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
HAO2	51179	genome.wustl.edu	37	1	119925645	119925645	+	Missense_Mutation	SNP	T	T	C	rs41306185	byCluster;byFrequency;by1000genomes	TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005783.1	+1	reviewed	p.F80S	1.000	67	0%	44	27.3%	0	-	benign(0.281)	deleterious(0.03)	neutral(0.451)	HMMPfam_FMN_dh,superfamily_FMN-linked oxidoreductases
C1orf53	388722	genome.wustl.edu	37	1	197871863	197871863	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001024594.2	+1	validated	p.W28*	0.005	4	0.000	8	0.750	15	73.3%	-	-	-	NULL
OR2T1	26696	genome.wustl.edu	37	1	248569858	248569858	+	Missense_Mutation	SNP	G	G	A	rs141385938	by1000genomes	TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030904.1	+1	provisional	p.R188H	0.000	166	0%	182	50%	0	-	benign(0.065)	tolerated(0.39)	neutral(0.021)	HMMPfam_7tm_1,superfamily_SSF81321
TTC21B	79809	genome.wustl.edu	37	2	166781179	166781179	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024753.3	-1	validated	p.P466S	1.000	99	0%	177	24.9%	3	0%	benign(0.011)	tolerated(0.81)	neutral(0.001)	NULL
SPEG	10290	genome.wustl.edu	37	2	220338272	220338272	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005876.4	+1	validated	p.I1398	0.004	93	0%	64	42.2%	0	-	-	-	-	HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin
ASIC4	55515	genome.wustl.edu	37	2	220397136	220397136	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018674.4	+1	reviewed	p.R446W	1.000	50	0%	26	30.8%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_ASC,PatternScan_ASC
SLC6A20	54716	genome.wustl.edu	37	3	45812919	45812919	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020208.3	-1	reviewed	p.I242T	1.000	64	0%	64	35.9%	3	0%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_SNF
UBXN7	26043	genome.wustl.edu	37	3	196096311	196096311	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015562.1	-1	validated	p.S229	1.000	84	0%	122	39.3%	2	50%	-	-	-	HMMSmart_SM00594
POLR2B	5431	genome.wustl.edu	37	4	57876368	57876368	+	Splice_Site	SNP	T	T	G	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000510355	+1	known	NULL	0.001	27	0%	25	28%	1	0%	-	-	-	-
PIK3R1	5295	genome.wustl.edu	37	5	67591126	67591134	+	In_Frame_Del	DEL	GAGAAAGAC	GAGAAAGAC	-	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	GAGAAAGAC	GAGAAAGAC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_181523.1	+1	reviewed	p.KTR575in_frame_del	1.000:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.999	-	-	-	-	-	-	-	-	-	NULL
PCDHA11	56138	genome.wustl.edu	37	5	140248834	140248834	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018902.3	+1	reviewed	p.A49V	0.997	58	0%	47	27.7%	0	-	possibly_damaging(0.9)	tolerated(0.05)	deleterious(0.702)	HMMSmart_SM00112,HMMPfam_Cadherin_2,superfamily_Cadherin-like
DHX16	8449	genome.wustl.edu	37	6	30622963	30622963	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003587.4	-1	reviewed	p.R938C	1.000	248	0%	169	17.8%	69	30.4%	possibly_damaging(0.882)	tolerated(0.05)	deleterious(0.690)	HMMPfam_DUF1605
VARS	7407	genome.wustl.edu	37	6	31750214	31750214	+	Silent	SNP	C	C	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000428445	-1	known	p.E23K	0.984	47	0%	20	45%	88	59%	-	-	-	superfamily_Nucleotidylyl transferase
FIG4	9896	genome.wustl.edu	37	6	110056484	110056484	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014845.5	+1	reviewed	p.I210N	1.000	250	0%	331	19.6%	8	12.5%	benign(0.014)	tolerated(0.13)	neutral(0.253)	HMMPfam_Syja_N
FZD1	8321	genome.wustl.edu	37	7	90895880	90895880	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003505.1	+1	reviewed	p.R562P	1.000	37	0%	17	29.4%	5	80%	probably_damaging(0.997)	deleterious(0.01)	deleterious(0.872)	HMMPfam_Frizzled
NEFL	4747	genome.wustl.edu	37	8	24813310	24813310	+	Silent	SNP	G	G	A	rs58975336		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000221169	-1	known	p.Y240	1.000	56	0%	29	17.2%	0	-	-	-	-	HMMPfam_Filament
LAPTM4B	55353	genome.wustl.edu	37	8	98787930	98787931	+	Frame_Shift_Ins	INS	-	-	TGCTTGGAGCTCCAGCAGC	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000378722	+1	known	p.W37fs	0.000:0.000	-	-	-	-	-	-	-	-	-	NULL
NFIL3	4783	genome.wustl.edu	37	9	94171833	94171833	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005384.2	-1	validated	p.S395L	0.892	273	0%	233	32.2%	25	12%	benign(0.071)	deleterious(0)	neutral(0.450)	HMMPfam_Vert_IL3-reg_TF
GARNL3	84253	genome.wustl.edu	37	9	130075772	130075772	+	Silent	SNP	C	C	T	rs143970041	by1000genomes	TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032293.4	+1	validated	p.S124	0.129	225	0%	190	30.5%	0	-	-	-	-	superfamily_Rap/Ran-GAP (Pfam 02145)
