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
SPOCD1	90853	genome.wustl.edu	37	1	32279606	32279606	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144569.4	-1	provisional	p.D443E	0.000	48	0%	37	45.9%	0	-	possibly_damaging(0.507)	-	-	NULL
PIGK	10026	genome.wustl.edu	37	1	77672356	77672356	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005482.2	-1	reviewed	p.R70G	1.000	258	0%	226	41.2%	26	38.4%	probably_damaging(0.999)	deleterious(0.01)	deleterious(0.896)	HMMPfam_Peptidase_C13
KCNC4	3749	genome.wustl.edu	37	1	110765724	110765724	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004978.3	+1	reviewed	p.R273W	0.998	138	0%	87	42.5%	2	50%	possibly_damaging(0.763)	tolerated(0.15)	deleterious(0.524)	superfamily_Voltage-gated potassium channels
C1orf110	339512	genome.wustl.edu	37	1	162824730	162824730	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178550.4	-1	validated	p.T245N	0.937	287	0%	223	43.9%	0	-	possibly_damaging(0.45)	deleterious(0.03)	deleterious(0.512)	NULL
CAPN9	10753	genome.wustl.edu	37	1	230883454	230883454	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006615.2	+1	reviewed	p.G71V	1.000	33	0%	30	26.7%	0	-	probably_damaging(0.993)	tolerated(0.27)	deleterious(0.484)	HMMPfam_Peptidase_C2,HMMSmart_SM00230,superfamily_Cysteine proteinases
CEP170	9859	genome.wustl.edu	37	1	243327801	243327801	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014812.2	-1	reviewed	p.R1154L	1.000	101	0%	64	32.8%	2	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
SEMA4F	10505	genome.wustl.edu	37	2	74901700	74901700	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004263.3	+1	provisional	p.P300A	0.998	102	0%	72	43.1%	2	50%	possibly_damaging(0.878)	deleterious(0.01)	deleterious(0.748)	HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain
COL3A1	1281	genome.wustl.edu	37	2	189859516	189859516	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000090.3	+1	reviewed	p.E472Q	1.000	72	0%	57	43.9%	69	0%	unknown(0)	tolerated(0.17)	-	HMMPfam_Collagen
COL3A1	1281	genome.wustl.edu	37	2	189859517	189859517	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000090.3	+1	reviewed	p.E472A	1.000	72	0%	54	42.6%	68	0%	unknown(0)	tolerated(0.27)	-	HMMPfam_Collagen
ATG7	10533	genome.wustl.edu	37	3	11468323	11468323	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006395.2	+1	validated	p.V668M	1.000	82	0%	51	41.2%	20	25%	probably_damaging(0.997)	deleterious(0.03)	deleterious(0.831)	superfamily_Activating enzymes of the ubiquitin-like proteins
SYN2	6854	genome.wustl.edu	37	3	12182150	12182150	+	Splice_Site	DEL	G	G	-	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000341648	+1	known	e3-1	1.000	-	-	-	-	-	-	-	-	-	-
ZNF852	285346	genome.wustl.edu	37	3	44541759	44541759	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000436261	-1	known	p.W170C	0.035	222	0%	116	33.6%	2	0%	possibly_damaging(0.943)	tolerated(0.17)	neutral(0.447)	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
PIK3CA	5290	genome.wustl.edu	37	3	178916944	178916944	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.K111E	1.000	165	0%	119	46.2%	5	60%	probably_damaging(0.984)	deleterious(0.04)	deleterious(0.779)	superfamily_SSF54236
TLR10	81793	genome.wustl.edu	37	4	38775102	38775102	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001017388.1	-1	reviewed	p.E704K	1.000	296	0%	124	85.5%	1	0%	probably_damaging(0.975)	deleterious(0)	deleterious(0.861)	HMMPfam_TIR,HMMSmart_TIR,superfamily_TIR
NPY5R	4889	genome.wustl.edu	37	4	164272660	164272660	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006174.2	+1	provisional	p.L412*	1.000	169	0.6%	108	46.3%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
C5orf42	65250	genome.wustl.edu	37	5	37125420	37125423	+	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	TTCT	TTCT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_023073.3	-1	predicted	p.R1805fs	1.000:0.989:0.999:0.996	-	-	-	-	-	-	-	-	-	NULL
PCDHA7	56141	genome.wustl.edu	37	5	140216005	140216005	+	Silent	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018910.2	+1	reviewed	p.S679	0.000	40	0%	38	47.4%	12	0%	-	-	-	NULL
MAT2B	27430	genome.wustl.edu	37	5	162945356	162945356	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_013283.3	+1	reviewed	p.T331M	1.000	90	0%	59	39%	31	32.2%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
