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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov_SOL	TVarCov_SOL	TVaf_SOL	NTotCov_SOL	NVarCov_SOL	NVaf_SOL	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	Ttot_rna	Tvar_rna	Tvaf_rna	note	germline-maf-frequency	IGV
SSBP3	23648	broad.mit.edu	37	1	54871665	54871665	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	SSBP3	NM_001009955	exon1	c.A17G	p.K6R	GAGCCTTTGCCTT		55	5	0.09	96	1	0.0104166667		65		83	0	0.00			
SEC22B	9554	broad.mit.edu	37	1	145116147	145116148	+	RNA	INS	-	-	A	rs113058116	bycluster	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	.	.	.	.	GATTGTTATTTCG		11	4	0.36	5	0	0				131	0	0.00			
NBPF10	100132406	hgsc.bcm.edu	37	1	145293535	145293535	+	Missense_Mutation	SNP	C	C	G	rs55936365		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	NBPF10,NS,carcinoma,0,2	NBPF10	NM_001039703	exon1	c.C130G	p.L44V	TGTTTTCTAACTC		65	4	0.06	50	2	0.04		0	2	5	0	0.00			
TDRKH	11022	broad.mit.edu	37	1	151747281	151747281	+	Splice_Site	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	TDRKH	NM_001083965	exon12	c.C1538A	p.A513D	TCTGTGGCCTGAG		95	4	0.04	80	0	0		45		52	0	0.00			
PROX1	5629	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	1	214170542	214170542	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001270616	exon2	c.C664T	p.Q222X	AGTTTCCAGCAGC		80	6	0.08	61	0	0				2	0	0.00			
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	215847769	215847769	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_206933	exon63	c.G13484A	p.R4495H	AAATCACGATAGC		112	22	0.20	112	0	0				0	0				
SIRT1	23411	mdanderson.org	37	10	69676305	69676305	+	Silent	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_012238	exon9	c.G2199T	p.V733V	ATCTGTGAAACAG		33	3	0.09	44	0	0				149	0	0.00			
DNMBP	23268	mdanderson.org	37	10	101643788	101643788	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_015221	exon15	c.G3977A	p.R1326H	AGCCAGCGGTTCT		48	3	0.06	73	0	0				22	0	0.00			
PDZD8	118987	hgsc.bcm.edu;mdanderson.org	37	10	119044191	119044191	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_173791	exon5	c.C2053A	p.L685I	GATAAAGAATTTC		111	5	0.05	125	0	0				37	0	0.00			
DCHS1	8642	mdanderson.org	37	11	6653321	6653321	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_003737	exon6	c.C3422A	p.T1141N	CTGTAGGTCAGAC		21	2	0.10	17	0	0				15	0	0.00			
OR1S2	219958	broad.mit.edu	37	11	57970760	57970760	+	Missense_Mutation	SNP	C	C	T	rs200054918		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	OR1S2,NS,carcinoma,0,3	OR1S2	NM_001004459	exon1	c.G894A	p.M298I	GGGGTTCATCATG		79	5	0.06	83	1	0.0120481928		119	3	0	0				
INTS5	80789	mdanderson.org	37	11	62416258	62416258	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_030628	exon2	c.C1294T	p.R432C	CCTCACGCACGGT		88	4	0.05	121	0	0				48	1	0.02			
MYO7A	4647	mdanderson.org	37	11	76913417	76913417	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_000260	exon37	c.G5116T	p.E1706X	GAGCCCGAGGTGC		46	3	0.07	45	0	0				8	0	0.00			
WBP11	51729	broad.mit.edu	37	12	14940229	14940229	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	WBP11	NM_016312	exon12	c.C1696A	p.P566T	TCTGTGGCTTGGC		223	5	0.02	63	0	0		66		1950	1	0.00			
CAPRIN2	65981	broad.mit.edu	37	12	30863206	30863206	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	CAPRIN2	NM_001002259	exon18	c.C3014A	p.T1005N	TTAGAGGTTCTGG		331	6	0.02	125	0	0		109		278	0	0.00			
LOC100240735	0	broad.mit.edu	37	12	54472994	54472996	+	RNA	DEL	TTC	TTC	-	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	TTC	TTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	.	.	.	.	TGTTCTTTCTTCT		6	3	0.50	6	0	0				3	0	0.00			
RPGRIP1	57096	mdanderson.org	37	14	21769151	21769151	+	Missense_Mutation	SNP	C	C	T	rs371371555		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_020366	exon3	c.C245T	p.T82I	GGTTGACCGCTGC		49	3	0.06	62	0	0				0	0				