SEC16A	9919	genome.wustl.edu	37	9	139357402	139357402	+	Silent	SNP	G	G	A	rs149236979	by1000genomes	TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014866.1	-1	validated	p.A1610	0.000	81	0%	42	31%	12	41.6%	-	-	-	NULL
PTEN	5728	genome.wustl.edu	37	10	89692905	89692905	+	Missense_Mutation	SNP	G	G	C	rs121913292		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.R130P	1.000	240	0%	331	31.7%	78	41%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II
PTEN	5728	genome.wustl.edu	37	10	89711891	89711891	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.S170N	1.000	218	0%	319	26%	78	30.7%	benign(0.392)	deleterious(0)	deleterious(0.570)	HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II
OR51G2	81282	genome.wustl.edu	37	11	4936283	4936283	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005238.1	-1	provisional	p.G204D	1.000	112	0.9%	79	38%	0	-	possibly_damaging(0.795)	deleterious(0)	deleterious(0.743)	HMMPfam_7tm_1,superfamily_SSF81321
ABCC8	6833	genome.wustl.edu	37	11	17428295	17428295	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000352.3	-1	reviewed	p.T1068M	0.996	173	0%	89	41.6%	0	-	benign(0.001)	deleterious(0.05)	neutral(0.345)	HMMPfam_ABC_membrane,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain
C11orf9	745	genome.wustl.edu	37	11	61544842	61544842	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127392.1	+1	validated	p.R566Q	1.000	27	0%	23	34.8%	8	37.5%	possibly_damaging(0.791)	deleterious(0.04)	deleterious(0.645)	NULL
METAP2	10988	genome.wustl.edu	37	12	95879657	95879657	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006838.3	+1	reviewed	p.K110E	1.000	388	0%	458	27.3%	49	26.5%	possibly_damaging(0.648)	tolerated(0.42)	neutral(0.242)	superfamily_Creatinase/aminopeptidase
ANKS1B	56899	genome.wustl.edu	37	12	99166884	99166884	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152788.3	-1	validated	p.A1147D	1.000	49	0%	59	28.8%	1	100%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_PID,HMMSmart_SM00462,superfamily_PH domain-like
TMEM132B	114795	genome.wustl.edu	37	12	125834187	125834187	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_052907.2	+1	provisional	p.P81L	0.101	373	0%	273	26.7%	0	-	benign(0.006)	tolerated(1)	-	NULL
ZNF268	10795	genome.wustl.edu	37	12	133781031	133781031	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003415.2	+1	validated	p.C920F	0.000	39	0%	26	34.6%	8	75%	benign(0.075)	tolerated(0.09)	neutral(0.301)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
AHNAK2	113146	genome.wustl.edu	37	14	105410491	105410492	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	AG	AG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_138420.2	-1	validated	p.L3766fs	0.001:0.000	-	-	-	-	-	-	-	-	-	NULL
IGHG4	3503	genome.wustl.edu	37	14	106091238	106091238	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000390543	-1	known	p.A219D	0.847	1101	0%	665	14.3%	20	0%	benign(0.001)	tolerated(0.06)	neutral(0.323)	superfamily_SSF48726
TMC3	342125	genome.wustl.edu	37	15	81636316	81636316	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080532.1	-1	provisional	p.R530Q	1.000	81	0%	57	26.3%	0	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_TMC
ARSG	22901	genome.wustl.edu	37	17	66391299	66391299	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014960.3	+1	validated	p.E393K	0.001	67	0%	50	36%	7	42.8%	benign(0.001)	tolerated(0.63)	neutral(0.004)	HMMPfam_Sulfatase,superfamily_Alkaline_phosphatase_core
TMC4	147798	genome.wustl.edu	37	19	54666489	54666489	+	Silent	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145303.1	-1	validated	p.V479	0.006	44	0%	29	31%	102	43.1%	-	-	-	HMMPfam_TMC
ENSG00000210077	0	genome.wustl.edu	37	MT	1669	1669	+	RNA	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387342	+1	novel	NULL	NULL	46	0%	50	10%	145	32.4%	-	-	-	-
ENSG00000210082	0	genome.wustl.edu	37	MT	2773	2773	+	RNA	SNP	A	A	G	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387347	+1	known	NULL	NULL	52	0%	42	11.9%	8012	6.2%	-	-	-	-
FRMPD4	9758	genome.wustl.edu	37	X	12627868	12627868	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014728.3	+1	reviewed	p.D63N	1.000	153	0.7%	117	30.8%	0	-	probably_damaging(0.983)	deleterious(0)	deleterious(0.873)	superfamily_PDZ
PLXNA3	55558	genome.wustl.edu	37	X	153699494	153699494	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A0LO-01	TCGA-AP-A0LO-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017514.3	+1	reviewed	p.V1735M	1.000	43	0%	29	31%	16	0%	probably_damaging(0.999)	tolerated(0.07)	deleterious(0.809)	superfamily_Rho_GAP,HMMPfam_Plexin_cytopl
