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
ARID1A	8289	genome.wustl.edu	37	1	27099947	27099947	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006015.4	+1	reviewed	p.R1276*	1.000	111	0%	116	64.7%	11	45.4%	-	-	-	NULL
TESK2	10420	genome.wustl.edu	37	1	45810620	45810620	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007170.2	-1	reviewed	p.A536	0.000	177	0.6%	176	26.1%	4	0%	-	-	-	NULL
CR2	1380	genome.wustl.edu	37	1	207651364	207651364	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001006658.2	+1	reviewed	p.Q1013K	1.000	234	0.4%	270	26.7%	4	50%	benign(0.19)	tolerated(0.17)	neutral(0.077)	HMMPfam_Sushi,HMMSmart_CCP,superfamily_Complement_control_module
RCOR3	55758	genome.wustl.edu	37	1	211486784	211486784	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001136223.1	+1	validated	p.P446S	0.998	379	0%	459	28.3%	6	50%	benign(0.001)	deleterious(0)	neutral(0.445)	NULL
SIPA1L2	57568	genome.wustl.edu	37	1	232601076	232601076	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020808.3	-1	validated	p.R777Q	1.000	71	0%	122	30.3%	7	57.1%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Rap_GAP,superfamily_Rap/Ran-GAP (Pfam 02145)
PRKCE	5581	genome.wustl.edu	37	2	46234657	46234657	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005400.2	+1	reviewed	p.E374K	1.000	74	0%	89	23.6%	7	57.1%	benign(0)	tolerated(0.44)	neutral(0.013)	NULL
LMAN2L	81562	genome.wustl.edu	37	2	97377602	97377602	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142292.1	-1	validated	p.T234M	1.000	78	0%	90	28.9%	42	28.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Lectin_leg-like,superfamily_ConA_like_lec_gl
MBD5	55777	genome.wustl.edu	37	2	149226743	149226743	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018328.4	+1	reviewed	p.T411A	1.000	157	0%	192	29.2%	4	75%	probably_damaging(0.984)	tolerated(0.07)	deleterious(0.750)	NULL
NFE2L2	4780	genome.wustl.edu	37	2	178098918	178098918	+	Missense_Mutation	SNP	G	G	C	rs182428269	by1000genomes	TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006164.3	-1	validated	p.R43G	1.000	277	0%	322	30.1%	59	38.9%	unknown(0)	deleterious(0.01)	-	NULL
CASR	846	genome.wustl.edu	37	3	121980530	121980530	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000388.3	+1	reviewed	p.D216	0.993	216	0%	238	23.9%	0	-	-	-	-	HMMPfam_ANF_receptor,superfamily_Periplasmic binding protein-like I
PIK3CA	5290	genome.wustl.edu	37	3	178916917	178916919	+	In_Frame_Del	DEL	ATT	ATT	-	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	ATT	ATT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.I102in_frame_del	1.000:1.000:0.996	-	-	-	-	-	-	-	-	-	HMMPfam_PI3K_p85B,HMMSmart_PI3K_p85B
CCKAR	886	genome.wustl.edu	37	4	26483547	26483547	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000730.2	-1	reviewed	p.A334T	1.000	282	0%	310	21.9%	0	-	benign(0)	tolerated(1)	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
WDFY3	23001	genome.wustl.edu	37	4	85658480	85658480	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014991.4	-1	reviewed	p.T2205I	1.000	252	0%	235	29.8%	7	42.8%	benign(0.001)	deleterious(0.03)	neutral(0.364)	NULL
FREM3	166752	genome.wustl.edu	37	4	144620080	144620080	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000329798	-1	known	p.L583	0.951	119	0%	115	28.7%	0	-	-	-	-	NULL
RFESD	317671	genome.wustl.edu	37	5	94989941	94989941	+	Splice_Site	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001131065.1	+1	validated	e3+1	1.000	235	0.4%	263	27.4%	0	-	-	-	-	-
PSD2	84249	genome.wustl.edu	37	5	139201585	139201585	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032289.2	+1	provisional	p.S402L	0.980	99	0%	118	29.7%	1	0%	benign(0.109)	deleterious(0)	neutral(0.453)	HMMPfam_Sec7,HMMSmart_SM00222,superfamily_Sec7 domain
SOX30	11063	genome.wustl.edu	37	5	157078220	157078220	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178424.1	-1	reviewed	p.V289	0.998	141	0%	154	31.8%	0	-	-	-	-	NULL
