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
SRSF4	6429	genome.wustl.edu	37	1	29476622	29476622	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005626.4	-1	reviewed	p.R221W	1.000	185	0%	158	36.7%	49	42.8%	unknown(0)	deleterious(0)	-	NULL
INADL	10207	genome.wustl.edu	37	1	62234986	62234986	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_176877.2	+1	reviewed	p.R139Q	0.999	125	0%	128	43%	5	60%	possibly_damaging(0.934)	deleterious(0.02)	deleterious(0.763)	HMMPfam_PDZ,superfamily_PDZ domain-like
EXO1	9156	genome.wustl.edu	37	1	242015642	242015642	+	Silent	SNP	G	G	T	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006027.4	+1	reviewed	p.G70	0.232	93	0%	84	41.7%	1	100%	-	-	-	HMMPfam_XPG_N,HMMSmart_SM00485,superfamily_PIN domain-like
OR2T2	401992	genome.wustl.edu	37	1	248616705	248616711	+	Frame_Shift_Del	DEL	TGCTGCG	TGCTGCG	-	rs35380868		TCGA-AX-A05U-01	TCGA-AX-A05U-01	TGCTGCG	TGCTGCG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004136.1	+1	provisional	p.C204fs	0.000:0.001:0.000:0.000:0.000:0.000:0.001	-	-	-	-	-	-	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
INPP4A	3631	genome.wustl.edu	37	2	99155410	99155410	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001134224.1	+1	reviewed	p.Y212fs	1.000	-	-	-	-	-	-	-	-	-	NULL
STK11IP	114790	genome.wustl.edu	37	2	220472928	220472928	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000456909	+1	known	p.Q461fs	0.000	-	-	-	-	-	-	-	-	-	NULL
CTNNB1	1499	genome.wustl.edu	37	3	41266097	41266097	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098209.1	+1	reviewed	p.D32N	1.000	93	0%	85	40%	134	36.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
PCCB	5096	genome.wustl.edu	37	3	136048867	136048867	+	Nonstop_Mutation	SNP	A	A	C	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000532.4	+1	reviewed	p.*540S	0.981	172	0%	202	41.1%	34	50%	-	-	-	NULL
PIK3R1	5295	genome.wustl.edu	37	5	67589606	67589623	+	In_Frame_Del	DEL	CAAGAAAAAAGTCGAGAA	CAAGAAAAAAGTCGAGAA	-	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	CAAGAAAAAAGTCGAGAA	CAAGAAAAAAGTCGAGAA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181523.1	+1	reviewed	p.QEKSRE457in_frame_del	1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999:0.929:0.484:0.483:0.234:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
PCDHB3	56132	genome.wustl.edu	37	5	140481691	140481691	+	Silent	SNP	A	A	C	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018937.2	+1	reviewed	p.V486	0.258	144	0%	123	46.3%	3	100%	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
OR2V2	285659	genome.wustl.edu	37	5	180582876	180582876	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_206880.1	+1	provisional	p.G312S	0.014	46	0%	37	43.2%	0	-	possibly_damaging(0.638)	tolerated(0.2)	neutral(0.273)	NULL
PTPRK	5796	genome.wustl.edu	37	6	128718765	128718765	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001135648.1	-1	validated	p.W57G	0.999	345	0%	292	41.8%	18	38.8%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_MAM,HMMSmart_MAM
IL7	3574	genome.wustl.edu	37	8	79710386	79710386	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000880.2	-1	reviewed	p.A23V	0.999	237	0%	180	41.7%	0	-	benign(0.227)	deleterious(0.03)	neutral(0.387)	NULL
EXT1	2131	genome.wustl.edu	37	8	118847713	118847713	+	Silent	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000436216	-1	known	p.R168C	1.000	150	0%	107	14%	12	25%	-	-	-	HMMPfam_Exostosin
LOC100288108	100288108	genome.wustl.edu	37	8	140631011	140631011	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002342878.1	+1	model	p.V252I	0.999	78	0%	51	47.1%	0	-	-	-	-	NULL
KDM4C	23081	genome.wustl.edu	37	9	7174666	7174666	+	Silent	SNP	C	C	T	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015061.3	+1	reviewed	p.A1036	0.999	337	0%	226	45.1%	8	37.5%	-	-	-	NULL
TAF1L	138474	genome.wustl.edu	37	9	32631370	32631370	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153809.2	-1	provisional	p.T1403M	0.984	619	0%	444	46.8%	0	-	probably_damaging(1)	deleterious(0.02)	deleterious(0.883)	HMMSmart_BROMO,superfamily_Bromodomain
PTEN	5728	genome.wustl.edu	37	10	89685314	89685315	+	Frame_Shift_Del	DEL	TG	TG	-	rs121909226		TCGA-AX-A05U-01	TCGA-AX-A05U-01	TG	TG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.C71fs	1.000	-	-	-	-	-	-	-	-	-	HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II
PTEN	5728	genome.wustl.edu	37	10	89692904	89692904	+	Missense_Mutation	SNP	C	C	G	rs121909224	byCluster	TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.R130G	1.000	348	0%	491	30.5%	80	25%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II
PGAP2	27315	genome.wustl.edu	37	11	3846853	3846855	+	RNA	DEL	CTC	CTC	-	rs3217617	byCluster;by1000genomes	TCGA-AX-A05U-01	TCGA-AX-A05U-01	CTC	CTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_027014.1	+1	validated	NULL	0.231:0.226:0.001	-	-	-	-	-	-	-	-	-	-
FAT3	120114	genome.wustl.edu	37	11	92498155	92498155	+	Silent	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001008781.2	+1	validated	p.P1365	0.009	102	0%	115	47%	0	-	-	-	-	superfamily_Concanavalin A-like lectins/glucanases,superfamily_Cadherin-like
