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
NBPF1	55672	genome.wustl.edu	37	1	16891365	16891365	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017940.3	-1	predicted	p.T1022M	0.001	43	2.3%	44	31.8%	10	30%	-	-	-	NULL
EPHB2	2048	genome.wustl.edu	37	1	23110965	23110965	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004442.6	+1	reviewed	p.Q69	1.000	59	0%	61	24.6%	13	23%	-	-	-	HMMPfam_Ephrin_lbd,HMMSmart_EPH_lbd,superfamily_Gal_bind_like
RNPC3	55599	genome.wustl.edu	37	1	104078803	104078803	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017619.3	+1	reviewed	p.A204V	0.992	146	0%	161	21.7%	2	50%	benign(0.027)	tolerated(0.11)	neutral(0.273)	NULL
EFNA4	1945	genome.wustl.edu	37	1	155041445	155041445	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005227.2	+1	reviewed	p.R196C	0.988	243	0%	225	23.1%	8	25%	unknown(0)	-	-	NULL
CYP27C1	339761	genome.wustl.edu	37	2	127957048	127957048	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001001665.3	-1	reviewed	p.S152	0.008	179	0%	163	24.5%	0	-	-	-	-	HMMPfam_p450,superfamily_Cytochrome P450
XIRP2	129446	genome.wustl.edu	37	2	168110547	168110547	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152381.4	+1	validated	p.A3521S	0.246	100	0%	103	23.3%	0	-	possibly_damaging(0.586)	tolerated(0.13)	neutral(0.455)	NULL
RAD18	56852	genome.wustl.edu	37	3	8944096	8944098	+	In_Frame_Del	DEL	TCA	TCA	-	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	TCA	TCA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020165.3	-1	reviewed	p.D378in_frame_del	0.779:0.981:0.987	-	-	-	-	-	-	-	-	-	NULL
PLXNB1	5364	genome.wustl.edu	37	3	48452292	48452292	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130082.1	-1	validated	p.R1801C	0.963	66	0%	86	15.1%	41	46.3%	benign(0.001)	tolerated(0.23)	neutral(0.042)	superfamily_GTPase activation domain GAP,HMMPfam_Plexin_cytopl
PIK3CA	5290	genome.wustl.edu	37	3	178936094	178936094	+	Missense_Mutation	SNP	C	C	A	rs121913286	byCluster	TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.Q546K	1.000	207	0%	236	34.3%	4	50%	probably_damaging(0.978)	tolerated(0.11)	deleterious(0.692)	HMMPfam_PI3Ka,HMMSmart_PI3Ka,superfamily_ARM-type_fold
NAA15	80155	genome.wustl.edu	37	4	140306014	140306014	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_057175.3	+1	validated	p.D728fs	0.984	-	-	-	-	-	-	-	-	-	NULL
FBXW7	55294	genome.wustl.edu	37	4	153250883	153250883	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033632.2	-1	reviewed	p.R393*	1.000	171	0%	174	20.1%	4	25%	-	-	-	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40
ZDHHC14	79683	genome.wustl.edu	37	6	158066798	158066798	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024630.2	+1	provisional	p.S261F	0.936	229	0%	237	23.6%	5	40%	possibly_damaging(0.858)	tolerated(0.1)	deleterious(0.617)	NULL
LPA	4018	genome.wustl.edu	37	6	161027548	161027548	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005577.2	-1	reviewed	p.I916V	0.000	143	0%	132	11.4%	0	-	benign(0)	tolerated(1)	-	superfamily_Kringle-like
INTS1	26173	genome.wustl.edu	37	7	1510261	1510261	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001080453.2	-1	validated	p.A2175	0.909	27	0%	44	20.5%	147	40.1%	-	-	-	NULL
MUC12	10071	genome.wustl.edu	37	7	100646182	100646182	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000379442	+1	known	p.S4256*	0.006	300	0.3%	376	9.8%	0	-	-	-	-	NULL
PRKAG2	51422	genome.wustl.edu	37	7	151483613	151483613	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016203.3	-1	reviewed	p.F43	0.996	66	0%	63	25.4%	0	-	-	-	-	NULL
CACNA1B	774	genome.wustl.edu	37	9	140777292	140777292	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000718.2	+1	validated	p.R163W	1.000	265	0%	241	13.7%	0	-	possibly_damaging(0.943)	deleterious(0)	deleterious(0.832)	HMMPfam_Ion_trans,superfamily_Voltage-gated potassium channels
LSP1	4046	genome.wustl.edu	37	11	1874398	1874398	+	Silent	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002339.2	+1	reviewed	p.P8	0.000	141	0%	134	32.8%	5	0%	-	-	-	NULL
KDM2A	22992	genome.wustl.edu	37	11	66985227	66985227	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012308.2	+1	reviewed	p.A238V	1.000	255	0%	273	33%	16	56.2%	benign(0.092)	tolerated(0.25)	neutral(0.044)	HMMSmart_SM00558,HMMPfam_JmjC,superfamily_Clavaminate synthase-like
