048	139912048	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_212533.2	-1	reviewed	p.A800T	1.000	4	0.000	6	0.667	0	-	possibly_damaging(0.793)	tolerated(0.06)	deleterious(0.621)	NULL
TUBB8	347688	genome.wustl.edu	37	10	93256	93256	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_177987.2	-1	validated	p.R359Q	1.000	231	0.4%	293	29.4%	8	25%	benign(0.258)	deleterious(0)	deleterious(0.472)	superfamily_Tub_FtsZ_C,HMMPfam_Tubulin_C
ZMYND11	10771	genome.wustl.edu	37	10	298377	298377	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006624.4	+1	reviewed	p.A552	0.015	233	0%	263	28.5%	16	12.5%	-	-	-	HMMPfam_zf-MYND,PatternScan_ZF_MYND_1
CCDC3	83643	genome.wustl.edu	37	10	13040504	13040504	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031455.3	-1	validated	p.E128G	1.000	96	0%	123	29.3%	3	0%	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	NULL
ARMC3	219681	genome.wustl.edu	37	10	23287152	23287152	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173081.3	+1	validated	p.N417	0.995	87	0%	102	20.6%	0	-	-	-	-	HMMPfam_Arm,HMMSmart_SM00185,superfamily_ARM repeat
KIAA1462	57608	genome.wustl.edu	37	10	30336625	30336625	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020848.2	-1	validated	p.A39	0.000	69	0%	91	20.9%	0	-	-	-	-	NULL
CUL2	8453	genome.wustl.edu	37	10	35343422	35343422	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003591.2	-1	provisional	p.A121	0.997	153	0%	175	24.6%	0	-	-	-	-	HMMPfam_Cullin,superfamily_Cullin repeat
SLC18A3	6572	genome.wustl.edu	37	10	50819136	50819136	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003055.2	+1	reviewed	p.T117M	0.495	38	0%	71	28.2%	0	-	benign(0.003)	tolerated(0.26)	neutral(0.034)	HMMPfam_MFS_1,superfamily_MFS general substrate transporter
ANK3	288	genome.wustl.edu	37	10	61833451	61833453	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	TTC	TTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020987.2	-1	reviewed	p.E2396in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
ARID5B	84159	genome.wustl.edu	37	10	63852248	63852248	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032199.2	+1	validated	p.A1009G	0.876	130	0%	166	26.5%	3	33.3%	possibly_damaging(0.885)	deleterious(0)	deleterious(0.790)	NULL
MYPN	84665	genome.wustl.edu	37	10	69933886	69933886	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032578.2	+1	validated	p.N679K	0.068	253	0.4%	289	28%	0	-	benign(0.059)	tolerated(1)	neutral(0.004)	NULL
PBLD	64081	genome.wustl.edu	37	10	70048415	70048415	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022129.3	-1	validated	p.S172	0.951	107	0%	138	31.9%	1	0%	-	-	-	HMMPfam_PhzC-PhzF,superfamily_SSF54506
TET1	80312	genome.wustl.edu	37	10	70333770	70333770	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030625.2	+1	validated	p.T559A	0.003	177	0%	189	37.6%	0	-	benign(0.025)	tolerated(0.78)	neutral(0.002)	NULL
NODAL	4838	genome.wustl.edu	37	10	72195614	72195614	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018055.4	-1	reviewed	p.G107C	0.000	79	0%	97	29.9%	2	0%	benign(0.313)	tolerated(0.05)	neutral(0.443)	NULL
DDIT4	54541	genome.wustl.edu	37	10	74034519	74034519	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019058.2	+1	validated	p.H91R	1.000	60	0%	61	21.3%	79	34.1%	benign(0.041)	tolerated(0.69)	neutral(0.005)	NULL
POLR3A	11128	genome.wustl.edu	37	10	79739977	79739977	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007055.3	-1	validated	p.L1316	1.000	55	0%	85	27.1%	16	43.7%	-	-	-	HMMPfam_RNA_pol_Rpb1_5,superfamily_SSF64484
C10orf99	387695	genome.wustl.edu	37	10	85944484	85944484	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207373.2	+1	validated	p.R70C	0.000	116	0%	130	36.2%	0	-	possibly_damaging(0.933)	-	-	NULL
PTEN	5728	genome.wustl.edu	37	10	89653829	89653829	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.E43*	1.000	254	0%	255	57.3%	0	-	-	-	-	HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II
PTEN	5728	genome.wustl.edu	37	10	89717683	89717684	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.F237fs	1.000:1.000	-	-	-	-	-	-	-	-	-	superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_PTEN_C2
BTAF1	9044	genome.wustl.edu	37	10	93719751	93719751	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003972.2	+1	validated	p.R368H	1.000	298	0%	331	25.1%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_ARM repeat
PLCE1	51196	genome.wustl.edu	37	10	96033395	96033395	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016341.3	+1	reviewed	p.P1528H	1.000	137	0%	152	25.7%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_PI-PLC-X,HMMSmart_SM00148,superfamily_PLC-like phosphodiesterases
CRTAC1	55118	genome.wustl.edu	37	10	99677301	99677301	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018058.4	-1	validated	p.A224V	0.868	42	0%	46	26.1%	1	100%	benign(0.002)	tolerated(0.48)	neutral(0.011)	superfamily_Integrin alpha N-terminal domain
PDCD11	22984	genome.wustl.edu	37	10	105176299	105176299	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014976.1	+1	validated	p.T524P	1.000	275	0%	286	26.9%	0	-	probably_damaging(0.998)	deleterious(0.01)	deleterious(0.880)	superfamily_Nucleic_acid_OB
ENSG00000246977	0	genome.wustl.edu	37	10	106074044	106074044	+	RNA	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000499336	+1	novel	NULL	0.006	44	0%	50	26%	1	100%	-	-	-	-
EIF3A	8661	genome.wustl.edu	37	10	120795673	120795673	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003750.2	-1	validated	p.R1343*	0.988	53	0%	75	28%	30	36.6%	-	-	-	NULL
DMBT1	1755	genome.wustl.edu	37	10	124345885	124345885	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007329.2	+1	reviewed	p.G590D	0.226	161	0%	169	57.4%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_SRCR,HMMSmart_SM00202,superfamily_SRCR-like
OAT	4942	genome.wustl.edu	37	10	126086581	126086581	+	Missense_Mutation	SNP	G	G	T	rs121965044		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000274.3	-1	reviewed	p.P417Q	1.000	115	0%	165	27.3%	26	23%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_PyrdxlP-dep_Trfase_major
C10orf137	26098	genome.wustl.edu	37	10	127442264	127442264	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015608.2	+1	validated	p.P1098L	0.026	282	0%	328	23.8%	4	50%	benign(0.001)	tolerated(0.27)	neutral(0.034)	NULL
DOCK1	1793	genome.wustl.edu	37	10	129202618	129202618	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000398025	+1	known	p.I1394	1.000	19	0%	34	20.6%	1	0%	-	-	-	NULL
AP2A2	161	genome.wustl.edu	37	11	970267	970267	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012305.2	+1	validated	p.A79T	1.000	55	0%	39	46.2%	0	-	probably_damaging(0.997)	tolerated(0.08)	deleterious(0.766)	HMMPfam_Adaptin_N,superfamily_ARM repeat
NAP1L4	4676	genome.wustl.edu	37	11	2975808	2975808	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005969.3	-1	reviewed	p.V328	0.948	134	0%	108	40.7%	49	44.8%	-	-	-	HMMPfam_NAP
OR51B6	390058	genome.wustl.edu	37	11	5373540	5373540	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004750.1	+1	provisional	p.H268R	0.004	379	0%	262	37.8%	0	-	benign(0.001)	tolerated(0.16)	neutral(0.059)	HMMPfam_7tm_1,superfamily_SSF81321
OR52N5	390075	genome.wustl.edu	37	11	5799486	5799486	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001922.2	-1	validated	p.M127V	1.000	336	0%	260	44.6%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_Family A G protein-coupled receptor-like
OR2AG2	338755	genome.wustl.edu	37	11	6789985	6789986	+	Frame_Shift_Del	DEL	GA	GA	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	GA	GA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004490.1	-1	provisional	p.L68fs	0.006:0.023	-	-	-	-	-	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
