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
GTF2B	2959	genome.wustl.edu	37	1	89325589	89325589	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001514.5	-1	reviewed	p.E171K	1.000	267	0%	287	15.3%	8	0%	probably_damaging(0.994)	deleterious(0.01)	deleterious(0.858)	HMMSmart_SM00385,superfamily_Cyclin-like,HMMPfam_TFIIB
DCST1	149095	genome.wustl.edu	37	1	155014046	155014046	+	Silent	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152494.2	+1	validated	p.S235	0.984	52	0%	77	46.8%	0	-	-	-	-	NULL
LOC648822	648822	genome.wustl.edu	37	1	155120990	155120990	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_001718420.1	+1	model	p.R9C	0.430	31	0%	75	42.7%	0	-	-	-	-	NULL
ACTN2	88	genome.wustl.edu	37	1	236918491	236918491	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001103.2	+1	reviewed	p.T716M	1.000	212	0%	270	36.7%	2	0%	probably_damaging(0.954)	deleterious(0)	deleterious(0.842)	HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_Spectrin repeat
ARHGAP25	9938	genome.wustl.edu	37	2	69053219	69053219	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001007231.2	+1	validated	p.R611C	1.000	418	0%	554	38.3%	1	0%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	NULL
ANKRD36BP2	645784	genome.wustl.edu	37	2	89084249	89084249	+	RNA	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_015424.1	+1	predicted	NULL	0.000	143	0%	138	37%	0	-	-	-	-	-
PIK3CA	5290	genome.wustl.edu	37	3	178921552	178921552	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.N345I	1.000	137	0%	140	38.6%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_C2,HMMSmart_PI3K_C2,superfamily_C2_CaLB
PITX2	5308	genome.wustl.edu	37	4	111542361	111542361	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000325.5	-1	reviewed	p.E124Q	1.000	27	0%	34	35.3%	0	-	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_Homeobox,HMMSmart_SM00389,superfamily_Homeodomain-like
PCDHB15	56121	genome.wustl.edu	37	5	140627002	140627002	+	Missense_Mutation	SNP	C	C	T	rs17844634		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018935.2	+1	reviewed	p.A619V	0.432	56	0%	59	25.4%	26	0%	possibly_damaging(0.89)	tolerated(0.07)	deleterious(0.669)	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin
TCERG1	10915	genome.wustl.edu	37	5	145862223	145862223	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006706.3	+1	reviewed	p.R652Q	1.000	240	0%	218	40.8%	5	60%	unknown(0)	tolerated(0.06)	-	superfamily_FF domain
PDE6A	5145	genome.wustl.edu	37	5	149313501	149313501	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000440.2	-1	reviewed	p.R237C	0.741	38	0%	42	38.1%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_SSF55781
LRFN2	57497	genome.wustl.edu	37	6	40400623	40400623	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020737.1	-1	provisional	p.G77E	0.968	35	0%	48	47.9%	0	-	benign(0.218)	deleterious(0.04)	neutral(0.370)	HMMSmart_SM00369,superfamily_L domain-like
CEP41	95681	genome.wustl.edu	37	7	130051012	130051012	+	Silent	SNP	G	G	C	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018718.1	-1	provisional	p.L76	0.929	326	0%	332	42.2%	3	66.6%	-	-	-	superfamily_Rhodanese/Cell cycle control phosphatase
PRSS37	136242	genome.wustl.edu	37	7	141537752	141537752	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001008270.2	-1	validated	p.P113L	0.000	219	0%	218	17.9%	0	-	benign(0)	tolerated(0.12)	neutral(0.261)	HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys
CBWD1	55871	genome.wustl.edu	37	9	154618	154618	+	Nonstop_Mutation	SNP	T	T	G	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000377447	-1	known	p.*251Y	0.006	78	0%	62	32.3%	0	-	-	-	-	NULL
HSPA5	3309	genome.wustl.edu	37	9	128003035	128003035	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005347.3	-1	validated	p.V92I	1.000	80	0%	97	54.6%	1227	96.6%	benign(0.004)	tolerated(0.85)	neutral(0.001)	HMMPfam_HSP70,superfamily_Actin-like ATPase domain
LOC645954	645954	genome.wustl.edu	37	10	30974305	30974305	+	RNA	SNP	C	C	G	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_017086.3	+1	model	NULL	1.000	62	0%	93	43%	18	0%	-	-	-	-
C11orf48	79081	genome.wustl.edu	37	11	62430624	62430624	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024099.3	-1	validated	p.P257T	0.915	56	0%	101	42.6%	86	50%	unknown(0)	-	-	NULL
FIBP	9158	genome.wustl.edu	37	11	65653878	65653878	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_198897.1	-1	reviewed	p.R143W	1.000	81	0%	127	17.3%	102	17.6%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_FIBP
CATSPER1	117144	genome.wustl.edu	37	11	65792818	65792818	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_053054.3	-1	reviewed	p.R345C	0.000	28	0%	37	37.8%	0	-	probably_damaging(0.983)	deleterious(0.01)	deleterious(0.835)	superfamily_Voltage-gated potassium channels
CHD4	1108	genome.wustl.edu	37	12	6701583	6701583	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001273.2	-1	reviewed	p.R975H	1.000	183	0%	326	41.7%	78	47.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_SNF2_N