SLC7A7	9056	mdanderson.org	37	14	23244708	23244708	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001126105	exon8	c.C1040A	p.A347D	CAGATGGCATCAG		35	3	0.09	42	0	0				73	0	0.00			
VPS13C	54832	mdanderson.org	37	15	62204118	62204118	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_020821	exon63	c.C8636A	p.S2879X	TCTAATGATGACT		75	4	0.05	85	0	0				6	0	0.00			
NUBP2	10101	mdanderson.org	37	16	1838172	1838172	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_012225	exon6	c.G634T	p.E212X	GGCGGAGAGGAGC		32	3	0.09	35	0	0				214	0	0.00			
TK2	7084	broad.mit.edu	37	16	66565284	66565284	+	Splice_Site	SNP	T	T	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	TK2	NM_004614	exon5	c.A374T	p.Q125L	CCTACCTGAGGAC		65	3	0.05	70	0	0		17		20	0	0.00			
FUK	197258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	70502854	70502854	+	Missense_Mutation	SNP	G	G	A	rs200140905		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_145059	exon9	c.G766A	p.G256R	GACTCCGGAGCCC		77	18	0.23	67	0	0	0.001			34	14	0.41			
IL34	146433	broad.mit.edu	37	16	70693984	70693984	+	Missense_Mutation	SNP	C	C	T	rs201277640	bycluster;by1000genomes	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	IL34,bladder,carcinoma,0,3	IL34	NM_152456	exon7	c.C623T	p.A208V	AGTATGCGGCCAC		234	6	0.03	256	0	0		26	3	104	0	0.00			
HSDL1	83693	mdanderson.org	37	16	84163181	84163181	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_031463	exon5	c.C866A	p.T289N	CCTGTGGTCCTTT		44	3	0.07	55	0	0				47	0	0.00			
C1QBP	708	mdanderson.org	37	17	5341589	5341589	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001212	exon2	c.C237A	p.D79E	AGCTTTGTCTCCT		52	3	0.06	63	0	0				515	0	0.00			
KIF18B	146909	broad.mit.edu	37	17	43009468	43009468	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	KIF18B	NM_001264573	exon10	c.C1381A	p.Q461K	GCTCCTGGTCTGA		102	4	0.04	100	0	0		63		67	0	0.00			
MRPL45P2	653479	hgsc.bcm.edu	37	17	45560578	45560578	+	RNA	SNP	T	T	C	rs199837409	bycluster	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	.	.	.	.	TTTTTTTCTTTTT		140	6	0.04	131	0	0				0	0				
CASKIN2	57513	mdanderson.org	37	17	73498038	73498038	+	Silent	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_020753	exon18	c.C3117A	p.P1039P	GGGCTCGGGCTGG		55	3	0.05	49	0	0				60	0	0.00			
TBCD	6904	mdanderson.org	37	17	80739475	80739475	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_005993	exon7	c.C649T	p.R217C	ATCACACGTCCTG		41	3	0.07	37	0	0				422	0	0.00			
ANKRD30B	374860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	14748512	14748512	+	Missense_Mutation	SNP	G	G	C	rs372583134	alternate_allele	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001145029	exon1	c.G94C	p.G32R	GACTACGGGACCA		74	16	0.22	70	0	0				0	0				
GREB1L	80000	mdanderson.org	37	18	19080093	19080093	+	Silent	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001142966	exon22	c.G3795T	p.V1265V	CTGGGTGAGCTCC		50	3	0.06	59	0	0				2	0	0.00			
HNRNPM	4670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	8539106	8539106	+	Silent	SNP	G	G	C	rs375739833	alternate_allele	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	HNRNPM,NS,malignant_melanoma,+2,1	HNRNPM	NM_005968	exon12	c.G1098C	p.G366G	ATCTGGGATGAAC		141	19	0.13	132	0	0		2	1	1490	338	0.23			
ZNF224	7767	mdanderson.org	37	19	44611473	44611473	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_013398	exon6	c.T1160A	p.L387H	CGTGTCTTTTGAA		58	4	0.07	47	0	0				37	0	0.00			
MYPOP	339344	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	19	46394069	46394069	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001012643	exon3	c.G1012A	p.V338M	CGGACACGGGCTC		30	5	0.17	26	0	0				1	1	1.00			
KCNC3	3748	mdanderson.org	37	19	50831872	50831872	+	Silent	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_004977	exon1	c.G468A	p.L156L	GCAGTGCAGCTTG		44	3	0.07	60	0	0				2	0	0.00			
ATRAID	51374	broad.mit.edu	37	2	27438402	27438402	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_080592	exon4	c.G519T	p.Q173H	TACTCAGCTCCAG		177	5	0.03	167	0	0				518	1	0.00			