ST5	6764	genome.wustl.edu	37	11	8737161	8737161	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005418.3	-1	reviewed	p.R612C	1.000	28	0%	37	35.1%	7	42.8%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
DENND5A	23258	genome.wustl.edu	37	11	9202353	9202353	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015213.2	-1	validated	p.L472	0.925	311	0%	275	45.1%	2	0%	-	-	-	NULL
ARNTL	406	genome.wustl.edu	37	11	13407264	13407264	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001030272.1	+1	reviewed	p.P548H	1.000	143	0%	171	46.2%	1	100%	benign(0.131)	deleterious(0)	neutral(0.456)	NULL
PDE3B	5140	genome.wustl.edu	37	11	14839801	14839801	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000922.3	+1	validated	p.R532Q	1.000	130	0%	96	40.6%	0	-	benign(0.038)	tolerated(0.07)	neutral(0.321)	NULL
TRIM48	79097	genome.wustl.edu	37	11	55038010	55038010	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000357530	+1	known	p.P242	0.001	115	0%	81	35.8%	0	-	-	-	-	NULL
OR5T2	219464	genome.wustl.edu	37	11	56000159	56000159	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004746.1	-1	provisional	p.P168H	1.000	537	0%	386	39.6%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_7tm_1,superfamily_SSF81321
APLNR	187	genome.wustl.edu	37	11	57003536	57003536	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005161.4	-1	reviewed	p.R315C	1.000	66	0%	44	40.9%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_SSF81321
OSBP	5007	genome.wustl.edu	37	11	59345683	59345683	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002556.2	-1	reviewed	p.R667*	1.000	323	0%	257	27.2%	3	33.3%	-	-	-	HMMPfam_Oxysterol_BP
MS4A6A	64231	genome.wustl.edu	37	11	59947360	59947360	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152852.1	-1	reviewed	p.T76A	0.075	159	0%	158	39.2%	0	-	possibly_damaging(0.608)	tolerated(0.09)	deleterious(0.507)	HMMPfam_CD20
SLC15A3	51296	genome.wustl.edu	37	11	60714276	60714276	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016582.2	-1	validated	p.R192	0.898	40	0%	35	48.6%	0	-	-	-	-	HMMPfam_PTR2,superfamily_MFS general substrate transporter
NRXN2	9379	genome.wustl.edu	37	11	64390261	64390261	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015080.2	-1	reviewed	p.R1379	1.000	41	0%	46	41.3%	1	0%	-	-	-	NULL
EFEMP2	30008	genome.wustl.edu	37	11	65637375	65637375	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016938.3	-1	reviewed	p.R227L	1.000	19	0%	23	39.1%	146	34.2%	probably_damaging(0.98)	tolerated(0.26)	neutral(0.458)	PatternScan_ASX_HYDROXYL,HMMSmart_EGF_CA,PatternScan_EGF_2,HMMPfam_EGF_CA,superfamily_SSF57196
ALDH3B2	222	genome.wustl.edu	37	11	67433852	67433852	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000695.3	-1	reviewed	p.P58S	1.000	39	0%	30	50%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Aldedh,superfamily_ALDH-like
PPP6R3	55291	genome.wustl.edu	37	11	68341578	68341578	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018312.4	+1	validated	p.A398T	1.000	88	0%	72	41.7%	1	0%	benign(0.003)	tolerated(0.41)	neutral(0.015)	HMMPfam_SAPS
CCDC83	220047	genome.wustl.edu	37	11	85597249	85597249	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173556.3	+1	provisional	p.R117H	0.985	71	0%	42	38.1%	0	-	benign(0.029)	tolerated(0.24)	neutral(0.039)	NULL
GRM5	2915	genome.wustl.edu	37	11	88780442	88780442	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001143831.2	-1	reviewed	p.R200M	0.805	143	0%	104	37.5%	0	-	benign(0.156)	deleterious(0.03)	neutral(0.379)	HMMPfam_ANF_receptor,superfamily_Periplasmic binding protein-like I
SIK2	23235	genome.wustl.edu	37	11	111594777	111594777	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015191.1	+1	validated	p.E902G	0.998	23	0%	27	22.2%	2	100%	benign(0.029)	deleterious(0)	neutral(0.446)	NULL
BUD13	84811	genome.wustl.edu	37	11	116633494	116633494	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032725.3	-1	validated	p.S271P	0.967	383	0.3%	319	38.9%	4	0%	probably_damaging(0.954)	deleterious(0)	deleterious(0.842)	NULL
TECTA	7007	genome.wustl.edu	37	11	121000393	121000393	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005422.2	+1	reviewed	p.K805R	0.276	187	0%	212	45.3%	0	-	benign(0.008)	tolerated(1)	-	HMMPfam_VWD,HMMSmart_SM00216
CLMP	79827	genome.wustl.edu	37	11	122944335	122944335	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024769.2	-1	validated	p.A323	0.140	53	0%	53	35.8%	0	-	-	-	-	NULL
OR10G4	390264	genome.wustl.edu	37	11	123886579	123886579	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004462.1	+1	provisional	p.L100V	1.000	483	0%	356	38.2%	0	-	possibly_damaging(0.77)	tolerated(0.15)	deleterious(0.527)	HMMPfam_7tm_1,superfamily_SSF81321
STT3A	3703	genome.wustl.edu	37	11	125488318	125488318	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152713.3	+1	validated	p.G609S	1.000	116	0%	94	37.2%	195	52.8%	probably_damaging(0.985)	tolerated(0.89)	neutral(0.432)	HMMPfam_STT3
FOXRED1	55572	genome.wustl.edu	37	11	126145272	126145272	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017547.2	+1	provisional	p.R228W	0.997	15	0%	13	30.8%	7	42.8%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DAO,superfamily_FAD/NAD(P)-binding domain
NCAPD3	23310	genome.wustl.edu	37	11	134055332	134055332	+	Missense_Mutation	SNP	G	G	A	rs143833204	by1000genomes	TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015261.2	-1	validated	p.T712M	0.931	111	0%	98	33.7%	0	-	benign(0.013)	tolerated(0.09)	neutral(0.297)	superfamily_ARM-type_fold
LRRC23	10233	genome.wustl.edu	37	12	7022149	7022149	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135217.1	+1	validated	p.P338	0.000	114	0%	106	41.5%	27	51.8%	-	-	-	NULL
TAS2R8	50836	genome.wustl.edu	37	12	10958911	10958911	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_023918.1	-1	reviewed	p.R223	0.103	214	0%	160	43.1%	0	-	-	-	-	HMMPfam_TAS2R,superfamily_SSF81321
WBP11	51729	genome.wustl.edu	37	12	14943518	14943518	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016312.2	-1	reviewed	p.P394L	1.000	149	0%	126	40.5%	25	72%	unknown(0)	deleterious(0.04)	-	NULL
KRAS	3845	genome.wustl.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529	byCluster	TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033360.2	-1	reviewed	p.G12D	1.000	52	0%	51	31.4%	3	100%	possibly_damaging(0.886)	deleterious(0)	deleterious(0.791)	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases
KIF21A	55605	genome.wustl.edu	37	12	39724563	39724563	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017641.3	-1	validated	p.G1089C	1.000	170	0%	126	45.2%	0	-	probably_damaging(1)	tolerated(0.17)	deleterious(0.559)	superfamily_Prefoldin,superfamily_WD40 repeat-like
NELL2	4753	genome.wustl.edu	37	12	44915955	44915955	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145107.1	-1	reviewed	p.G718E	1.000	138	0%	113	39.8%	6	16.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_VWC,HMMSmart_VWC,PatternScan_EGF_2
ADCY6	112	genome.wustl.edu	37	12	49169126	49169126	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015270.3	-1	reviewed	p.R647Q	1.000	60	1.7%	58	41.4%	0	-	possibly_damaging(0.754)	tolerated(0.27)	neutral(0.311)	HMMPfam_DUF1053
MLL2	8085	genome.wustl.edu	37	12	49441824	49441824	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003482.3	-1	validated	p.G1387A	1.000	44	0%	21	19%	0	-	unknown(0)	-	-	HMMSmart_SM00184,HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger,PatternScan_ZF_PHD_1,HMMPfam_PHD
KRT83	3889	genome.wustl.edu	37	12	52711520	52711520	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002282.3	-1	reviewed	p.A232V	1.000	263	0%	213	40.8%	0	-	probably_damaging(0.97)	deleterious(0.01)	deleterious(0.818)	HMMPfam_Filament
KRT85	3891	genome.wustl.edu	37	12	52760986	52760986	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002283.3	-1	reviewed	p.V68	0.001	85	0%	62	35.5%	0	-	-	-	-	NULL
