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
SGIP1	84251	genome.wustl.edu	37	1	67206363	67206363	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032291.2	+1	validated	p.L753M	1.000	25	0%	48	22.9%	1	0%	probably_damaging(0.996)	deleterious(0.04)	deleterious(0.810)	NULL
ST6GALNAC3	256435	genome.wustl.edu	37	1	76877834	76877834	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152996.2	+1	validated	p.V119I	1.000	313	0%	429	35%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Glyco_transf_29
SETDB1	9869	genome.wustl.edu	37	1	150936496	150936496	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145415.1	+1	reviewed	p.V1232G	1.000	120	0%	148	43.2%	52	63.4%	probably_damaging(0.995)	deleterious(0.05)	deleterious(0.803)	HMMPfam_SET,HMMSmart_SM00317,superfamily_SET domain
GABPB2	126626	genome.wustl.edu	37	1	151090500	151090500	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144618.2	+1	validated	p.R372Q	1.000	110	0%	123	41.5%	2	0%	possibly_damaging(0.949)	deleterious(0)	deleterious(0.838)	NULL
LAMC1	3915	genome.wustl.edu	37	1	183111747	183111747	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002293.3	+1	reviewed	p.V1551A	0.997	201	0%	180	41.7%	57	42.1%	benign(0)	tolerated(0.77)	neutral(0.001)	NULL
ATP2B4	493	genome.wustl.edu	37	1	203691729	203691729	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001684.3	+1	reviewed	p.R979Q	1.000	478	0.2%	501	41.5%	6	83.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Cation_ATPase_C,superfamily_Calcium ATPase transmembrane domain M
IARS2	55699	genome.wustl.edu	37	1	220279397	220279397	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018060.3	+1	validated	p.M412fs	0.930	-	-	-	-	-	-	-	-	-	HMMPfam_tRNA-synt_1,superfamily_ValRS/IleRS/LeuRS editing domain,superfamily_Nucleotidylyl transferase
SULT1C3	442038	genome.wustl.edu	37	2	108875465	108875486	+	Frame_Shift_Del	DEL	AAACTTGGTCAGGTGATGTTAT	AAACTTGGTCAGGTGATGTTAT	-	rs72322214	byCluster	TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	AAACTTGGTCAGGTGATGTTAT	AAACTTGGTCAGGTGATGTTAT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000376700	+1	known	p.W224fs	0.420:0.382:0.018:0.002:0.000:0.000:0.001:0.000:0.000:0.000:0.002:0.395:0.396:0.268:0.312:0.255:0.004:0.004:0.004:0.002:0.004:0.025	-	-	-	-	-	-	-	-	-	HMMPfam_Sulfotransfer_1,superfamily_SSF52540
CNTNAP5	129684	genome.wustl.edu	37	2	124999812	124999812	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_130773.2	+1	reviewed	p.Q75K	0.368	46	0%	52	34.6%	0	-	benign(0.016)	tolerated(0.12)	neutral(0.261)	HMMPfam_F5_F8_type_C,HMMSmart_FA58C,superfamily_Gal_bind_like
LCT	3938	genome.wustl.edu	37	2	136562373	136562373	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002299.2	-1	reviewed	p.L1476	0.998	95	0%	74	37.8%	0	-	-	-	-	HMMPfam_Glyco_hydro_1,superfamily_Glyco_hydro_cat
PRKRA	8575	genome.wustl.edu	37	2	179306376	179306376	+	Silent	SNP	G	G	C	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003690.4	-1	reviewed	p.A190	0.997	76	0%	133	31.6%	13	38.4%	-	-	-	HMMPfam_dsrm,HMMSmart_SM00358,superfamily_dsRNA-binding domain-like
CTNNB1	1499	genome.wustl.edu	37	3	41266101	41266101	+	Missense_Mutation	SNP	C	C	A	rs121913400	byCluster	TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098209.1	+1	reviewed	p.S33Y	1.000	65	1.5%	75	40%	54	53.7%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
LIMD1	8994	genome.wustl.edu	37	3	45637446	45637446	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014240.2	+1	validated	p.G359C	0.025	42	0%	46	34.8%	1	100%	benign(0.018)	deleterious(0.01)	neutral(0.406)	NULL
