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	27057804	27057804	+	Frame_Shift_Del	DEL	A	A	-	rs61749357		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006015.4	+1	reviewed	p.Q505fs	0.049	-	-	-	-	-	-	-	-	-	NULL
CSF3R	1441	genome.wustl.edu	37	1	36931958	36931958	+	Nonstop_Mutation	SNP	C	C	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_156039.2	-1	reviewed	p.*864Y	0.256	28	0%	29	62.1%	-	-	-	-	-	NULL
COL11A1	1301	genome.wustl.edu	37	1	103461460	103461460	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080629.2	-1	reviewed	p.A779E	1.000	60	0%	46	28.3%	-	-	benign(0.158)	tolerated(0.3)	neutral(0.043)	HMMPfam_Collagen
PRRC2C	23215	genome.wustl.edu	37	1	171504709	171504710	+	Frame_Shift_Del	DEL	TT	TT	-	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	TT	TT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015172.3	+1	validated	p.L671fs	0.998:0.998	-	-	-	-	-	-	-	-	-	NULL
SLC8A1	6546	genome.wustl.edu	37	2	40366693	40366693	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021097.2	-1	validated	p.W798*	1.000	25	0%	87	59.8%	-	-	-	-	-	NULL
METAP1D	254042	genome.wustl.edu	37	2	172926339	172926339	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_199227.1	+1	validated	p.I52V	0.918	95	0%	122	46.7%	-	-	benign(0)	tolerated(0.85)	neutral(0.001)	NULL
PROK2	60675	genome.wustl.edu	37	3	71821941	71821941	+	Silent	SNP	T	T	C	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001126128.1	-1	reviewed	p.P108	0.117	40	0%	30	13.3%	-	-	-	-	-	HMMPfam_Prokineticin,superfamily_Colipase-like
KPNA1	3836	genome.wustl.edu	37	3	122145407	122145408	+	RNA	INS	-	-	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_026698.1	-1	reviewed	NULL	1.000:1.000	-	-	-	-	-	-	-	-	-	-
CLRN1	7401	genome.wustl.edu	37	3	150645803	150645803	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_174878.2	-1	reviewed	p.R207*	1.000	49	0%	72	30.6%	-	-	-	-	-	NULL
PIK3CA	5290	genome.wustl.edu	37	3	178952077	178952077	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.N1044K	1.000	36	0%	93	51.6%	-	-	probably_damaging(0.983)	tolerated(0.05)	deleterious(0.774)	HMMSmart_PI3Kc,superfamily_Kinase_like
APC	324	genome.wustl.edu	37	5	112154723	112154723	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000038.4	+1	reviewed	p.R332*	0.996	37	0%	36	63.9%	-	-	-	-	-	superfamily_ARM repeat
MEGF10	84466	genome.wustl.edu	37	5	126755818	126755818	+	Silent	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032446.2	+1	validated	p.N503	0.861	19	0%	23	60.9%	-	-	-	-	-	HMMSmart_SM00180,HMMSmart_SM00181
HFE	3077	genome.wustl.edu	37	6	26093114	26093114	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000410.3	+1	reviewed	p.P273L	0.003	43	0%	55	36.4%	-	-	benign(0.002)	tolerated(0.31)	neutral(0.027)	HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin
HIST1H4G	8369	genome.wustl.edu	37	6	26247065	26247065	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003547.2	-1	reviewed	p.I47M	1.000	37	0%	34	26.5%	-	-	probably_damaging(0.997)	deleterious(0)	deleterious(0.911)	HMMSmart_H4,HMMPfam_Histone,superfamily_Histone-fold
TCP10	6953	genome.wustl.edu	37	6	167791514	167791514	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004610.3	-1	validated	p.A116T	0.000	92	0%	134	48.5%	-	-	benign(0.039)	tolerated(0.15)	neutral(0.243)	NULL
MPPED2	744	genome.wustl.edu	37	11	30439158	30439158	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001584.2	-1	reviewed	p.G187C	1.000	50	0%	31	25.8%	-	-	probably_damaging(0.995)	deleterious(0.01)	deleterious(0.863)	HMMPfam_Metallophos,superfamily_Metallo-dependent phosphatases
OPCML	4978	genome.wustl.edu	37	11	132527164	132527164	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002545.3	-1	reviewed	p.T73N	1.000	59	0%	60	31.7%	-	-	benign(0.039)	tolerated(0.13)	neutral(0.255)	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin
PLBD1	79887	genome.wustl.edu	37	12	14688639	14688639	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024829.5	-1	validated	p.I266M	0.000	57	0%	112	27.7%	-	-	benign(0.004)	tolerated(0.11)	neutral(0.272)	HMMPfam_Phospholip_B
STRN3	29966	genome.wustl.edu	37	14	31388219	31388219	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001083893.1	-1	validated	p.S398L	1.000	65	0%	128	37.5%	-	-	possibly_damaging(0.694)	tolerated(0.08)	deleterious(0.549)	NULL
PAX9	5083	genome.wustl.edu	37	14	37145495	37145495	+	Silent	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006194.3	+1	reviewed	p.T288	1.000	61	0%	65	29.2%	-	-	-	-	-	NULL
CASC5	57082	genome.wustl.edu	37	15	40915288	40915288	+	Silent	SNP	T	T	C	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_170589.3	+1	validated	p.T968	0.654	28	0%	25	76%	-	-	-	-	-	NULL
CHRNA3	1136	genome.wustl.edu	37	15	78913068	78913070	+	In_Frame_Del	DEL	CAG	CAG	-	rs66793222	byCluster;by1000genomes	TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	CAG	CAG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000743.4	-1	reviewed	p.L23in_frame_del	0.172:0.251:0.463	-	-	-	-	-	-	-	-	-	NULL