KRT4	3851	genome.wustl.edu	37	12	53204577	53204577	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002272.2	-1	reviewed	p.R308H	0.909	63	0%	64	20.3%	0	-	possibly_damaging(0.905)	deleterious(0.05)	deleterious(0.705)	HMMPfam_Filament
KRT8	3856	genome.wustl.edu	37	12	53294418	53294418	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002273.3	-1	reviewed	p.E215V	1.000	80	0%	43	51.2%	600	44.6%	possibly_damaging(0.439)	deleterious(0)	deleterious(0.588)	superfamily_Prefoldin,HMMPfam_Filament
ZNF385A	25946	genome.wustl.edu	37	12	54769642	54769642	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130967.1	-1	validated	p.R82C	1.000	40	0%	39	30.8%	2	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00451,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355
ZBTB39	9880	genome.wustl.edu	37	12	57396904	57396904	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014830.1	-1	provisional	p.P600T	0.141	70	0%	47	44.7%	0	-	benign(0.001)	tolerated(1)	-	NULL
KIF5A	3798	genome.wustl.edu	37	12	57963868	57963868	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004984.2	+1	reviewed	p.V406M	1.000	23	0%	18	38.9%	0	-	possibly_damaging(0.822)	tolerated(0.27)	neutral(0.345)	NULL
SRGAP1	57522	genome.wustl.edu	37	12	64474113	64474113	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020762.2	+1	validated	p.Q457	1.000	134	0%	89	38.2%	0	-	-	-	-	NULL
TMBIM4	51643	genome.wustl.edu	37	12	66546086	66546086	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016056.2	-1	validated	p.K93E	1.000	164	0%	168	19.6%	25	24%	benign(0.003)	tolerated(0.09)	neutral(0.296)	HMMPfam_UPF0005
NUP107	57122	genome.wustl.edu	37	12	69128518	69128518	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020401.2	+1	reviewed	p.K765E	1.000	133	0%	85	28.2%	56	21.4%	benign(0.002)	tolerated(0.55)	neutral(0.007)	HMMPfam_Nup84_Nup100
HAL	3034	genome.wustl.edu	37	12	96384268	96384268	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002108.2	-1	reviewed	p.A253V	1.000	219	0%	165	44.2%	0	-	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMPfam_PAL,PatternScan_PAL_HISTIDASE,superfamily_L-Aspartase-like
TXNRD1	7296	genome.wustl.edu	37	12	104720179	104720179	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000429002	+1	known	p.V459I	0.975	21	0%	27	37%	2	50%	benign(0.001)	tolerated(0.41)	neutral(0.015)	HMMPfam_Pyr_redox_2,superfamily_FAD/NAD(P)-binding domain
IQCD	115811	genome.wustl.edu	37	12	113633535	113633535	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138451.1	-1	provisional	p.R297C	1.000	82	0%	78	35.9%	26	61.5%	probably_damaging(0.99)	deleterious(0.02)	deleterious(0.825)	HMMSmart_IQ
GCN1L1	10985	genome.wustl.edu	37	12	120572359	120572359	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006836.1	-1	validated	p.A2394T	0.250	37	0%	25	44%	11	18.1%	benign(0)	tolerated(1)	-	NULL
COQ5	84274	genome.wustl.edu	37	12	120954447	120954447	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032314.3	-1	validated	p.R166H	0.015	349	0%	275	47.3%	8	50%	benign(0.002)	tolerated(1)	-	HMMPfam_Ubie_methyltran,superfamily_S-adenosyl-L-methionine-dependent methyltransferases
MPHOSPH9	10198	genome.wustl.edu	37	12	123649857	123649857	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022782.2	-1	validated	p.T768N	0.063	250	0%	247	41.3%	0	-	benign(0.076)	deleterious(0.03)	neutral(0.370)	NULL
IFT88	8100	genome.wustl.edu	37	13	21212594	21212594	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_175605.3	+1	reviewed	p.A513T	1.000	240	0.4%	255	41.2%	4	75%	benign(0.037)	tolerated(0.25)	neutral(0.039)	HMMPfam_TPR_1,HMMSmart_SM00671,HMMSmart_SM00028,superfamily_TPR-like
LOC122038	122038	genome.wustl.edu	37	13	33528272	33528274	+	RNA	DEL	GCT	GCT	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	GCT	GCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_040920.1	-1	model	NULL	0.987:0.990:1.000	-	-	-	-	-	-	-	-	-	-
RFC3	5983	genome.wustl.edu	37	13	34404107	34404134	+	Frame_Shift_Del	DEL	CGTAGTAGGTGCTTGGCGGTTCGTGTGC	CGTAGTAGGTGCTTGGCGGTTCGTGTGC	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	CGTAGTAGGTGCTTGGCGGTTCGTGTGC	CGTAGTAGGTGCTTGGCGGTTCGTGTGC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002915.3	+1	reviewed	p.R176fs	1.000:1.000:0.967:1.000:1.000:0.942:0.953:1.000:0.989:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.988:0.991:0.995:0.875:1.000:1.000:0.880:1.000:1.000:0.993:1.000	-	-	-	-	-	-	-	-	-	HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases
AKAP11	11215	genome.wustl.edu	37	13	42876961	42876961	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016248.2	+1	reviewed	p.S1360N	0.009	177	0%	128	43%	0	-	benign(0.15)	tolerated(1)	neutral(0.013)	NULL
TSC22D1	8848	genome.wustl.edu	37	13	45148708	45148708	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_183422.2	-1	validated	p.Q501	0.000	89	0%	51	47.1%	3	66.6%	-	-	-	NULL
ZC3H13	23091	genome.wustl.edu	37	13	46553969	46553969	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015070.3	-1	validated	p.R631C	1.000	294	0%	194	41.2%	35	48.5%	unknown(0)	deleterious(0)	-	NULL
NEK5	341676	genome.wustl.edu	37	13	52676102	52676102	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_199289.1	-1	provisional	p.P287S	0.000	161	0%	115	31.3%	0	-	benign(0)	tolerated(0.4)	neutral(0.016)	superfamily_Kinase_like
MCF2L	23263	genome.wustl.edu	37	13	113739263	113739263	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001112732.1	+1	validated	p.L764M	1.000	35	0%	31	32.3%	8	0%	possibly_damaging(0.789)	deleterious(0.01)	deleterious(0.702)	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain)
TMCO3	55002	genome.wustl.edu	37	13	114149930	114149930	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017905.4	+1	validated	p.L12	0.100	32	0%	40	37.5%	1	100%	-	-	-	NULL
SALL2	6297	genome.wustl.edu	37	14	21992835	21992835	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005407.1	-1	validated	p.A343T	0.961	51	0%	43	48.8%	1	0%	benign(0.005)	tolerated(0.46)	neutral(0.012)	NULL
LRRC16B	90668	genome.wustl.edu	37	14	24529364	24529364	+	Splice_Site	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138360.3	+1	validated	e24-2	1.000	31	0%	23	47.8%	0	-	-	-	-	-
C14orf21	161424	genome.wustl.edu	37	14	24769849	24769850	+	In_Frame_Ins	INS	-	-	GAG	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_174913.1	+1	provisional	p.165in_frame_insE	0.000:0.015	-	-	-	-	-	-	-	-	-	superfamily_ARM-type_fold
GZMH	2999	genome.wustl.edu	37	14	25077580	25077580	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033423.3	-1	provisional	p.R32C	0.013	263	0%	217	51.2%	1	0%	probably_damaging(0.99)	deleterious(0.01)	deleterious(0.847)	HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys
STXBP6	29091	genome.wustl.edu	37	14	25443991	25443991	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014178.6	-1	provisional	p.F12I	1.000	36	0%	21	52.4%	45	51.1%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
KLHL28	54813	genome.wustl.edu	37	14	45403630	45403630	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017658.3	-1	validated	p.R344H	1.000	208	0%	150	38%	0	-	possibly_damaging(0.95)	tolerated(0.37)	neutral(0.413)	HMMPfam_Kelch_1,HMMSmart_SM00612,superfamily_Galactose oxidase central domain
KLHDC2	23588	genome.wustl.edu	37	14	50246335	50246335	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014315.2	+1	validated	p.A219V	1.000	99	0%	59	33.9%	19	31.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2
ARF6	382	genome.wustl.edu	37	14	50360872	50360872	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001663.3	+1	reviewed	p.G140C	1.000	63	0%	38	47.4%	57	49.1%	possibly_damaging(0.952)	deleterious(0)	deleterious(0.840)	HMMSmart_SM00175,HMMSmart_SM00178,HMMSmart_SM00177,HMMPfam_Arf,superfamily_P-loop containing nucleoside triphosphate hydrolases