USP19	10869	genome.wustl.edu	37	3	49148196	49148196	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006677.1	-1	provisional	p.R1113C	1.000	102	0%	77	29.9%	30	50%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_UCH,superfamily_Cysteine proteinases
MYH15	22989	genome.wustl.edu	37	3	108205290	108205290	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014981.1	-1	validated	p.E339Q	0.690	209	0%	286	34.6%	0	-	benign(0.258)	deleterious(0.02)	neutral(0.410)	HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	byCluster	TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.E545K	1.000	56	0%	112	40.2%	2	50%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_PI3Ka,HMMSmart_PI3Ka,superfamily_ARM-type_fold
DMP1	1758	genome.wustl.edu	37	4	88583803	88583803	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004407.3	+1	reviewed	p.V291	0.000	188	0%	224	40.6%	0	-	-	-	-	HMMPfam_DMP1
NPR3	4883	genome.wustl.edu	37	5	32780847	32780847	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000908.2	+1	validated	p.S405	1.000	109	0%	106	34.9%	0	-	-	-	-	HMMPfam_ANF_receptor,superfamily_Periplasmic binding protein-like I
NIPBL	25836	genome.wustl.edu	37	5	37022151	37022171	+	Splice_Site	DEL	AATGTTTGCTTGGCAGATCCT	AATGTTTGCTTGGCAGATCCT	-	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	AATGTTTGCTTGGCAGATCCT	AATGTTTGCTTGGCAGATCCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_133433.3	+1	reviewed	e27-1	1.000:1.000:1.000:1.000:0.999:1.000:1.000	-	-	-	-	-	-	-	-	-	-
ZNF366	167465	genome.wustl.edu	37	5	71756624	71756624	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152625.1	-1	provisional	p.V234M	1.000	146	0%	110	39.1%	0	-	probably_damaging(0.993)	deleterious(0)	deleterious(0.895)	NULL
PCDHB7	56129	genome.wustl.edu	37	5	140554386	140554386	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018940.2	+1	reviewed	p.T657M	0.593	66	0%	57	33.3%	15	0%	possibly_damaging(0.811)	tolerated(0.17)	neutral(0.364)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
PGM3	5238	genome.wustl.edu	37	6	83892650	83892650	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015599.1	-1	provisional	p.R169*	0.978	123	0%	214	12.1%	6	0%	-	-	-	superfamily_Phosphoglucomutase first 3 domains
ZNF292	23036	genome.wustl.edu	37	6	87967133	87967133	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015021.1	+1	validated	p.F1262L	1.000	100	0%	125	11.2%	3	0%	probably_damaging(0.998)	deleterious(0.04)	deleterious(0.823)	NULL
IL22RA2	116379	genome.wustl.edu	37	6	137476207	137476207	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052962.2	-1	reviewed	p.E115K	0.003	279	0%	411	35.3%	0	-	possibly_damaging(0.829)	tolerated(0.8)	neutral(0.315)	superfamily_Fibronectin type III,HMMPfam_IL10Ra-bind
TBRG4	9238	genome.wustl.edu	37	7	45142001	45142001	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004749.2	-1	validated	p.R423fs	0.001	-	-	-	-	-	-	-	-	-	HMMPfam_FAST_1
PTPRD	5789	genome.wustl.edu	37	9	8331643	8331643	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002839.3	-1	reviewed	p.G1825R	1.000	229	0.4%	310	30.3%	1	0%	probably_damaging(1)	deleterious(0.04)	deleterious(0.849)	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II
QRFP	347148	genome.wustl.edu	37	9	133769001	133769001	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198180.1	-1	validated	p.Q75	0.724	47	0%	31	12.9%	0	-	-	-	-	NULL
RAPGEF1	2889	genome.wustl.edu	37	9	134467551	134467551	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000414781	-1	known	p.G145S	1.000	88	0%	60	33.3%	9	11.1%	-	-	-	HMMPfam_RasGEF_N,HMMSmart_SM00229,superfamily_Ras GEF