COG7	91949	genome.wustl.edu	37	16	23453825	23453825	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153603.3	-1	reviewed	p.V193I	0.743	30	0%	45	33.3%	-	-	probably_damaging(0.994)	tolerated(0.13)	deleterious(0.705)	HMMPfam_COG7
EXOC3L1	283849	genome.wustl.edu	37	16	67218471	67218471	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000314553	-1	known	p.G622*	0.922	5	0.000	7	1.000	-	-	-	-	-	HMMPfam_Sec6
TP53	7157	genome.wustl.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343	byCluster	TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000546.4	-1	reviewed	p.R273C	0.830	39	0%	56	67.9%	-	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_p53-like transcription factors,HMMPfam_P53
MED9	55090	genome.wustl.edu	37	17	17394705	17394707	+	In_Frame_Del	DEL	CAG	CAG	-	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	CAG	CAG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018019.2	+1	reviewed	p.Q116in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_CSE2
CDK12	51755	genome.wustl.edu	37	17	37687543	37687543	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016507.2	+1	validated	p.G1483R	1.000	8	0.000	19	1.000	-	-	unknown(0)	deleterious(0)	-	NULL
KRT36	8689	genome.wustl.edu	37	17	39643668	39643675	+	Frame_Shift_Del	DEL	CCGTCTGG	CCGTCTGG	-	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	CCGTCTGG	CCGTCTGG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003771.4	-1	reviewed	p.C305fs	0.989:0.000:0.409:0.421:0.790:0.909:0.960:0.979	-	-	-	-	-	-	-	-	-	superfamily_Prefoldin,HMMPfam_Filament
CBX1	10951	genome.wustl.edu	37	17	46152382	46152387	+	In_Frame_Del	DEL	CATGAG	CATGAG	-	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	CATGAG	CATGAG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001127228.1	-1	reviewed	p.LM132in_frame_del	1.000:1.000:1.000:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMSmart_SM00298,HMMPfam_Chromo_shadow,superfamily_Chromo domain-like,HMMSmart_SM00300
UNC13D	201294	genome.wustl.edu	37	17	73826490	73826491	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_199242.2	-1	reviewed	p.R928fs	0.000:0.106	-	-	-	-	-	-	-	-	-	HMMPfam_C2,HMMSmart_SM00239,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)
OSBPL1A	114876	genome.wustl.edu	37	18	21819342	21819342	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080597.2	-1	reviewed	p.R429T	1.000	33	0%	30	46.7%	-	-	benign(0.139)	tolerated(0.15)	neutral(0.253)	NULL
CDH19	28513	genome.wustl.edu	37	18	64235735	64235735	+	Silent	SNP	G	G	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021153.2	-1	reviewed	p.I136	1.000	73	0%	125	41.6%	-	-	-	-	-	HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,superfamily_Cadherin
ZNF726	730087	genome.wustl.edu	37	19	24116696	24116696	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000322487	+1	known	p.Y593C	0.165	18	0%	16	43.8%	-	-	possibly_damaging(0.751)	deleterious(0.03)	deleterious(0.640)	HMMPfam_zf-C2H2,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
MYH14	79784	genome.wustl.edu	37	19	50753885	50753885	+	Silent	SNP	C	C	T	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001077186.1	+1	reviewed	p.F590	1.000	23	0%	35	37.1%	-	-	-	-	-	HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases
MIS18A	54069	genome.wustl.edu	37	21	33651308	33651308	+	Silent	SNP	T	T	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018944.2	-1	validated	p.S6	0.000	15	0.000	4	1.000	-	-	-	-	-	NULL
C21orf119	84996	genome.wustl.edu	37	21	33765457	33765472	+	RNA	DEL	GGGATCCAGAGTCTTG	GGGATCCAGAGTCTTG	-	rs150903996	by1000genomes	TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	GGGATCCAGAGTCTTG	GGGATCCAGAGTCTTG					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NR_026845.1	+1	validated	NULL	0.001:0.002:0.003:0.000:0.000:0.000:0.000:0.001:0.002:0.003:0.004:0.005:0.005:0.004:0.003:0.002	-	-	-	-	-	-	-	-	-	-
PKNOX1	5316	genome.wustl.edu	37	21	44430314	44430314	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004571.3	+1	validated	p.D111H	1.000	27	0%	17	82.4%	-	-	possibly_damaging(0.768)	deleterious(0)	deleterious(0.730)	NULL
GAB4	128954	genome.wustl.edu	37	22	17450989	17450989	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001037814.1	-1	provisional	p.D261H	1.000	53	0%	90	43.3%	-	-	probably_damaging(0.995)	deleterious(0.01)	deleterious(0.863)	NULL
SEPT5	5413	genome.wustl.edu	37	22	19709391	19709391	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000438754	+1	known	p.H293D	1.000	16	0%	33	27.3%	-	-	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	NULL
ENSG00000210077	0	genome.wustl.edu	37	MT	1632	1632	+	RNA	SNP	T	T	C	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387342	+1	novel	NULL	NULL	17	0%	641	93.9%	-	-	-	-	-	-
ENSG00000210100	0	genome.wustl.edu	37	MT	4264	4264	+	RNA	SNP	G	G	A	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000387365	+1	novel	NULL	NULL	22	0%	443	52.1%	-	-	-	-	-	-
FAM9A	171482	genome.wustl.edu	37	X	8763175	8763175	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AX-A2HF-01	TCGA-AX-A2HF-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_174951.3	-1	validated	p.E259Q	0.000	63	0%	28	82.1%	-	-	unknown(0)	-	-	NULL