TRIM9	114088	genome.wustl.edu	37	14	51561076	51561076	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015163.5	-1	reviewed	p.R194	1.000	28	0%	30	33.3%	1	0%	-	-	-	HMMSmart_SM00336
KIAA0586	9786	genome.wustl.edu	37	14	58953762	58953762	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014749.3	+1	validated	p.T985M	1.000	113	0%	115	46.1%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
VTI1B	10490	genome.wustl.edu	37	14	68126450	68126450	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006370.2	-1	validated	p.M122V	0.802	81	0%	79	40.5%	90	43.3%	benign(0)	tolerated(0.76)	neutral(0.001)	HMMPfam_V-SNARE
ESRRB	2103	genome.wustl.edu	37	14	76964698	76964698	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004452.3	+1	reviewed	p.R400Q	1.000	17	0%	19	57.9%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Hormone_recep,HMMSmart_HOLI,superfamily_Str_ncl_receptor
ADCK1	57143	genome.wustl.edu	37	14	78392234	78392234	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020421.3	+1	validated	p.C379Y	1.000	218	0%	176	23.9%	5	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
EML5	161436	genome.wustl.edu	37	14	89083152	89083152	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_183387.2	-1	validated	p.V1905A	0.999	155	0%	120	35.8%	0	-	probably_damaging(0.997)	tolerated(0.11)	deleterious(0.738)	HMMSmart_SM00320,superfamily_WD40 repeat-like
BAG5	9529	genome.wustl.edu	37	14	104026273	104026273	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001015049.1	-1	reviewed	p.D451G	1.000	102	0%	69	37.7%	2	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_BAG,HMMSmart_SM00264,superfamily_BAG domain
HERC2	8924	genome.wustl.edu	37	15	28506000	28506000	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004667.4	-1	reviewed	p.V747M	0.982	88	0%	86	40.7%	1	0%	benign(0.004)	tolerated(0.22)	neutral(0.042)	superfamily_RCC1/BLIP-II
ZNF770	54989	genome.wustl.edu	37	15	35275052	35275052	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014106.2	-1	validated	p.K195I	1.000	104	0%	65	44.6%	1	100%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667
MGA	23269	genome.wustl.edu	37	15	42003323	42003323	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080541.2	+1	validated	p.F954fs	0.080	-	-	-	-	-	-	-	-	-	NULL
GANC	2595	genome.wustl.edu	37	15	42602661	42602661	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198141.2	+1	reviewed	p.E301D	0.991	116	0%	107	43.9%	0	-	benign(0.001)	tolerated(0.24)	neutral(0.037)	NULL
FAM214A	56204	genome.wustl.edu	37	15	52902259	52902259	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019600.2	-1	validated	p.K284N	0.048	77	0%	57	38.6%	0	-	probably_damaging(0.981)	deleterious(0)	deleterious(0.870)	NULL
FAM63B	54629	genome.wustl.edu	37	15	59064436	59064436	+	Splice_Site	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001040450.1	+1	validated	e1+2	1.000	88	0%	57	28.1%	1	100%	-	-	-	-
HERC1	8925	genome.wustl.edu	37	15	63986651	63986651	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003922.3	-1	reviewed	p.N1780	0.928	197	0%	139	43.2%	0	-	-	-	-	NULL
CYP1A1	1543	genome.wustl.edu	37	15	75014822	75014822	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000499.3	-1	reviewed	p.R206H	1.000	74	0%	69	34.8%	0	-	benign(0.022)	tolerated(0.09)	neutral(0.297)	HMMPfam_p450,superfamily_Cytochrome P450
ETFA	2108	genome.wustl.edu	37	15	76577985	76577985	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000126.3	-1	reviewed	p.V219	0.973	238	0%	233	49.4%	25	32%	-	-	-	HMMPfam_ETF_alpha,superfamily_DHS-like NAD/FAD-binding domain
CHRNA3	1136	genome.wustl.edu	37	15	78894498	78894498	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000743.4	-1	reviewed	p.D162	0.997	191	0%	135	37%	2	50%	-	-	-	HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like,PatternScan_NEUROTR_ION_CHANNEL
MTHFS	10588	genome.wustl.edu	37	15	80137600	80137600	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006441.2	-1	validated	p.N188	0.012	289	0%	221	40.7%	101	42.5%	-	-	-	HMMPfam_5-FTHF_cyc-lig,superfamily_SSF100950
MAN2A2	4122	genome.wustl.edu	37	15	91455333	91455333	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006122.2	+1	validated	p.L724M	0.995	24	0%	34	47.1%	0	-	benign(0.007)	tolerated(0.13)	neutral(0.253)	superfamily_Gal_mut_like,HMMPfam_Glyco_hydro_38C
UNC45A	55898	genome.wustl.edu	37	15	91479620	91479620	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018671.3	+1	validated	p.V119A	1.000	19	0%	21	47.6%	0	-	benign(0.001)	tolerated(0.49)	neutral(0.011)	HMMPfam_TPR_2,HMMSmart_SM00028,superfamily_TPR-like
IGF1R	3480	genome.wustl.edu	37	15	99442775	99442775	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000875.3	+1	reviewed	p.R391H	1.000	111	0%	99	40.4%	0	-	possibly_damaging(0.762)	tolerated(0.07)	deleterious(0.601)	HMMPfam_Recep_L_domain,superfamily_SSF52058
IGF1R	3480	genome.wustl.edu	37	15	99500563	99500563	+	Silent	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000875.3	+1	reviewed	p.G1332	0.042	38	0%	23	17.4%	13	53.8%	-	-	-	NULL
ADAMTS17	170691	genome.wustl.edu	37	15	100649240	100649240	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139057.2	-1	reviewed	p.P657H	1.000	35	0%	28	32.1%	0	-	probably_damaging(0.999)	deleterious(0.02)	deleterious(0.873)	NULL
LUC7L	55692	genome.wustl.edu	37	16	249138	249138	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_201412.1	-1	validated	p.R204S	1.000	95	0%	72	27.8%	189	38.6%	probably_damaging(0.991)	tolerated(0.07)	deleterious(0.763)	HMMPfam_LUC7
DECR2	26063	genome.wustl.edu	37	16	456360	456360	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020664.3	+1	validated	p.T55M	0.990	12	0%	10	40%	7	71.4%	probably_damaging(1)	deleterious(0.03)	deleterious(0.865)	HMMPfam_adh_short,superfamily_NAD(P)-binding Rossmann-fold domains
TBC1D24	57465	genome.wustl.edu	37	16	2546986	2546986	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020705.1	+1	provisional	p.T279	0.000	36	0%	42	33.3%	1	0%	-	-	-	superfamily_RabGAP_TBC
ZSCAN10	84891	genome.wustl.edu	37	16	3142551	3142551	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032805.1	-1	provisional	p.G75W	0.845	9	0.000	11	0.727	0	-	probably_damaging(0.973)	deleterious(0)	deleterious(0.859)	HMMPfam_SCAN,HMMSmart_SCAN
SLX4	84464	genome.wustl.edu	37	16	3647844	3647844	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032444.2	-1	provisional	p.A440	0.000	30	0%	24	41.7%	0	-	-	-	-	NULL
UBN1	29855	genome.wustl.edu	37	16	4903005	4903005	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001079514.1	+1	validated	p.A29	0.039	54	0%	65	47.7%	0	-	-	-	-	NULL
KIAA0430	9665	genome.wustl.edu	37	16	15733069	15733069	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014647.3	-1	validated	p.E8K	1.000	317	0%	227	42.7%	3	100%	possibly_damaging(0.615)	tolerated(0.07)	deleterious(0.532)	NULL
NOMO2	283820	genome.wustl.edu	37	16	18549884	18549884	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004060.1	-1	reviewed	p.P395L	1.000	477	0%	307	35.8%	1	0%	probably_damaging(0.999)	tolerated(1)	deleterious(0.490)	superfamily_Starch-binding domain-like
TMC5	79838	genome.wustl.edu	37	16	19498568	19498568	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001105248.1	+1	validated	p.Q831H	1.000	142	0%	127	45.7%	3	66.6%	possibly_damaging(0.815)	tolerated(0.52)	neutral(0.316)	NULL
ERI2	112479	genome.wustl.edu	37	16	20812683	20812683	+	Splice_Site	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142725.1	-1	validated	e5-2	0.990	169	0%	141	36.9%	0	-	-	-	-	-
ANKS4B	257629	genome.wustl.edu	37	16	21245068	21245068	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145865.2	+1	validated	p.R4C	1.000	258	0%	215	40%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_Ankyrin repeat
