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
USP24	23358	genome.wustl.edu	37	1	55564204	55564204	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015306.2	-1	validated	p.N1640Y	1.000	43	0%	25	16%	0	-	probably_damaging(0.983)	deleterious(0.01)	deleterious(0.835)	HMMPfam_UCH,superfamily_Cysteine proteinases
ARNT	405	genome.wustl.edu	37	1	150814904	150814904	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001668.2	-1	reviewed	p.A90T	1.000	266	0%	246	44.7%	0	-	probably_damaging(0.992)	deleterious(0.04)	deleterious(0.796)	HMMPfam_HLH,superfamily_HLH helix-loop-helix DNA-binding domain
DDR2	4921	genome.wustl.edu	37	1	162740317	162740317	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000458105	+1	known	p.V117M	0.000	43	0%	94	66%	0	-	possibly_damaging(0.819)	deleterious(0.01)	deleterious(0.715)	NULL
PROX1	5629	genome.wustl.edu	37	1	214171027	214171027	+	Silent	SNP	C	C	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002763.3	+1	provisional	p.F383	1.000	393	0%	271	42.8%	1	0%	-	-	-	HMMPfam_Prox1
CYP27C1	339761	genome.wustl.edu	37	2	127957069	127957069	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001665.3	-1	reviewed	p.M145I	0.884	44	0%	26	30.8%	0	-	benign(0.001)	tolerated(0.06)	neutral(0.323)	HMMPfam_p450,superfamily_Cytochrome P450
CPB1	1360	genome.wustl.edu	37	3	148575316	148575316	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001871.2	+1	reviewed	p.A352S	1.000	122	0%	69	42%	0	-	benign(0.044)	tolerated(0.58)	neutral(0.007)	HMMPfam_Peptidase_M14,HMMSmart_SM00631,superfamily_Zn-dependent exopeptidases
PIK3CA	5290	genome.wustl.edu	37	3	178916854	178916854	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.E81K	1.000	255	0%	164	53%	2	0%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B
ARAP3	64411	genome.wustl.edu	37	5	141041613	141041613	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022481.5	-1	reviewed	p.A1004S	1.000	268	0%	126	34.1%	4	25%	possibly_damaging(0.832)	tolerated(0.2)	neutral(0.366)	HMMPfam_RhoGAP,HMMSmart_RhoGAP,superfamily_Rho_GAP
COL14A1	7373	genome.wustl.edu	37	8	121228617	121228617	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021110.1	+1	validated	p.R542T	1.000	252	0%	209	32.5%	3	0%	possibly_damaging(0.712)	tolerated(0.22)	neutral(0.299)	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
PSIP1	11168	genome.wustl.edu	37	9	15486823	15486900	+	Splice_Site	DEL	GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT	GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT	-	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT	GTTTAAAATGTTAGGAGAAATAGAACATACCTCATTGCTGGCTTTTTCTTCATGGTCGGTATCTTCCTTTGAAACACT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001128217.1	-1	validated	e5-1	0.997:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.989:0.288:0.306:0.481:0.989:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999:0.994:0.993:0.984:0.997:0.997:0.983:0.993:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.995:0.984:0.937	-	-	-	-	-	-	-	-	-	-
NUP214	8021	genome.wustl.edu	37	9	134073775	134073775	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005085.2	+1	reviewed	p.A1632T	0.033	194	0%	125	43.2%	27	37%	benign(0)	tolerated(1)	-	NULL
MS4A4A	51338	genome.wustl.edu	37	11	60059853	60059853	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_148975.1	+1	reviewed	p.L66P	0.478	121	0%	141	39%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
SOCS4	122809	genome.wustl.edu	37	14	55511039	55511039	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080867.2	+1	reviewed	p.K427R	1.000	115	0%	77	42.9%	4	75%	probably_damaging(0.983)	tolerated(0.51)	neutral(0.438)	NULL
TMED8	283578	genome.wustl.edu	37	14	77812811	77812811	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_213601.1	-1	provisional	p.V70L	0.996	279	0%	169	27.8%	1	0%	possibly_damaging(0.643)	deleterious(0)	deleterious(0.670)	NULL
GABRB3	2562	genome.wustl.edu	37	15	26866466	26866466	+	Silent	SNP	C	C	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000814.4	-1	reviewed	p.G152	0.948	269	0%	91	47.3%	0	-	-	-	-	HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like