NSD1	64324	genome.wustl.edu	37	5	176637232	176637232	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022455.4	+1	reviewed	p.R611L	0.002	196	0%	261	60.9%	8	62.5%	benign(0.005)	tolerated(0.07)	neutral(0.319)	NULL
PPP1R18	170954	genome.wustl.edu	37	6	30647119	30647119	+	Silent	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001134870.1	-1	validated	p.Y553	1.000	30	0%	27	25.9%	27	3.7%	-	-	-	NULL
TAAR8	83551	genome.wustl.edu	37	6	132874535	132874535	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_053278.1	+1	provisional	p.S235N	0.000	178	0.6%	168	44.6%	0	-	benign(0.001)	tolerated(0.45)	neutral(0.012)	HMMPfam_7tm_1,superfamily_SSF81321
C7orf25	79020	genome.wustl.edu	37	7	42949865	42949865	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001099858.1	-1	validated	p.S270*	0.978	94	0%	66	43.9%	22	59%	-	-	-	HMMPfam_DUF1308
GPR85	54329	genome.wustl.edu	37	7	112724695	112724695	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018970.6	-1	validated	p.G28C	1.000	120	0%	71	43.7%	1	100%	probably_damaging(0.998)	tolerated(0.08)	deleterious(0.774)	superfamily_Family A G protein-coupled receptor-like
KLF10	7071	genome.wustl.edu	37	8	103663816	103663816	+	Silent	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005655.2	-1	validated	p.V248	0.002	32	0%	47	42.6%	29	58.6%	-	-	-	NULL
SMARCA2	6595	genome.wustl.edu	37	9	2104095	2104095	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003070.3	+1	reviewed	p.C1073F	1.000	285	0%	190	42.6%	0	-	possibly_damaging(0.449)	tolerated(0.85)	neutral(0.147)	superfamily_P-loop containing nucleoside triphosphate hydrolases
CAMK1D	57118	genome.wustl.edu	37	10	12867710	12867710	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020397.2	+1	reviewed	p.E354K	0.001	523	0%	501	26.7%	5	40%	unknown(0)	tolerated(0.33)	-	NULL
KIAA1217	56243	genome.wustl.edu	37	10	24833991	24833991	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019590.3	+1	validated	p.G1765S	0.055	216	0%	115	46.1%	163	45.3%	benign(0.006)	tolerated(0.39)	neutral(0.016)	NULL
PLAC9	219348	genome.wustl.edu	37	10	81904097	81904098	+	In_Frame_Ins	INS	-	-	AGA	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001012973.1	+1	provisional	p.95in_frame_insE	0.062:0.007	-	-	-	-	-	-	-	-	-	NULL
TMEM180	79847	genome.wustl.edu	37	10	104230835	104230835	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024789.3	+1	validated	p.R222Q	0.998	35	0%	44	59.1%	12	50%	benign(0.174)	tolerated(0.57)	neutral(0.022)	superfamily_MFS_gen_substrate_transporter
OR51A4	401666	genome.wustl.edu	37	11	4967776	4967776	+	Silent	SNP	A	A	G	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005329.1	-1	provisional	p.D185	0.000	91	0%	50	42%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
OR51A2	401667	genome.wustl.edu	37	11	4976389	4976389	+	Silent	SNP	A	A	G	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004748.1	-1	provisional	p.D185	0.976	403	0%	306	42.5%	0	-	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
OR52B2	255725	genome.wustl.edu	37	11	6190819	6190819	+	Silent	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004052.1	-1	provisional	p.H246	1.000	138	0%	141	51.8%	1	100%	-	-	-	HMMPfam_7tm_1,superfamily_SSF81321
MRVI1	10335	genome.wustl.edu	37	11	10603430	10603430	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098579.1	-1	reviewed	p.E773K	1.000	71	0%	87	40.2%	3	0%	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_MRVI1
CHST1	8534	genome.wustl.edu	37	11	45671886	45671886	+	Silent	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003654.4	-1	validated	p.A196	0.997	41	0%	26	57.7%	7	100%	-	-	-	HMMPfam_Sulfotransfer_1,superfamily_SSF52540
OR5A1	219982	genome.wustl.edu	37	11	59211290	59211290	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004728.1	+1	provisional	p.L217I	0.751	352	0%	510	29.4%	0	-	benign(0.007)	tolerated(1)	-	HMMPfam_7tm_1,superfamily_SSF81321
CLPB	81570	genome.wustl.edu	37	11	72005148	72005148	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030813.3	-1	provisional	p.T598M	1.000	49	0%	24	45.8%	25	60%	probably_damaging(0.998)	tolerated(0.06)	deleterious(0.797)	HMMPfam_ClpB_D2-small,superfamily_P-loop containing nucleoside triphosphate hydrolases
ARHGEF17	9828	genome.wustl.edu	37	11	73022287	73022287	+	Silent	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014786.3	+1	validated	p.E868	0.995	31	0%	22	27.3%	7	57.1%	-	-	-	NULL
IGSF9B	22997	genome.wustl.edu	37	11	133815984	133815985	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014987.1	-1	validated	p.P80fs	0.999:1.000	-	-	-	-	-	-	-	-	-	HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726