GTF3C1	2975	genome.wustl.edu	37	16	27497391	27497391	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001520.3	-1	validated	p.R1262H	0.999	180	0%	158	38%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
ZNF267	10308	genome.wustl.edu	37	16	31926579	31926579	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003414.4	+1	validated	p.L337I	0.362	402	0%	259	47.9%	0	-	benign(0.353)	deleterious(0.01)	deleterious(0.517)	HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
CES1	1066	genome.wustl.edu	37	16	55855389	55855389	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001025195.1	-1	reviewed	p.Q195R	1.000	55	0%	52	50%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_COesterase,superfamily_SSF53474
KIFC3	3801	genome.wustl.edu	37	16	57803524	57803524	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005550.3	-1	validated	p.R401G	0.004	10	0%	12	41.7%	4	50%	benign(0.001)	tolerated(0.46)	neutral(0.012)	superfamily_P-loop containing nucleoside triphosphate hydrolases
NAE1	8883	genome.wustl.edu	37	16	66850556	66850556	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003905.3	-1	reviewed	p.N256	1.000	98	0%	96	30.2%	10	60%	-	-	-	superfamily_Activating enzymes of the ubiquitin-like proteins
KIAA0895L	653319	genome.wustl.edu	37	16	67210794	67210794	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001040715.1	-1	validated	p.R446C	0.918	215	0%	203	40.9%	68	48.5%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	NULL
KIAA0895L	653319	genome.wustl.edu	37	16	67213752	67213752	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001040715.1	-1	validated	p.R227H	1.000	116	0%	95	42.1%	6	16.6%	probably_damaging(0.984)	deleterious(0.04)	deleterious(0.779)	NULL
GFOD2	81577	genome.wustl.edu	37	16	67709514	67709515	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	AC	AC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030819.3	-1	validated	p.C234fs	0.992:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_GFO_IDH_MocA_C,superfamily_Glyceraldehyde-3-phosphate dehydrogenase-like C-terminal domain
PSMB10	5699	genome.wustl.edu	37	16	67968568	67968568	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002801.2	-1	reviewed	p.G239	0.000	145	0%	106	40.6%	684	40.6%	-	-	-	superfamily_N-terminal nucleophile aminohydrolases (Ntn hydrolases)
SMPD3	55512	genome.wustl.edu	37	16	68405139	68405139	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018667.3	-1	validated	p.E316K	0.959	17	0%	20	30%	0	-	benign(0.237)	tolerated(0.79)	neutral(0.025)	NULL
ZFHX3	463	genome.wustl.edu	37	16	72828912	72828913	+	Frame_Shift_Del	DEL	GC	GC	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	GC	GC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006885.3	-1	reviewed	p.Q2557fs	1.000:0.725	-	-	-	-	-	-	-	-	-	superfamily_C2H2 and C2HC zinc fingers
GLG1	2734	genome.wustl.edu	37	16	74486002	74486002	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012201.5	-1	validated	p.A1188	0.000	46	0%	41	43.9%	655	43.3%	-	-	-	NULL
CHST5	23563	genome.wustl.edu	37	16	75563999	75563999	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024533.3	-1	validated	p.A95V	0.914	29	0%	20	40%	0	-	probably_damaging(0.993)	tolerated(0.33)	deleterious(0.474)	HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases
CDH13	1012	genome.wustl.edu	37	16	83711856	83711856	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001257.3	+1	reviewed	p.K443R	1.000	49	0%	50	42%	0	-	probably_damaging(0.998)	tolerated(0.39)	deleterious(0.490)	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
RNMTL1	55178	genome.wustl.edu	37	17	686504	686504	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018146.2	+1	provisional	p.I166V	1.000	90	0%	51	35.3%	5	60%	benign(0.015)	deleterious(0)	neutral(0.445)	HMMPfam_SpoU_sub_bind,superfamily_SSF55315
NLRP1	22861	genome.wustl.edu	37	17	5445178	5445178	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033004.3	-1	reviewed	p.Q900*	0.002	118	0%	101	41.6%	3	66.6%	-	-	-	HMMSmart_SM00368,superfamily_RNI-like
DNAH2	146754	genome.wustl.edu	37	17	7681677	7681677	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020877.2	+1	validated	p.E1811K	1.000	66	0%	69	53.6%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases
ARHGEF15	22899	genome.wustl.edu	37	17	8215628	8215628	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173728.2	+1	reviewed	p.P91S	0.981	108	0%	97	38.1%	0	-	possibly_damaging(0.771)	deleterious(0)	deleterious(0.731)	NULL
MYH8	4626	genome.wustl.edu	37	17	10315784	10315784	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002472.2	-1	reviewed	p.L440P	1.000	615	0%	448	42.4%	0	-	probably_damaging(0.991)	tolerated(0.27)	deleterious(0.478)	HMMPfam_Myosin_head,HMMSmart_MYSc,superfamily_SSF52540
MAP2K4	6416	genome.wustl.edu	37	17	12044469	12044469	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003010.2	+1	reviewed	p.H364	1.000	144	0%	122	49.2%	2	50%	-	-	-	HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase
MYOCD	93649	genome.wustl.edu	37	17	12639554	12639554	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153604.2	+1	reviewed	p.P164	0.901	308	0%	284	45.1%	0	-	-	-	-	NULL
MPRIP	23164	genome.wustl.edu	37	17	17083923	17083923	+	Silent	SNP	C	C	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000414263	+1	known	p.P1082R	1.000	113	0%	85	34.1%	32	9.3%	-	-	-	NULL
SPAG5	10615	genome.wustl.edu	37	17	26919200	26919200	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006461.3	-1	reviewed	p.V354	0.976	103	0%	86	39.5%	8	37.5%	-	-	-	NULL
TRAF4	9618	genome.wustl.edu	37	17	27076536	27076536	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004295.3	+1	reviewed	p.R452W	1.000	28	0%	20	60%	277	59.2%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_MATH,superfamily_TRAF domain-like
ENSG00000226049	0	genome.wustl.edu	37	17	32364804	32364804	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000430493	-1	known	p.R639*	0.997	129	0%	100	40%	1	0%	-	-	-	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase
TMEM132E	124842	genome.wustl.edu	37	17	32964757	32964757	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_207313.1	+1	provisional	p.V821I	0.722	18	0%	22	40.9%	0	-	probably_damaging(0.987)	tolerated(0.13)	deleterious(0.689)	NULL
LIG3	3980	genome.wustl.edu	37	17	33328351	33328351	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013975.2	+1	reviewed	p.R803*	1.000	77	0%	60	36.7%	18	22.2%	-	-	-	NULL
RAD51D	5892	genome.wustl.edu	37	17	33445607	33445607	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002878.3	-1	reviewed	p.A59D	1.000	61	0%	48	50%	1	0%	probably_damaging(0.983)	deleterious(0)	deleterious(0.873)	HMMPfam_HhH-GPD
GAS2L2	246176	genome.wustl.edu	37	17	34073153	34073153	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139285.2	-1	validated	p.P455S	0.212	53	0%	40	45%	0	-	benign(0.013)	tolerated(0.6)	neutral(0.005)	NULL
C17orf98	388381	genome.wustl.edu	37	17	36997552	36997552	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080465.2	-1	validated	p.R31C	0.000	53	0%	48	35.4%	0	-	possibly_damaging(0.921)	deleterious(0.01)	deleterious(0.776)	NULL
TOP2A	7153	genome.wustl.edu	37	17	38555153	38555153	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001067.2	-1	reviewed	p.E1109K	0.999	129	0.8%	91	48.4%	4	50%	benign(0.003)	tolerated(0.27)	neutral(0.034)	HMMPfam_DNA_topoisoIV,HMMSmart_SM00434,superfamily_Type II DNA topoisomerase
KRTAP9-9	81870	genome.wustl.edu	37	17	39411768	39411768	+	Splice_Site	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000431129	+1	known	e2-2	0.201	398	0%	296	47.3%	0	-	-	-	-	-
KRT19	3880	genome.wustl.edu	37	17	39680132	39680132	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002276.4	-1	reviewed	p.S356G	0.825	42	0%	26	34.6%	4978	48.4%	benign(0.025)	deleterious(0)	neutral(0.446)	HMMPfam_Filament