BRD3	8019	genome.wustl.edu	37	9	136901309	136901309	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007371.3	-1	reviewed	p.R594Q	1.000	48	0%	38	44.7%	13	53.8%	possibly_damaging(0.627)	deleterious(0.01)	deleterious(0.624)	NULL
ANK3	288	genome.wustl.edu	37	10	61835222	61835222	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020987.2	-1	reviewed	p.S1806*	1.000	305	0%	495	53.1%	0	-	-	-	-	NULL
PTEN	5728	genome.wustl.edu	37	10	89624237	89624240	+	Frame_Shift_Del	DEL	TCAT	TCAT	-	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	TCAT	TCAT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.I4fs	1.000:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
PTEN	5728	genome.wustl.edu	37	10	89692889	89692915	+	In_Frame_Del	DEL	AAAGCTGGAAAGGGACGAACTGGTGTA	AAAGCTGGAAAGGGACGAACTGGTGTA	-	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	AAAGCTGGAAAGGGACGAACTGGTGTA	AAAGCTGGAAAGGGACGAACTGGTGTA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.KAGKGRTGV125in_frame_del	1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999:1.000:1.000:1.000:1.000:1.000:0.998:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II
OR5I1	10798	genome.wustl.edu	37	11	55703430	55703430	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006637.1	-1	reviewed	p.L149	0.001	200	0%	264	34.8%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
CACNA1C	775	genome.wustl.edu	37	12	2788637	2788637	+	Missense_Mutation	SNP	G	G	A	rs147896322	by1000genomes	TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_199460.2	+1	reviewed	p.V1755I	1.000	23	0%	22	27.3%	2	0%	benign(0.366)	tolerated(0.29)	neutral(0.146)	NULL
CHD4	1108	genome.wustl.edu	37	12	6686952	6686952	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001273.2	-1	reviewed	p.K1787R	1.000	179	0%	208	43.8%	107	49.5%	probably_damaging(0.987)	deleterious(0)	deleterious(0.881)	HMMPfam_CHDCT2
H3F3C	440093	genome.wustl.edu	37	12	31944998	31944998	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001013699.2	-1	validated	p.G35R	0.999	116	0%	105	42.9%	0	-	possibly_damaging(0.764)	-	-	HMMSmart_H3,superfamily_Histone-fold
MTUS2	23281	genome.wustl.edu	37	13	29599207	29599207	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001033602.2	+1	validated	p.T134	0.000	284	0%	299	33.1%	0	-	-	-	-	NULL
DACT1	51339	genome.wustl.edu	37	14	59113045	59113045	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016651.5	+1	validated	p.R568S	0.003	53	0%	77	46.8%	4	25%	possibly_damaging(0.689)	deleterious(0.04)	deleterious(0.595)	NULL
PAPLN	89932	genome.wustl.edu	37	14	73719926	73719926	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000216658	+1	known	p.C384*	0.025	23	0%	22	50%	1	0%	-	-	-	superfamily_TSP1
RYR3	6263	genome.wustl.edu	37	15	34042429	34042429	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001036.3	+1	validated	p.R2781W	1.000	84	0%	90	35.6%	0	-	probably_damaging(0.985)	-	-	HMMPfam_RyR
FAM96A	84191	genome.wustl.edu	37	15	64385872	64385896	+	Frame_Shift_Del	DEL	GATCCGGGGCTGCCGGGCAGCTCCC	GATCCGGGGCTGCCGGGCAGCTCCC	-	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	GATCCGGGGCTGCCGGGCAGCTCCC	GATCCGGGGCTGCCGGGCAGCTCCC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032231.4	-1	validated	p.G25fs	1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.966:0.862	-	-	-	-	-	-	-	-	-	NULL
OR1F1	4992	genome.wustl.edu	37	16	3255097	3255097	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012360.1	+1	provisional	p.M284K	1.000	160	0%	165	38.8%	1	100%	benign(0.229)	deleterious(0)	neutral(0.468)	HMMPfam_7tm_1,superfamily_SSF81321
WDR59	79726	genome.wustl.edu	37	16	74943479	74943479	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030581.3	-1	validated	p.R521Q	1.000	142	0%	188	41.5%	11	45.4%	possibly_damaging(0.723)	tolerated(0.2)	neutral(0.311)	NULL