CHD4	1108	genome.wustl.edu	37	12	6697096	6697096	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001273.2	-1	reviewed	p.R1162Q	1.000	104	0%	113	22.1%	74	56.7%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_Helicase_C,HMMSmart_SM00490,superfamily_P-loop containing nucleoside triphosphate hydrolases
SOX5	6660	genome.wustl.edu	37	12	23818392	23818392	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006940.4	-1	reviewed	p.Y306C	1.000	82	0%	96	12.5%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
SRRM4	84530	genome.wustl.edu	37	12	119588923	119588923	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_194286.2	+1	validated	p.S393F	0.990	131	0%	125	26.4%	0	-	probably_damaging(0.978)	deleterious(0.03)	deleterious(0.785)	NULL
C12orf65	91574	genome.wustl.edu	37	12	123741495	123741495	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001143905.1	+1	validated	p.E140K	1.000	172	0%	116	22.4%	7	28.5%	unknown(0)	tolerated(0.37)	-	NULL
FBLN5	10516	genome.wustl.edu	37	14	92403397	92403397	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006329.3	-1	reviewed	p.P91	0.000	134	0%	163	23.3%	5	0%	-	-	-	NULL
TP53	7157	genome.wustl.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000546.4	-1	reviewed	p.R248Q	1.000	112	0%	110	52.7%	85	92.9%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53
CCDC144A	9720	genome.wustl.edu	37	17	16631011	16631011	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014695.1	+1	provisional	p.E688K	0.999	575	0%	611	10%	0	-	benign(0.096)	tolerated(0.21)	neutral(0.051)	NULL
NPEPPS	9520	genome.wustl.edu	37	17	45691041	45691041	+	Silent	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006310.3	+1	reviewed	p.L749	1.000	571	0%	568	23.8%	50	50%	-	-	-	NULL
ARHGAP35	2909	genome.wustl.edu	37	19	47424736	47424736	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004491.4	+1	reviewed	p.H935fs	1.000	-	-	-	-	-	-	-	-	-	NULL
LIG1	3978	genome.wustl.edu	37	19	48626232	48626232	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000234.1	-1	reviewed	p.A731T	1.000	165	0%	128	29.7%	26	61.5%	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	HMMPfam_DNA_ligase_A_M,PatternScan_DNA_LIGASE_A2,superfamily_DNA ligase/mRNA capping enzyme catalytic domain
LIG1	3978	genome.wustl.edu	37	19	48653466	48653466	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000234.1	-1	reviewed	p.K192N	0.017	153	0%	112	28.6%	8	75%	benign(0)	tolerated(0.46)	neutral(0.012)	NULL
SALL4	57167	genome.wustl.edu	37	20	50405676	50405676	+	Silent	SNP	C	C	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020436.3	-1	reviewed	p.R822	0.879	38	0%	45	20%	0	-	-	-	-	NULL
CELSR1	9620	genome.wustl.edu	37	22	46860088	46860088	+	Silent	SNP	G	G	A	rs3747251	byCluster;byFrequency;by2Hit2Allele;by1000genomes	TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000454637	-1	known	p.P608L	0.015	39	0%	47	12.8%	10	10%	-	-	-	NULL
DMD	1756	genome.wustl.edu	37	X	31196794	31196794	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004006.2	-1	reviewed	p.N3405K	1.000	310	0.6%	279	30.1%	1	100%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	NULL
CACNA1F	778	genome.wustl.edu	37	X	49075803	49075803	+	Nonsense_Mutation	SNP	G	G	A	rs122456135		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005183.2	-1	reviewed	p.R895*	1.000	136	0%	143	20.3%	0	-	-	-	-	superfamily_Voltage-gated potassium channels
CDX4	1046	genome.wustl.edu	37	X	72667325	72667325	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005193.1	+1	provisional	p.P79L	0.999	51	0%	49	22.4%	0	-	benign(0.002)	deleterious(0)	neutral(0.445)	HMMPfam_Caudal_act
DACH2	117154	genome.wustl.edu	37	X	85969556	85969556	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_053281.3	+1	reviewed	p.D313Y	1.000	207	0%	189	25.4%	0	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	NULL
NXF2	56001	genome.wustl.edu	37	X	101572395	101572395	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_017809.3	+1	reviewed	p.R98H	0.000	456	0%	446	13.5%	0	-	benign(0)	tolerated(1)	-	NULL
COL4A5	1287	genome.wustl.edu	37	X	107826158	107826158	+	Silent	SNP	T	T	C	novel		TCGA-D1-A16G-01A-31D-A12J-09	TCGA-D1-A16G-10A-01D-A12J-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033380.1	+1	reviewed	p.D327	1.000	445	0%	417	23%	6	0%	-	-	-	HMMPfam_Collagen