CADM1	23705	genome.wustl.edu	37	11	115109307	115109307	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014333.3	-1	validated	p.N113D	1.000	122	0%	118	33.9%	71	43.6%	probably_damaging(0.999)	tolerated(0.84)	deleterious(0.491)	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin
RERG	85004	genome.wustl.edu	37	12	15262109	15262109	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032918.1	-1	provisional	p.R179*	1.000	274	0%	110	51.8%	1	0%	-	-	-	superfamily_P-loop containing nucleoside triphosphate hydrolases
COL4A1	1282	genome.wustl.edu	37	13	110864923	110864923	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001845.4	-1	reviewed	p.P108S	1.000	108	0%	110	39.1%	20	5%	unknown(0)	tolerated(0.45)	-	HMMPfam_Collagen
RNASE7	84659	genome.wustl.edu	37	14	21511572	21511572	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032572.3	+1	validated	p.D141Y	0.002	562	0%	370	42.4%	0	-	benign(0.055)	deleterious(0)	neutral(0.448)	HMMPfam_RnaseA,HMMSmart_SM00092,superfamily_RNase A-like
SLC8A3	6547	genome.wustl.edu	37	14	70634329	70634329	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_183002.1	-1	reviewed	p.R271*	1.000	153	0.7%	130	40.8%	0	-	-	-	-	NULL
GREM1	26585	genome.wustl.edu	37	15	33023162	33023162	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013372.5	+1	reviewed	p.R91*	1.000	151	0%	32	46.9%	1	0%	-	-	-	HMMPfam_DAN
PIGQ	9091	genome.wustl.edu	37	16	633130	633130	+	Silent	SNP	T	T	C	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_148920.1	+1	reviewed	p.A593	0.001	3	0.000	16	0.562	64	40.6%	-	-	-	NULL
CYB5B	80777	genome.wustl.edu	37	16	69496358	69496358	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030579.2	+1	validated	p.I130V	0.998	94	0%	55	78.2%	98	95.9%	benign(0.002)	tolerated(0.72)	neutral(0.002)	NULL
OR3A3	8392	genome.wustl.edu	37	17	3324433	3324433	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012373.2	+1	validated	p.P191Q	0.585	287	0%	219	37.4%	0	-	probably_damaging(0.988)	tolerated(0.18)	deleterious(0.493)	HMMPfam_7tm_1,superfamily_SSF81321
TRPV3	162514	genome.wustl.edu	37	17	3436191	3436191	+	Silent	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_145068.2	-1	reviewed	p.P275	0.181	29	0%	25	40%	0	-	-	-	-	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat
KANSL1	284058	genome.wustl.edu	37	17	44249046	44249068	+	Frame_Shift_Del	DEL	TTTACAGGTGCTTGTGGCAGAGC	TTTACAGGTGCTTGTGGCAGAGC	-	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	TTTACAGGTGCTTGTGGCAGAGC	TTTACAGGTGCTTGTGGCAGAGC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015443.2	-1	validated	p.A148fs	1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	NULL
ZNF700	90592	genome.wustl.edu	37	19	12059258	12059258	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144566.1	+1	provisional	p.S140Y	0.012	178	0%	223	46.2%	2	100%	probably_damaging(0.999)	tolerated(0.06)	deleterious(0.813)	NULL
NFKBIB	4793	genome.wustl.edu	37	19	39397877	39397877	+	Silent	SNP	C	C	T	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002503.3	+1	validated	p.H212	0.737	46	0%	30	46.7%	21	28.5%	-	-	-	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat
ARHGAP35	2909	genome.wustl.edu	37	19	47440623	47440623	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004491.4	+1	reviewed	p.P1262T	1.000	211	0%	204	39.2%	16	37.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_RhoGAP,HMMSmart_SM00324,superfamily_GTPase activation domain GAP
NCAM2	4685	genome.wustl.edu	37	21	22658642	22658642	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004540.2	+1	reviewed	p.D131H	0.872	64	0%	63	52.4%	0	-	benign(0.343)	deleterious(0.01)	deleterious(0.514)	HMMSmart_IGc2,HMMPfam_ig,superfamily_SSF48726
C22orf13	83606	genome.wustl.edu	37	22	24942937	24942937	+	Missense_Mutation	SNP	G	G	A	rs191716304	by1000genomes	TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_031444.2	-1	validated	p.R111W	1.000	66	0%	60	13.3%	26	23%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Guanylate_cyc_2
FOXP3	50943	genome.wustl.edu	37	X	49107964	49107964	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000455775	-1	known	p.P401L	0.001	19	0%	13	46.2%	0	-	unknown(0)	-	-	HMMPfam_Fork_head,HMMSmart_FH
P2RY10	27334	genome.wustl.edu	37	X	78216335	78216335	+	Silent	SNP	C	C	T	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014499.2	+1	reviewed	p.C106	1.000	635	0.2%	584	46.1%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
GUCY2F	2986	genome.wustl.edu	37	X	108652309	108652309	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001522.2	-1	reviewed	p.S627Y	0.964	409	0.2%	310	11.3%	0	-	probably_damaging(0.995)	deleterious(0.01)	deleterious(0.863)	HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like)
CT47B1	643311	genome.wustl.edu	37	X	120007855	120007855	+	Silent	SNP	G	G	A	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145718.1	-1	validated	p.P265	0.001	448	0.4%	338	40.8%	0	-	-	-	-	NULL
ZNF75D	7626	genome.wustl.edu	37	X	134424989	134424989	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AX-A05U-01	TCGA-AX-A05U-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007131.3	-1	reviewed	p.K257Q	0.869	457	0%	350	40%	0	-	possibly_damaging(0.952)	tolerated(0.17)	neutral(0.455)	HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box