UNC5A	90249	genome.wustl.edu	37	5	176305474	176305474	+	Splice_Site	SNP	A	A	G	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_133369.2	+1	validated	e13-2	1.000	79	0%	83	24.1%	0	-	-	-	-	-
ELOVL2	54898	genome.wustl.edu	37	6	10990626	10990626	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017770.3	-1	validated	p.S185	0.940	156	0.6%	172	29.7%	0	-	-	-	-	HMMPfam_ELO
GRM4	2914	genome.wustl.edu	37	6	34004089	34004089	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000841.1	-1	reviewed	p.A600T	0.966	41	0%	64	20.3%	0	-	benign(0.023)	tolerated(0.14)	neutral(0.251)	HMMPfam_7tm_3
ECT2L	345930	genome.wustl.edu	37	6	139210147	139210150	+	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	AAGA	AAGA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001077706.1	+1	validated	p.E799fs	1.000:0.997:0.952:0.724	-	-	-	-	-	-	-	-	-	superfamily_SSF50729
INTS1	26173	genome.wustl.edu	37	7	1520024	1520024	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080453.2	-1	validated	p.G1335R	1.000	161	0%	186	29.6%	44	34%	possibly_damaging(0.625)	tolerated(0.35)	neutral(0.238)	NULL
BRAT1	221927	genome.wustl.edu	37	7	2584590	2584590	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152743.2	-1	provisional	p.R128H	0.413	22	0%	22	40.9%	52	32.6%	benign(0.002)	tolerated(0.59)	neutral(0.004)	superfamily_ARM repeat
SEMA3C	10512	genome.wustl.edu	37	7	80427428	80427428	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006379.2	-1	validated	p.P371S	1.000	63	0%	95	24.2%	15	53.3%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Sema,HMMSmart_Sema,superfamily_Sema
TAF6	6878	genome.wustl.edu	37	7	99709599	99709599	+	Silent	SNP	C	C	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005641.2	-1	reviewed	p.T248	0.098	102	0%	126	37.3%	77	37.6%	-	-	-	NULL
ARHGEF10	9639	genome.wustl.edu	37	8	1877480	1877480	+	Missense_Mutation	SNP	T	T	A	rs17683288	byCluster;byFrequency;by1000genomes	TCGA-D1-A16E-01	TCGA-D1-A16E-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014629.2	+1	reviewed	p.S984T	1.000	49	0%	82	45.1%	4	50%	benign(0.008)	tolerated(0.65)	neutral(0.003)	superfamily_WD40_like
ATP6V1H	51606	genome.wustl.edu	37	8	54708309	54708309	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015941.2	-1	reviewed	p.M256I	1.000	98	0%	92	28.3%	44	38.6%	benign(0)	tolerated(0.96)	-	HMMPfam_V-ATPase_H,superfamily_ARM repeat
HNF4G	3174	genome.wustl.edu	37	8	76471108	76471108	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004133.4	+1	validated	p.Y310C	1.000	200	0%	193	53.9%	3	66.6%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Hormone_recep,HMMSmart_HOLI,superfamily_Str_ncl_receptor
ESRP1	54845	genome.wustl.edu	37	8	95676982	95676982	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017697.3	+1	validated	p.W234*	1.000	290	0%	344	56.4%	4	50%	-	-	-	HMMSmart_SM00360,superfamily_RNA-binding domain RBD
IFNA13	3447	genome.wustl.edu	37	9	21367853	21367853	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006900.3	-1	validated	p.C53S	0.003	330	0%	360	13.9%	0	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_Interferon,superfamily_4-helical cytokines
PHF2	5253	genome.wustl.edu	37	9	96428110	96428110	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005392.3	+1	reviewed	p.R694W	1.000	95	0%	98	32.7%	10	40%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
FUT11	170384	genome.wustl.edu	37	10	75532984	75532987	+	Frame_Shift_Del	DEL	CTGC	CTGC	-	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	CTGC	CTGC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173540.2	+1	validated	p.T251fs	1.000:1.000:0.991:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_Glyco_transf_10
PTEN	5728	genome.wustl.edu	37	10	89685312	89685313	+	Frame_Shift_Del	DEL	TC	TC	-	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	TC	TC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.A72fs	1.000:1.000	-	-	-	-	-	-	-	-	-	HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II