STAT3	6774	genome.wustl.edu	37	17	40485756	40485756	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139276.2	-1	reviewed	p.C328	1.000	35	0%	36	25%	4	50%	-	-	-	superfamily_p53-like transcription factors,HMMPfam_STAT_bind
KANSL1	284058	genome.wustl.edu	37	17	44144966	44144966	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015443.2	-1	validated	p.L534P	0.940	179	0%	138	36.2%	1	0%	possibly_damaging(0.852)	tolerated(0.19)	neutral(0.377)	NULL
XYLT2	64132	genome.wustl.edu	37	17	48434462	48434462	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022167.2	+1	reviewed	p.Y597C	1.000	30	0%	25	48%	5	60%	probably_damaging(0.993)	tolerated(0.07)	deleterious(0.769)	NULL
CACNA1G	8913	genome.wustl.edu	37	17	48667850	48667850	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018896.3	+1	validated	p.A774T	1.000	155	0%	99	32.3%	0	-	probably_damaging(0.977)	tolerated(0.27)	neutral(0.453)	superfamily_Voltage-gated potassium channels
MPO	4353	genome.wustl.edu	37	17	56356957	56356957	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000250.1	-1	reviewed	p.A159T	0.998	19	0%	23	47.8%	0	-	benign(0.027)	tolerated(0.62)	neutral(0.005)	NULL
BZRAP1	9256	genome.wustl.edu	37	17	56385265	56385265	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004758.2	-1	validated	p.S1590Y	0.663	15	0%	10	40%	18	11.1%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	NULL
BRIP1	83990	genome.wustl.edu	37	17	59885948	59885948	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032043.1	-1	reviewed	p.T266	0.994	201	0%	172	46.5%	0	-	-	-	-	HMMSmart_SM00488,HMMPfam_DEAD_2,HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases
HELZ	9931	genome.wustl.edu	37	17	65103751	65103751	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014877.3	-1	validated	p.R1592Q	1.000	239	0%	199	43.7%	0	-	unknown(0)	deleterious(0.02)	-	NULL
ABCA10	10349	genome.wustl.edu	37	17	67150143	67150143	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080282.3	-1	reviewed	p.L1265S	0.007	212	0%	176	11.9%	0	-	probably_damaging(0.975)	deleterious(0)	deleterious(0.861)	HMMPfam_ABC_tran,HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases
SDK2	54549	genome.wustl.edu	37	17	71364671	71364671	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001144952.1	-1	provisional	p.A1681V	1.000	12	0%	19	31.6%	0	-	benign(0.004)	tolerated(0.07)	neutral(0.319)	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
SLC16A5	9121	genome.wustl.edu	37	17	73096323	73096323	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004695.2	+1	provisional	p.I189V	0.959	47	0%	53	37.7%	6	83.3%	benign(0)	deleterious(0)	neutral(0.445)	HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter
RNF213	57674	genome.wustl.edu	37	17	78360648	78360648	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000508628	+1	known	p.I4960T	0.192	19	0%	30	33.3%	4	0%	benign(0.315)	deleterious(0.02)	deleterious(0.482)	NULL
FASN	2194	genome.wustl.edu	37	17	80041083	80041083	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004104.4	-1	reviewed	p.V1854L	0.022	8	0.000	11	0.455	20	50%	benign(0)	tolerated(0.55)	neutral(0.007)	NULL
THOC1	9984	genome.wustl.edu	37	18	216591	216591	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005131.2	-1	validated	p.L499	0.044	287	0%	231	42.9%	49	55.1%	-	-	-	NULL
LOC646359	646359	genome.wustl.edu	37	18	14378440	14378440	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_929288.3	-1	model	p.T108M	0.012	112	0%	90	42.2%	0	-	-	-	-	HMMPfam_TRF,superfamily_Telomeric repeat binding factor (TRF) dimerisation domain
C18orf8	29919	genome.wustl.edu	37	18	21099098	21099098	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013326.3	+1	validated	p.V270A	1.000	96	1%	70	47.1%	2	50%	possibly_damaging(0.938)	deleterious(0.03)	deleterious(0.748)	NULL
LAMA3	3909	genome.wustl.edu	37	18	21396448	21396448	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198129.1	+1	reviewed	p.Q715R	1.000	26	0%	32	34.4%	0	-	benign(0.006)	tolerated(0.51)	neutral(0.009)	HMMPfam_Laminin_EGF,HMMSmart_SM00180,superfamily_EGF/Laminin
ZNF521	25925	genome.wustl.edu	37	18	22804943	22804943	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015461.2	-1	validated	p.T980M	1.000	233	0%	183	44.8%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
DSC1	1823	genome.wustl.edu	37	18	28714669	28714669	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024421.2	-1	reviewed	p.V581A	0.652	75	0%	39	46.2%	0	-	benign(0.041)	tolerated(0.6)	neutral(0.007)	HMMPfam_Cadherin,superfamily_Cadherin-like
B4GALT6	9331	genome.wustl.edu	37	18	29210978	29210978	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004775.3	-1	reviewed	p.Y240	0.340	309	0%	239	38.1%	0	-	-	-	-	HMMPfam_Galactosyl_T_2,superfamily_SSF53448
DCC	1630	genome.wustl.edu	37	18	50683792	50683792	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005215.3	+1	reviewed	p.R443Q	1.000	344	0%	329	41%	0	-	probably_damaging(0.987)	deleterious(0)	deleterious(0.881)	HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
MC4R	4160	genome.wustl.edu	37	18	58038893	58038893	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005912.2	-1	reviewed	p.P230	0.001	185	0%	132	42.4%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
ADNP2	22850	genome.wustl.edu	37	18	77896075	77896075	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014913.3	+1	validated	p.T927A	1.000	77	0%	68	30.9%	5	20%	probably_damaging(0.959)	deleterious(0.01)	deleterious(0.808)	NULL
KDM4B	23030	genome.wustl.edu	37	19	5033005	5033005	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015015.2	+1	validated	p.I35K	1.000	59	0%	52	44.2%	0	-	benign(0.293)	deleterious(0)	deleterious(0.535)	HMMPfam_JmjN,HMMSmart_SM00545
XAB2	56949	genome.wustl.edu	37	19	7686072	7686072	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020196.2	-1	validated	p.R577W	0.933	10	0%	10	50%	64	43.7%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_HAT,superfamily_SSF48452
C19orf59	199675	genome.wustl.edu	37	19	7742554	7742554	+	Silent	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_174918.2	+1	reviewed	p.T42	1.000	88	0%	78	37.2%	0	-	-	-	-	NULL
TYK2	7297	genome.wustl.edu	37	19	10476448	10476448	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003331.4	-1	reviewed	p.Q252	0.033	15	0%	10	70%	2	50%	-	-	-	HMMSmart_B41
ZNF20	7568	genome.wustl.edu	37	19	12244737	12244737	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021143.2	-1	validated	p.Q88	0.000	430	0%	301	43.9%	1	100%	-	-	-	NULL
ZNF563	147837	genome.wustl.edu	37	19	12433415	12433415	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145276.2	-1	validated	p.R38	0.084	158	0%	100	39%	2	50%	-	-	-	HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352)
AKAP8L	26993	genome.wustl.edu	37	19	15510131	15510131	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014371.2	-1	validated	p.R380Q	1.000	27	0%	26	38.5%	90	52.2%	probably_damaging(0.994)	tolerated(0.07)	deleterious(0.771)	NULL
OR10H5	284433	genome.wustl.edu	37	19	15905717	15905717	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004466.1	+1	provisional	p.S287G	0.993	199	0.5%	134	45.5%	0	-	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	HMMPfam_7tm_1,superfamily_SSF81321
CERS1	10715	genome.wustl.edu	37	19	18990092	18990092	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021267.3	-1	reviewed	p.A286	0.002	17	0%	16	43.8%	43	41.8%	-	-	-	HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724
ZNF90	7643	genome.wustl.edu	37	19	20229666	20229666	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007138.1	+1	validated	p.K435E	0.027	226	0%	128	45.3%	0	-	benign(0.253)	tolerated(0.41)	neutral(0.041)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667