LRP6	4040	genome.wustl.edu	37	12	12339881	12339881	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002336.2	-1	reviewed	p.F274V	1.000	521	0%	716	34.9%	0	-	benign(0.07)	tolerated(0.19)	neutral(0.054)	HMMPfam_Ldl_recept_b,superfamily_YWTD domain
KRT83	3889	genome.wustl.edu	37	12	52708439	52708439	+	Silent	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002282.3	-1	reviewed	p.G486	0.000	28	0%	30	56.7%	0	-	-	-	-	NULL
USP15	9958	genome.wustl.edu	37	12	62783435	62783435	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006313.1	+1	provisional	p.M507I	1.000	322	0%	309	35.9%	3	66.6%	benign(0)	tolerated(0.33)	neutral(0.024)	HMMPfam_UCH,superfamily_RNA3apos_cycl/enolpyr_transf_A/B,superfamily_SSF54001
SLC46A3	283537	genome.wustl.edu	37	13	29287613	29287613	+	Silent	SNP	T	T	C	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135919.1	-1	validated	p.T88	0.000	65	0%	81	34.6%	0	-	-	-	-	HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter
CHAMP1	283489	genome.wustl.edu	37	13	115089640	115089640	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032436.2	+1	validated	p.S108I	0.998	401	0.2%	502	17.3%	6	50%	possibly_damaging(0.507)	tolerated(0.06)	deleterious(0.492)	NULL
RIN3	79890	genome.wustl.edu	37	14	93154538	93154540	+	In_Frame_Del	DEL	GGC	GGC	-	rs148538588	byCluster;by1000genomes	TCGA-AP-A05D-01	TCGA-AP-A05D-01	GGC	GGC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024832.3	+1	validated	p.G970in_frame_del	0.984:0.981:0.979	-	-	-	-	-	-	-	-	-	NULL
TLN2	83660	genome.wustl.edu	37	15	62942372	62942372	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015059.2	+1	reviewed	p.R76G	1.000	134	0%	146	44.5%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
ENSG00000184730	0	genome.wustl.edu	37	16	28507445	28507445	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000431282	+1	known	p.E352D	0.310	14	0%	43	23.3%	3	0%	benign(0)	tolerated(0.31)	neutral(0.027)	NULL
RPGRIP1L	23322	genome.wustl.edu	37	16	53726272	53726272	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015272.2	-1	reviewed	p.A79T	1.000	219	0%	171	34.5%	1	0%	probably_damaging(1)	tolerated(0.22)	deleterious(0.542)	NULL
TP53	7157	genome.wustl.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs121912651	byCluster	TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000546.4	-1	reviewed	p.R248W	1.000	85	0%	78	56.4%	120	95%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53
PPP2R1A	5518	genome.wustl.edu	37	19	52715971	52715971	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014225.5	+1	reviewed	p.P179R	1.000	82	0%	91	42.9%	349	46.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_HEAT,superfamily_ARM repeat
TMC4	147798	genome.wustl.edu	37	19	54671947	54671961	+	In_Frame_Del	DEL	CAGGTAGGTGACCGC	CAGGTAGGTGACCGC	-	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	CAGGTAGGTGACCGC	CAGGTAGGTGACCGC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145303.1	-1	validated	p.AVTYL251in_frame_del	0.997:1.000:1.000:1.000:1.000:1.000:0.992:0.932:0.436:0.423:0.191:0.002:0.000:0.667:0.727	-	-	-	-	-	-	-	-	-	NULL
FOXA2	3170	genome.wustl.edu	37	20	22563345	22563345	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021784.4	-1	reviewed	p.Q179*	1.000	101	0%	127	31.5%	12	66.6%	-	-	-	HMMPfam_Fork_head,HMMSmart_FH,superfamily_SSF46785
CTSA	5476	genome.wustl.edu	37	20	44520238	44520240	+	In_Frame_Del	DEL	CTG	CTG	-	rs11467527	byCluster;by1000genomes	TCGA-AP-A05D-01	TCGA-AP-A05D-01	CTG	CTG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000308.2	+1	reviewed	p.L32in_frame_del	0.155:0.311:0.361	-	-	-	-	-	-	-	-	-	NULL
NPBWR2	2832	genome.wustl.edu	37	20	62737797	62737799	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	AGA	AGA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005286.2	-1	reviewed	p.F129in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
ETS2	2114	genome.wustl.edu	37	21	40193586	40193592	+	Frame_Shift_Del	DEL	GACTGGA	GACTGGA	-	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	GACTGGA	GACTGGA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005239.4	+1	validated	p.G386fs	1.000:1.000:0.996:0.088:1.000:1.000:0.996	-	-	-	-	-	-	-	-	-	HMMPfam_Ets,HMMSmart_ETS,superfamily_SSF46785
COL18A1	80781	genome.wustl.edu	37	21	46924426	46924434	+	In_Frame_Del	DEL	GGCCCCCCA	GGCCCCCCA	-	rs149296338	byCluster;by1000genomes	TCGA-AP-A05D-01	TCGA-AP-A05D-01	GGCCCCCCA	GGCCCCCCA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_130444.2	+1	reviewed	p.GPP1360in_frame_del	0.307:0.391:0.336:0.964:0.952:0.917:0.918:0.919:0.837	-	-	-	-	-	-	-	-	-	NULL
SCML1	6322	genome.wustl.edu	37	X	17768092	17768092	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001037540.1	+1	validated	p.Y128H	0.000	464	0%	263	51%	1	100%	benign(0)	tolerated(0.43)	neutral(0.013)	NULL
PCDH19	57526	genome.wustl.edu	37	X	99551837	99551837	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A05D-01	TCGA-AP-A05D-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001105243.1	-1	reviewed	p.R915Q	1.000	296	0%	285	24.6%	7	0%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