ZBTB4	57659	genome.wustl.edu	37	17	7365800	7365800	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001128833.1	-1	validated	p.G834E	0.071	62	0%	40	40%	12	41.6%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
TRPV2	51393	genome.wustl.edu	37	17	16332137	16332137	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016113.3	+1	reviewed	p.F476L	0.949	159	0%	137	36.5%	3	0%	benign(0)	tolerated(0.57)	neutral(0.006)	HMMPfam_Ion_trans
ASXL3	80816	genome.wustl.edu	37	18	31314318	31314318	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030632.1	+1	provisional	p.E341Q	1.000	65	0%	141	37.6%	0	-	possibly_damaging(0.871)	deleterious(0.02)	deleterious(0.722)	NULL
CDC37	11140	genome.wustl.edu	37	19	10504112	10504112	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007065.3	-1	reviewed	p.A244	0.465	93	0%	85	32.9%	218	44.4%	-	-	-	HMMPfam_CDC37_M,superfamily_Hsp90 co-chaperone CDC37
ATRN	8455	genome.wustl.edu	37	20	3543024	3543024	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_139321.2	+1	reviewed	p.H517D	1.000	277	0.4%	316	11.4%	5	0%	probably_damaging(0.999)	deleterious(0.02)	deleterious(0.873)	superfamily_Galactose oxidase central domain
RALGAPA2	57186	genome.wustl.edu	37	20	20610075	20610075	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020343.2	-1	validated	p.E389K	1.000	129	0%	170	36.5%	1	100%	probably_damaging(0.978)	tolerated(0.08)	deleterious(0.720)	NULL
DSCAM	1826	genome.wustl.edu	37	21	41725648	41725648	+	Silent	SNP	G	G	C	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001389.3	-1	validated	p.S226	1.000	65	0%	61	37.7%	0	-	-	-	-	HMMPfam_I-set,superfamily_Immunoglobulin
ABCG1	9619	genome.wustl.edu	37	21	43708177	43708177	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004915.3	+1	reviewed	p.L384F	0.001	300	0%	237	35%	7	14.2%	benign(0)	tolerated(0.7)	neutral(0.002)	NULL
SEZ6L	23544	genome.wustl.edu	37	22	26736414	26736414	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021115.4	+1	validated	p.S676R	1.000	510	0%	513	40.9%	4	50%	benign(0.02)	tolerated(0.61)	neutral(0.005)	HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain
DCAF8L1	139425	genome.wustl.edu	37	X	27998092	27998092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001017930.1	-1	reviewed	p.V454M	0.975	146	0%	171	47.4%	0	-	possibly_damaging(0.704)	tolerated(0.13)	deleterious(0.506)	HMMSmart_WD40,superfamily_WD40_like
USP51	158880	genome.wustl.edu	37	X	55515340	55515340	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_201286.3	-1	validated	p.S11	0.015	21	0%	28	25%	0	-	-	-	-	NULL
ARHGEF9	23229	genome.wustl.edu	37	X	62885817	62885817	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015185.2	-1	reviewed	p.N335K	1.000	138	0%	111	44.1%	7	0%	benign(0.023)	tolerated(0.31)	neutral(0.028)	HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729
LPAR4	2846	genome.wustl.edu	37	X	78011376	78011376	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005296.2	+1	reviewed	p.E337G	1.000	316	0.3%	475	34.7%	0	-	benign(0.318)	tolerated(0.2)	neutral(0.149)	NULL
GLUD2	2747	genome.wustl.edu	37	X	120183199	120183199	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012084.3	+1	reviewed	p.G554V	1.000	185	0%	228	27.6%	0	-	probably_damaging(0.994)	deleterious(0)	deleterious(0.897)	superfamily_NAD(P)-bd
HTATSF1	27336	genome.wustl.edu	37	X	135579893	135579893	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LN-01A-11W-A062-09	TCGA-AP-A0LN-10A-01W-A062-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014500.4	+1	reviewed	p.R17Q	1.000	54	0%	95	28.4%	22	0%	possibly_damaging(0.902)	tolerated(0.31)	neutral(0.384)	NULL