CCNE1	898	genome.wustl.edu	37	19	30311680	30311680	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001238.1	+1	reviewed	p.A178	1.000	33	0%	32	12.5%	1	0%	-	-	-	HMMSmart_SM00385,HMMPfam_Cyclin_N,superfamily_Cyclin-like
THAP8	199745	genome.wustl.edu	37	19	36530946	36530946	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152658.2	-1	provisional	p.S59N	0.981	21	0%	30	50%	4	0%	probably_damaging(0.978)	deleterious(0.03)	deleterious(0.785)	HMMPfam_THAP,HMMSmart_DM3
CEACAM5	1048	genome.wustl.edu	37	19	42223893	42223893	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004363.2	+1	validated	p.V513M	0.000	281	0%	233	38.2%	0	-	benign(0.345)	tolerated(0.07)	neutral(0.428)	HMMSmart_SM00409,superfamily_Immunoglobulin
RTN2	6253	genome.wustl.edu	37	19	45997944	45997944	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005619.3	-1	reviewed	p.S133	0.000	33	0%	29	51.7%	1	0%	-	-	-	NULL
PNMAL2	57469	genome.wustl.edu	37	19	46997631	46997631	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020709.1	-1	validated	p.D364	0.001	93	0%	47	40.4%	0	-	-	-	-	NULL
CCDC114	93233	genome.wustl.edu	37	19	48800674	48800674	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144577.3	-1	validated	p.Q524	0.000	15	0%	21	38.1%	19	47.3%	-	-	-	NULL
KCNA7	3743	genome.wustl.edu	37	19	49574060	49574060	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031886.2	-1	reviewed	p.V211M	0.976	29	0%	20	35%	0	-	benign(0.004)	tolerated(0.33)	neutral(0.024)	superfamily_SSF81324
TRPM4	54795	genome.wustl.edu	37	19	49671309	49671309	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017636.2	+1	provisional	p.Q135*	1.000	29	0%	23	52.2%	4	75%	-	-	-	NULL
SIGLEC12	89858	genome.wustl.edu	37	19	52000673	52000673	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_053003.2	-1	reviewed	p.T478A	0.000	122	0%	106	47.2%	0	-	benign(0.016)	tolerated(0.29)	neutral(0.030)	NULL
HAS1	3036	genome.wustl.edu	37	19	52222539	52222539	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001523.2	-1	reviewed	p.V208M	1.000	69	0%	36	25%	0	-	possibly_damaging(0.903)	deleterious(0)	deleterious(0.802)	superfamily_SSF53448
FPR1	2357	genome.wustl.edu	37	19	52249306	52249306	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002029.3	-1	validated	p.H314	0.786	229	0%	173	44.5%	0	-	-	-	-	superfamily_Family A G protein-coupled receptor-like
ZNF808	388558	genome.wustl.edu	37	19	53057769	53057769	+	Missense_Mutation	SNP	A	A	G	rs144248619	by1000genomes	TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001039886.3	+1	validated	p.T534A	0.989	724	0%	426	35.9%	0	-	benign(0.032)	tolerated(0.11)	neutral(0.273)	superfamily_C2H2 and C2HC zinc fingers
CCDC106	29903	genome.wustl.edu	37	19	56162699	56162699	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013301.2	+1	validated	p.R122C	0.351	18	0%	11	36.4%	94	51%	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	NULL
ZSCAN1	284312	genome.wustl.edu	37	19	58565340	58565340	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_182572.3	+1	validated	p.S383I	0.873	28	0%	27	40.7%	0	-	possibly_damaging(0.726)	deleterious(0.02)	deleterious(0.647)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
NOP56	10528	genome.wustl.edu	37	20	2638866	2638866	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006392.2	+1	reviewed	p.G571W	0.067	31	0%	51	51%	147	53%	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	NULL
PRND	23627	genome.wustl.edu	37	20	4705357	4705357	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012409.2	+1	reviewed	p.N54D	0.062	53	0%	45	44.4%	0	-	benign(0.032)	tolerated(0.34)	neutral(0.025)	superfamily_Prion-like
FAM83C	128876	genome.wustl.edu	37	20	33875192	33875192	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178468.4	-1	validated	p.R464W	0.137	36	0%	28	39.3%	0	-	probably_damaging(0.992)	deleterious(0)	deleterious(0.892)	NULL
PLCG1	5335	genome.wustl.edu	37	20	39792735	39792735	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002660.2	+1	reviewed	p.G371S	1.000	117	0%	93	40.9%	9	33.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_PI-PLC-X,HMMSmart_PLCXc,superfamily_PLC-like_Pdiesterase_TIM-brl
C20orf111	51526	genome.wustl.edu	37	20	42826354	42826354	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016470.6	-1	provisional	p.A73T	1.000	161	0%	103	38.8%	11	54.5%	benign(0.002)	tolerated(0.19)	neutral(0.050)	HMMPfam_DUF776
PLTP	5360	genome.wustl.edu	37	20	44527599	44527599	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006227.2	-1	reviewed	p.P488L	0.006	45	0%	36	41.7%	1521	44.6%	unknown(0)	tolerated(0.22)	-	NULL
SALL4	57167	genome.wustl.edu	37	20	50407849	50407849	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020436.3	-1	reviewed	p.F391L	0.998	83	0%	90	35.6%	2	0%	probably_damaging(0.998)	tolerated(0.07)	deleterious(0.793)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2
BMP7	655	genome.wustl.edu	37	20	55803352	55803352	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001719.2	-1	reviewed	p.R182W	1.000	186	0%	191	49.2%	0	-	possibly_damaging(0.836)	deleterious(0.02)	deleterious(0.703)	HMMPfam_TGFb_propeptide
CDH4	1002	genome.wustl.edu	37	20	60448937	60448937	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001794.2	+1	reviewed	p.A344V	1.000	17	0%	28	35.7%	0	-	probably_damaging(0.994)	tolerated(0.06)	deleterious(0.774)	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
PRPF6	24148	genome.wustl.edu	37	20	62626421	62626421	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012469.3	+1	reviewed	p.H197	0.993	144	0%	136	36.8%	6	33.3%	-	-	-	NULL
PRPF6	24148	genome.wustl.edu	37	20	62632577	62632577	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012469.3	+1	reviewed	p.R391W	1.000	66	0%	38	34.2%	17	58.8%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMSmart_HAT,superfamily_SSF48452
USP16	10600	genome.wustl.edu	37	21	30403007	30403007	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001032410.1	+1	reviewed	p.C51	1.000	111	0%	106	44.3%	0	-	-	-	-	HMMPfam_zf-UBP,HMMSmart_SM00290
WRB	7485	genome.wustl.edu	37	21	40765168	40765168	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004627.4	+1	reviewed	p.P138H	1.000	115	0%	96	38.5%	10	50%	unknown(0)	-	-	HMMPfam_CHD5
MX1	4599	genome.wustl.edu	37	21	42807786	42807786	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001144925.1	+1	reviewed	p.S43N	0.978	76	0%	73	43.8%	11	45.4%	benign(0.202)	tolerated(0.14)	neutral(0.269)	NULL
TRAPPC10	7109	genome.wustl.edu	37	21	45507714	45507714	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003274.4	+1	reviewed	p.G892R	0.000	66	0%	59	45.8%	1	0%	benign(0.001)	tolerated(0.81)	neutral(0.001)	NULL
KRTAP10-4	386672	genome.wustl.edu	37	21	45994008	45994008	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198687.1	+1	reviewed	p.C125S	0.665	343	0%	266	32.3%	0	-	unknown(0)	tolerated(0.4)	-	NULL
PPM1F	9647	genome.wustl.edu	37	22	22300346	22300346	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014634.2	-1	reviewed	p.T25	0.000	21	0%	32	53.1%	0	-	-	-	-	NULL
IGLV7-46	28775	genome.wustl.edu	37	22	22724027	22724027	+	Silent	SNP	T	T	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000390295	+1	known	p.T4	0.000	19	0%	21	33.3%	0	-	-	-	-	NULL
EWSR1	2130	genome.wustl.edu	37	22	29674198	29674198	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005243.3	+1	reviewed	p.P136S	1.000	70	0%	58	34.5%	18	38.8%	unknown(0)	tolerated(0.3)	-	NULL
LARGE	9215	genome.wustl.edu	37	22	34022286	34022286	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004737.4	-1	reviewed	p.A145T	1.000	93	0%	62	46.8%	0	-	possibly_damaging(0.54)	deleterious(0.01)	deleterious(0.589)	HMMPfam_Glyco_transf_8,superfamily_Nucleotide-diphospho-sugar transferases
APOL2	23780	genome.wustl.edu	37	22	36624081	36624081	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030882.2	-1	reviewed	p.G128D	0.833	174	0%	85	35.3%	2	0%	possibly_damaging(0.47)	tolerated(0.1)	neutral(0.442)	HMMPfam_ApoL