PTEN	5728	genome.wustl.edu	37	10	89692883	89692883	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000371953	+1	known	p.H123D	1.000	374	0%	433	31.4%	38	55.2%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_DSPc,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II
MKI67	4288	genome.wustl.edu	37	10	129901654	129901654	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002417.4	-1	reviewed	p.D2817fs	0.000	-	-	-	-	-	-	-	-	-	NULL
IGF2	3481	genome.wustl.edu	37	11	2161482	2161482	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127598.1	-1	reviewed	p.T15	0.037	53	0%	61	24.6%	0	-	-	-	-	NULL
ST5	6764	genome.wustl.edu	37	11	8734139	8734139	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005418.3	-1	reviewed	p.R711*	1.000	177	0%	199	28.1%	33	3%	-	-	-	HMMPfam_uDENN,HMMSmart_SM00800
PTH	5741	genome.wustl.edu	37	11	13514070	13514070	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000315.2	-1	reviewed	p.A77V	0.001	212	0%	257	38.5%	0	-	benign(0.013)	deleterious(0.01)	neutral(0.406)	HMMPfam_Parathyroid
CHD4	1108	genome.wustl.edu	37	12	6691814	6691814	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001273.2	-1	reviewed	p.R1446K	1.000	100	0%	131	28.2%	101	34.6%	benign(0.059)	deleterious(0.03)	neutral(0.368)	HMMPfam_DUF1086
PZP	5858	genome.wustl.edu	37	12	9345291	9345291	+	Silent	SNP	T	T	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002864.2	-1	validated	p.V433	0.000	135	0%	152	29.6%	0	-	-	-	-	NULL
PPFIA2	8499	genome.wustl.edu	37	12	81719572	81719572	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003625.2	-1	reviewed	p.R876*	0.289	318	0%	303	22.4%	0	-	-	-	-	NULL
POLR3B	55703	genome.wustl.edu	37	12	106848415	106848415	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018082.5	+1	validated	p.T740R	0.999	232	0%	246	26%	3	33.3%	possibly_damaging(0.771)	deleterious(0.01)	deleterious(0.692)	HMMPfam_RNA_pol_Rpb2_6,superfamily_beta and beta-prime subunits of DNA dependent RNA-polymerase
RBM26	64062	genome.wustl.edu	37	13	79911350	79911350	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022118.3	-1	validated	p.R847*	0.956	169	0%	228	32.9%	25	12%	-	-	-	superfamily_SSF54928
ZFYVE1	53349	genome.wustl.edu	37	14	73441497	73441497	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021260.1	-1	reviewed	p.N659	0.056	134	0%	114	28.9%	25	48%	-	-	-	HMMPfam_FYVE,HMMSmart_SM00064,superfamily_FYVE/PHD zinc finger
C14orf49	161176	genome.wustl.edu	37	14	95916409	95916409	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152592.3	-1	validated	p.A436	0.000	41	0%	49	22.4%	0	-	-	-	-	superfamily_Spectrin repeat
RTL1	388015	genome.wustl.edu	37	14	101349698	101349698	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001134888.2	-1	reviewed	p.T476	0.260	59	0%	66	39.4%	0	-	-	-	-	superfamily_Acid proteases
LOC100288273	100288273	genome.wustl.edu	37	14	106320630	106320630	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002343262.1	+1	model	p.A4V	0.000	119	0%	125	25.6%	400	0%	benign(0.002)	tolerated(0.46)	neutral(0.012)	NULL
LOC100289059	100289059	genome.wustl.edu	37	15	25414719	25414719	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XM_002343317.1	-1	model	p.S138	0.000	44	0%	58	43.1%	0	-	-	-	-	NULL
PIAS1	8554	genome.wustl.edu	37	15	68378839	68378839	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016166.1	+1	reviewed	p.D74N	1.000	211	0%	235	27.7%	16	43.7%	benign(0.019)	tolerated(0.3)	neutral(0.030)	NULL
SPSB3	90864	genome.wustl.edu	37	16	1828578	1828578	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080861.3	-1	validated	p.T54	0.785	61	0%	70	22.9%	76	50%	-	-	-	NULL
SRRM2	23524	genome.wustl.edu	37	16	2808540	2808540	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016333.3	+1	validated	p.D195	0.978	181	0%	220	28.6%	17	52.9%	-	-	-	NULL
PDILT	204474	genome.wustl.edu	37	16	20396149	20396149	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_174924.1	-1	provisional	p.R76K	0.586	404	0%	455	26.8%	0	-	possibly_damaging(0.746)	tolerated(1)	neutral(0.274)	superfamily_Thiordxn-like_fd