CHRM5	1133	genome.wustl.edu	37	15	34355985	34355985	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012125.3	+1	validated	p.Y356C	0.952	212	0%	98	56.1%	0	-	possibly_damaging(0.884)	tolerated(0.17)	neutral(0.404)	HMMPfam_7tm_1,superfamily_SSF81321
BMF	90427	genome.wustl.edu	37	15	40398215	40398215	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001003940.1	-1	reviewed	p.Q25*	1.000	67	0%	24	25%	1	0%	-	-	-	NULL
FBXL19	54620	genome.wustl.edu	37	16	30958263	30958263	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001099784.2	+1	provisional	p.L634V	1.000	20	0%	25	40%	81	6.1%	probably_damaging(0.973)	deleterious(0)	deleterious(0.859)	superfamily_RNI-like
ZNF267	10308	genome.wustl.edu	37	16	31926099	31926099	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003414.4	+1	validated	p.Q177E	0.021	156	0%	272	24.3%	1	0%	benign(0.017)	tolerated(0.57)	neutral(0.007)	NULL
ANKRD11	29123	genome.wustl.edu	37	16	89351187	89351187	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013275.4	-1	validated	p.S588*	1.000	54	0%	18	72.2%	5	100%	-	-	-	superfamily_Ankyrin repeat
OR3A2	4995	genome.wustl.edu	37	17	3181503	3181503	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002551.3	-1	validated	p.R243*	0.931	141	0%	117	64.1%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
TP53	7157	genome.wustl.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000546.4	-1	reviewed	p.R273H	0.864	166	0%	56	83.9%	27	88.8%	possibly_damaging(0.936)	deleterious(0.01)	deleterious(0.787)	superfamily_p53-like transcription factors,HMMPfam_P53
AOC3	8639	genome.wustl.edu	37	17	41003742	41003742	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003734.2	+1	reviewed	p.V128I	0.986	68	0%	28	75%	0	-	benign(0.007)	tolerated(1)	-	HMMPfam_Cu_amine_oxidN2,superfamily_Cu_amine_oxidase_N-reg
DCC	1630	genome.wustl.edu	37	18	50683801	50683801	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005215.3	+1	reviewed	p.R446H	1.000	368	0%	255	41.6%	0	-	probably_damaging(0.995)	tolerated(0.12)	deleterious(0.718)	HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
SALL3	27164	genome.wustl.edu	37	18	76757209	76757209	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_171999.2	+1	validated	p.R1264C	0.994	87	0%	52	44.2%	0	-	probably_damaging(0.997)	deleterious(0.02)	deleterious(0.849)	NULL
ZNF560	147741	genome.wustl.edu	37	19	9578900	9578900	+	Silent	SNP	C	C	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152476.2	-1	validated	p.T241	0.001	174	0%	139	43.9%	0	-	-	-	-	NULL
ZNF829	374899	genome.wustl.edu	37	19	37405898	37405929	+	Splice_Site	DEL	ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA	ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA	-	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA	ATTCTTTCCTCCTCTTCTGGGTGACACCTGGA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001037232.3	-1	validated	e2-1	0.973:0.975:0.954:0.937:0.735:0.707:0.359:0.040:0.031:0.031:0.033:0.049:0.049:0.050:0.060:0.059:0.048:0.064:0.057:0.002:0.002:0.000:0.000:0.000:0.002:0.001:0.002:0.000:0.000	-	-	-	-	-	-	-	-	-	-
ZNF135	7694	genome.wustl.edu	37	19	58578553	58578553	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003436.3	+1	validated	p.R234Q	0.003	333	0%	112	75.9%	0	-	probably_damaging(0.994)	tolerated(0.06)	deleterious(0.774)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
ENSG00000211459	0	genome.wustl.edu	37	MT	1105	1105	+	RNA	SNP	C	C	T	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000389680	+1	known	NULL	NULL	62	0%	28	46.4%	1425	43.7%	-	-	-	-
SYAP1	94056	genome.wustl.edu	37	X	16754330	16754330	+	Silent	SNP	T	T	G	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032796.3	+1	validated	p.V112	0.991	125	0%	61	34.4%	78	34.6%	-	-	-	NULL
MSN	4478	genome.wustl.edu	37	X	64956747	64956747	+	Missense_Mutation	SNP	G	G	T	rs182327269	by1000genomes	TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002444.2	+1	reviewed	p.R350S	0.969	136	0%	89	33.7%	50	0%	benign(0.265)	deleterious(0)	deleterious(0.472)	HMMPfam_ERM
ACSL4	2182	genome.wustl.edu	37	X	108911504	108911504	+	Splice_Site	SNP	T	T	G	novel		TCGA-AP-A052-01A-11W-A027-09	TCGA-AP-A052-10A-01W-A027-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022977.2	-1	reviewed	e9-2	0.996	233	0.4%	217	35.9%	0	-	-	-	-	-