TAS2R14	50840	genome.wustl.edu	37	12	11090897	11090897	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_023922.1	-1	reviewed	p.D304N	0.003	194	0%	187	44.4%	0	-	benign(0.059)	tolerated(0.56)	neutral(0.010)	superfamily_SSF81321
RASAL1	8437	genome.wustl.edu	37	12	113559348	113559348	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004658.1	-1	reviewed	p.G132C	0.846	194	0%	126	50%	14	50%	probably_damaging(0.992)	tolerated(0.06)	deleterious(0.770)	superfamily_C2 domain (Calcium/lipid-binding domain CaLB)
MZT1	440145	genome.wustl.edu	37	13	73293116	73293116	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001071775.2	-1	validated	p.L67F	1.000	362	0%	279	44.8%	30	66.6%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	NULL
MYCBP2	23077	genome.wustl.edu	37	13	77763183	77763183	+	Splice_Site	SNP	C	C	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015057.4	-1	validated	e30-1	1.000	87	0%	82	42.7%	0	-	-	-	-	-
PSEN1	5663	genome.wustl.edu	37	14	73659449	73659449	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000021.3	+1	reviewed	p.K216E	1.000	260	0%	173	41%	16	68.7%	probably_damaging(0.994)	deleterious(0)	deleterious(0.897)	HMMPfam_Presenilin,HMMSmart_SM00730
VPS35	55737	genome.wustl.edu	37	16	46706202	46706202	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018206.4	-1	reviewed	p.N448fs	1.000	-	-	-	-	-	-	-	-	-	HMMPfam_Vps35
TP53	7157	genome.wustl.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000546.4	-1	reviewed	p.R248Q	1.000	113	0%	39	79.5%	96	96.8%	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53
GSDMA	284110	genome.wustl.edu	37	17	38133276	38133276	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_178171.4	+1	validated	p.L435F	1.000	251	0%	1327	88.7%	4	75%	probably_damaging(0.998)	deleterious(0)	deleterious(0.919)	NULL
EFTUD2	9343	genome.wustl.edu	37	17	42940095	42940095	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004247.3	-1	validated	p.W531C	1.000	76	0%	39	79.5%	31	90.3%	probably_damaging(0.987)	deleterious(0.04)	deleterious(0.785)	HMMPfam_GTP_EFTU_D2,superfamily_Translat_factor
DHX40	79665	genome.wustl.edu	37	17	57682972	57682972	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_024612.4	+1	reviewed	p.R713C	0.999	103	0%	126	66.7%	62	66.1%	possibly_damaging(0.95)	deleterious(0.04)	deleterious(0.742)	NULL
BRIP1	83990	genome.wustl.edu	37	17	59871074	59871074	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032043.1	-1	reviewed	p.A453T	0.998	66	0%	53	18.9%	4	0%	benign(0)	tolerated(0.28)	neutral(0.032)	NULL
TEX2	55852	genome.wustl.edu	37	17	62290313	62290313	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018469.3	-1	validated	p.Y422C	1.000	194	0%	179	30.2%	7	28.5%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
ENSG00000173213	0	genome.wustl.edu	37	18	49030	49030	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000308911	-1	known	p.A63T	1.000	23	0%	26	69.2%	5	0%	possibly_damaging(0.88)	deleterious(0)	deleterious(0.788)	HMMPfam_Tubulin,superfamily_Tubulin_FtsZ
ELL	8178	genome.wustl.edu	37	19	18555601	18555601	+	Silent	SNP	G	G	A	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006532.3	-1	validated	p.I609	0.921	10	0%	15	33.3%	24	29.1%	-	-	-	HMMPfam_Occludin_ELL
IL29	282618	genome.wustl.edu	37	19	39787191	39787191	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_172140.1	+1	reviewed	p.P44S	0.020	177	0%	155	46.5%	1	0%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
UBE2V1	7335	genome.wustl.edu	37	20	48713345	48713345	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021988.4	-1	reviewed	p.P35H	1.000	217	0%	175	45.1%	85	56.4%	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_UBQ-conjugat/RWD-like
NFATC2	4773	genome.wustl.edu	37	20	50051757	50051757	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_173091.2	-1	reviewed	p.R667Q	1.000	332	0%	218	43.6%	1	0%	probably_damaging(0.991)	tolerated(0.07)	deleterious(0.763)	HMMPfam_TIG,HMMSmart_SM00429,superfamily_E set domains
PABPC5	140886	genome.wustl.edu	37	X	90691600	90691600	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-AP-A053-01	TCGA-AP-A053-01	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_080832.2	+1	reviewed	p.G342*	1.000	173	0%	74	58.1%	0	-	-	-	-	HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00361,superfamily_RNA-binding domain RBD