ADSL	158	genome.wustl.edu	37	22	40759064	40759064	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000026.2	+1	reviewed	p.V364M	1.000	169	0%	131	35.1%	171	27.4%	possibly_damaging(0.941)	deleterious(0)	deleterious(0.831)	superfamily_L-aspartase-like
PACSIN2	11252	genome.wustl.edu	37	22	43289518	43289518	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007229.3	-1	reviewed	p.A54	0.548	33	0%	16	75%	2	50%	-	-	-	HMMPfam_FCH,HMMSmart_SM00055
PKDREJ	10343	genome.wustl.edu	37	22	46656706	46656706	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006071.1	-1	reviewed	p.S838	0.925	41	0%	36	30.6%	0	-	-	-	-	NULL
ENSG00000210082	0	genome.wustl.edu	37	MT	2022	2022	+	RNA	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387347	+1	known	NULL	NULL	36	0%	10	100%	7075	89.7%	-	-	-	-
ENSG00000198888	0	genome.wustl.edu	37	MT	4216	4216	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000361390	+1	known	p.Y304H	NULL	66	0%	28	14.3%	7104	0%	benign(0.001)	tolerated(0.91)	-	HMMPfam_NADHdh
SHROOM2	357	genome.wustl.edu	37	X	9912900	9912900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001649.2	+1	reviewed	p.R1511W	1.000	39	0%	24	58.3%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_ASD2
CDKL5	6792	genome.wustl.edu	37	X	18616707	18616707	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001037343.1	+1	reviewed	p.H317	0.969	251	0.4%	191	44.5%	0	-	-	-	-	superfamily_Kinase_like
KLHL34	257240	genome.wustl.edu	37	X	21674198	21674198	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153270.1	-1	provisional	p.E570A	0.997	19	0.000	7	0.571	0	-	probably_damaging(0.963)	tolerated(0.19)	neutral(0.455)	HMMSmart_Kelch,superfamily_Gal_oxid_central
FAM48B2	170067	genome.wustl.edu	37	X	24329623	24329623	+	Missense_Mutation	SNP	C	C	T	rs184929479	by1000genomes	TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001136233.1	-1	provisional	p.A604T	0.000	58	0%	50	54%	0	-	-	-	-	NULL
POLA1	5422	genome.wustl.edu	37	X	24861772	24861772	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016937.3	+1	reviewed	p.R1336H	1.000	97	0%	72	38.9%	3	0%	probably_damaging(0.973)	tolerated(0.05)	deleterious(0.760)	HMMPfam_zf-DNA_Pol
DDX3X	1654	genome.wustl.edu	37	X	41201791	41201791	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001356.3	+1	reviewed	p.R110C	1.000	152	0%	105	34.3%	5	20%	probably_damaging(0.997)	deleterious(0.02)	deleterious(0.849)	NULL
UBA1	7317	genome.wustl.edu	37	X	47062184	47062184	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003334.3	+1	reviewed	p.G402W	1.000	39	0%	25	56%	28	17.8%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_MoeB
TIMP1	7076	genome.wustl.edu	37	X	47442935	47442935	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003254.2	+1	reviewed	p.V41I	0.986	65	0%	53	43.4%	635	0%	probably_damaging(0.976)	deleterious(0.01)	deleterious(0.824)	HMMPfam_TIMP,HMMSmart_SM00206,superfamily_TIMP-like
HDAC6	10013	genome.wustl.edu	37	X	48675000	48675000	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006044.2	+1	reviewed	p.G584D	0.993	24	0%	26	42.3%	5	80%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Hist_deacetyl,superfamily_SSF52768
TSPYL2	64061	genome.wustl.edu	37	X	53112308	53112308	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022117.3	+1	reviewed	p.E210K	0.507	33	0%	27	29.6%	11	0%	possibly_damaging(0.452)	tolerated(0.16)	neutral(0.207)	NULL
PHF8	23133	genome.wustl.edu	37	X	54037692	54037692	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015107.2	-1	reviewed	p.R270H	0.989	182	0%	136	43.4%	0	-	possibly_damaging(0.435)	tolerated(0.17)	neutral(0.201)	HMMSmart_SM00558,HMMPfam_JmjC,superfamily_Clavaminate synthase-like
APEX2	27301	genome.wustl.edu	37	X	55028709	55028709	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014481.2	+1	reviewed	p.N89	0.001	57	0%	41	22%	0	-	-	-	-	HMMPfam_Exo_endo_phos,superfamily_Exo_endo_phos
FAM123B	139285	genome.wustl.edu	37	X	63411272	63411272	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152424.3	-1	reviewed	p.E632V	0.088	106	0%	99	33.3%	0	-	possibly_damaging(0.919)	deleterious(0)	deleterious(0.814)	NULL
OPHN1	4983	genome.wustl.edu	37	X	67652807	67652807	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002547.2	-1	reviewed	p.R19H	1.000	46	0%	29	48.3%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
GDPD2	54857	genome.wustl.edu	37	X	69645624	69645624	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017711.3	+1	reviewed	p.R74H	0.001	58	0%	61	36.1%	1	0%	benign(0.016)	tolerated(0.14)	neutral(0.250)	NULL
ZMYM3	9203	genome.wustl.edu	37	X	70461176	70461176	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005096.3	-1	reviewed	p.R1274Q	1.000	92	0%	73	46.6%	7	0%	probably_damaging(0.975)	deleterious(0.01)	deleterious(0.823)	NULL
TBX22	50945	genome.wustl.edu	37	X	79281115	79281115	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001109878.1	+1	reviewed	p.S158G	1.000	109	0%	96	34.4%	2	0%	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	HMMPfam_T-box,HMMSmart_TBOX,superfamily_P53_like_DNA_bnd
CYLC1	1538	genome.wustl.edu	37	X	83126482	83126482	+	Silent	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021118.1	+1	provisional	p.S27	0.072	119	0%	119	46.2%	0	-	-	-	-	NULL
CYLC1	1538	genome.wustl.edu	37	X	83129608	83129608	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021118.1	+1	provisional	p.P631H	0.577	255	0%	286	33.9%	0	-	unknown(0)	deleterious(0)	-	NULL
NXF5	55998	genome.wustl.edu	37	X	101095986	101095986	+	Splice_Site	SNP	A	A	G	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032946.2	-1	reviewed	e6+2	0.950	735	0%	638	39.8%	0	-	-	-	-	-
ESX1	80712	genome.wustl.edu	37	X	103499131	103499131	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153448.3	-1	reviewed	p.D70	0.000	56	0%	65	47.7%	0	-	-	-	-	NULL
IL1RAPL2	26280	genome.wustl.edu	37	X	104440222	104440222	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017416.1	+1	reviewed	p.R50*	0.990	406	0%	283	46.6%	0	-	-	-	-	HMMSmart_SM00409,superfamily_Immunoglobulin
ALG13	79868	genome.wustl.edu	37	X	110987996	110987996	+	Silent	SNP	A	A	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000394780	+1	known	p.P932	0.007	22	0%	22	36.4%	1	0%	-	-	-	NULL
RNF113A	7737	genome.wustl.edu	37	X	119005256	119005256	+	Silent	SNP	T	T	C	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006978.2	-1	reviewed	p.K107	0.994	274	0%	231	44.2%	13	0%	-	-	-	NULL
CT47B1	643311	genome.wustl.edu	37	X	120009264	120009264	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145718.1	-1	validated	p.I87	0.000	28	0%	35	48.6%	0	-	-	-	-	NULL
THOC2	57187	genome.wustl.edu	37	X	122754770	122754770	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000432353	-1	known	p.P157H	1.000	600	0%	544	36%	7	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
FAM127B	26071	genome.wustl.edu	37	X	134186007	134186007	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001078172.1	-1	validated	p.I44	1.000	78	0%	100	48%	129	0%	-	-	-	NULL
RBMX	27316	genome.wustl.edu	37	X	135961586	135961588	+	In_Frame_Del	DEL	TGT	TGT	-	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	TGT	TGT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002139.3	-1	reviewed	p.MVEA1in_frame_delWLK	1.000	-	-	-	-	-	-	-	-	-	NULL
MAGEC1	9947	genome.wustl.edu	37	X	140994185	140994185	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005462.4	+1	reviewed	p.G332D	0.021	1121	0%	985	45.3%	0	-	unknown(0)	tolerated(0.15)	-	NULL
CNGA2	1260	genome.wustl.edu	37	X	150911739	150911739	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LD-01	TCGA-AP-A0LD-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005140.1	+1	reviewed	p.R255H	1.000	304	0%	301	47.2%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Ion_trans,superfamily_SSF81324