IRX6	79190	genome.wustl.edu	37	16	55363171	55363171	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024335.2	+1	validated	p.C427	1.000	23	0%	26	26.9%	8	62.5%	-	-	-	NULL
MBTPS1	8720	genome.wustl.edu	37	16	84100137	84100137	+	Silent	SNP	G	G	A	rs190946033	by1000genomes	TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003791.2	-1	reviewed	p.S770	0.958	112	0%	130	24.6%	152	50%	-	-	-	NULL
WSCD1	23302	genome.wustl.edu	37	17	6023780	6023780	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015253.1	+1	validated	p.N509	0.928	66	0%	95	31.6%	0	-	-	-	-	superfamily_SSF52540
MPRIP	23164	genome.wustl.edu	37	17	17053495	17053495	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015134.2	+1	validated	p.C438Y	1.000	97	0%	125	30.4%	33	33.3%	possibly_damaging(0.772)	deleterious(0.01)	deleterious(0.693)	HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729
MPP2	4355	genome.wustl.edu	37	17	41958179	41958179	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005374.3	-1	reviewed	p.R344C	1.000	95	0%	101	21.8%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	superfamily_P-loop containing nucleoside triphosphate hydrolases
DHX40	79665	genome.wustl.edu	37	17	57682855	57682855	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024612.4	+1	reviewed	p.L674	0.901	261	0%	293	18.4%	82	37.8%	-	-	-	HMMPfam_DUF1605
AFMID	125061	genome.wustl.edu	37	17	76201691	76201691	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145526.1	+1	validated	p.A218T	1.000	80	0%	108	25.9%	4	50%	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	superfamily_alpha/beta-Hydrolases
NOL4	8715	genome.wustl.edu	37	18	31432971	31432971	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003787.3	-1	validated	p.Q584	0.992	211	0%	298	30.2%	0	-	-	-	-	NULL
CYP2A13	1553	genome.wustl.edu	37	19	41599635	41599635	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000766.3	+1	reviewed	p.R311H	0.968	158	0%	174	25.9%	0	-	benign(0.163)	deleterious(0.02)	neutral(0.398)	HMMPfam_p450,superfamily_Cytochrome_P450
FOXA3	3171	genome.wustl.edu	37	19	46376055	46376055	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004497.2	+1	reviewed	p.G264	0.224	49	0%	41	36.6%	1	0%	-	-	-	NULL
TMEM143	55260	genome.wustl.edu	37	19	48846684	48846684	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018273.2	-1	provisional	p.V197I	0.439	42	0%	41	24.4%	5	20%	benign(0.004)	tolerated(0.21)	neutral(0.044)	NULL
CTSZ	1522	genome.wustl.edu	37	20	57581482	57581482	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001336.3	-1	reviewed	p.W68R	1.000	58	0%	73	26%	395	31.8%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMPfam_Peptidase_C1,HMMSmart_SM00645,superfamily_Cysteine proteinases
TIAM1	7074	genome.wustl.edu	37	21	32502549	32502549	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003253.2	-1	validated	p.R1343*	1.000	116	0%	107	30.8%	6	0%	-	-	-	HMMPfam_PH,HMMSmart_PH,superfamily_SSF50729
ENSG00000210082	0	genome.wustl.edu	37	MT	2593	2593	+	RNA	SNP	G	G	A	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387347	+1	known	NULL	NULL	82	0%	117	24.8%	5293	22.6%	-	-	-	-
XK	7504	genome.wustl.edu	37	X	37587534	37587534	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021083.2	+1	reviewed	p.S385F	0.953	255	0%	233	27%	0	-	possibly_damaging(0.51)	tolerated(0.1)	neutral(0.458)	NULL
BCOR	54880	genome.wustl.edu	37	X	39921444	39921444	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001123385.1	-1	reviewed	p.N1459S	1.000	149	0%	217	24.9%	26	80.7%	probably_damaging(0.985)	deleterious(0)	deleterious(0.877)	superfamily_Ankyrin repeat
PGK1	5230	genome.wustl.edu	37	X	77380399	77380399	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000291.3	+1	reviewed	p.K322T	1.000	358	0%	398	27.9%	986	0%	benign(0.008)	deleterious(0.01)	neutral(0.406)	HMMPfam_PGK,superfamily_Phosphoglycerate kinase
LAMP2	3920	genome.wustl.edu	37	X	119581762	119581762	+	Silent	SNP	A	A	C	novel		TCGA-D1-A16E-01	TCGA-D1-A16E-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001122606.1	-1	reviewed	p.V225	0.000	431	0.2%	503	24.7%	147	0%	-	-	-	HMMPfam_Lamp