RGPD4	285190	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	2	108496563	108496563	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_182588	exon21	c.G5064C	p.K1688N	AATTAAGGTGAGA		795	36	0.05	751	0	0				0	0				
STK35	140901	hgsc.bcm.edu	37	20	2083851	2083851	+	Silent	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_080836	exon2	c.G732T	p.A244A	GCTGGCGCTGGCT		64	5	0.08	46	0	0				67	0	0.00			
SIGLEC1	6614	mdanderson.org	37	20	3674127	3674127	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_023068	exon13	c.C3475A	p.R1159S	AGAGGCGGGGTGC		26	2	0.08	25	0	0				20	0	0.00			
FRG1B	284802	bcgsc.ca	37	20	29623214	29623214	+	Missense_Mutation	SNP	C	C	T	rs367590609		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	FRG1B	.	.	.	.	TGCACTCGACAAT		308	18	0.06	309	9	0.0291262136		181		208	2	0.01			
ZNF341	84905	mdanderson.org	37	20	32378974	32378974	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_032819	exon15	c.A2195G	p.K732R	AGGACAAGGACCT		63	3	0.05	72	0	0				28	0	0.00			
SEC22C	9117	mdanderson.org	37	3	42594863	42594863	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_032970	exon7	c.C789A	p.N263K	GTACATGTTGCCC		55	3	0.05	59	0	0				34	0	0.00			
ATRIP	84126	mdanderson.org	37	3	48505443	48505443	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_130384	exon10	c.G1886T	p.G629V	CAGAAGGCTGCCT		36	3	0.08	39	0	0				40	0	0.00			
ARIH2OS	646450	mdanderson.org	37	3	48955837	48955837	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001123040	exon1	c.G746A	p.R249H	ACTGCGCGGCGAA		46	3	0.07	51	0	0				4	0	0.00			
CDHR4	389118	mdanderson.org	37	3	49829387	49829387	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001007540	exon16	c.C2144A	p.A715D	AGCTGGGCCAACC		50	3	0.06	50	0	0				0	0				
C3orf72	401089	mdanderson.org	37	3	138666289	138666289	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001040061	exon1	c.C83T	p.A28V	TCCAAGCCTCCTC		43	4	0.09	55	0	0				0	0				
RBP1	5947	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	3	139257745	139257745	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_002899	exon2	c.G316C	p.V106L	CCTGCACGATCTC		120	8	0.07	134	0	0				172	15	0.09			
PCDH7	5099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	30725116	30725116	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_032457	exon1	c.C2072T	p.T691M	ATGACACGGGGAC		57	15	0.26	80	0	0				1	0	0.00			
BMP2K	55589	broad.mit.edu	37	4	79792085	79792085	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	BMP2K_ENST00000502871,NS,carcinoma,0,7	BMP2K	NM_017593	exon11	c.G1380C	p.Q460H	TCACCAGCAGCAG		76	3	0.04	54	0	0		169	7	48	0	0.00			
NKD2	85409	broad.mit.edu	37	5	1038447	1038449	+	In_Frame_Del	DEL	CAC	CAC	-	rs75431263	alternate_allele	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	CAC	CAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	NKD2	NM_033120	exon10	c.1315_1317del	p.439_439del	CACGAGCACCACC		6	2	0.33	8	0	0		39		8	0	0.00			
FST	10468	mdanderson.org	37	5	52781043	52781043	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_006350	exon5	c.C938A	p.S313Y	AGCACTCCGGATC		31	3	0.10	45	0	0				1	0	0.00			
TRIM23	373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	5	64906830	64906830	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	TRIM23,bladder,carcinoma,0,1	TRIM23	NM_033228	exon5	c.C686G	p.S229X	AAAATTGATGCTC		73	15	0.21	93	0	0		0	1	19	5	0.26			
NBPF22P	0	broad.mit.edu	37	5	85586764	85586764	+	RNA	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	.	.	.	.	TGTCTGCGACTAC		330	5	0.02	409	2	0.0048899756				0	0				
SLC26A2	1836	mdanderson.org	37	5	149361140	149361140	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_000112	exon3	c.G1984T	p.A662S	GATACAGCAGGGA		40	3	0.08	54	0	0				5	0	0.00			
LCP2	3937	mdanderson.org	37	5	169683547	169683547	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_005565	exon17	c.C1133A	p.P378Q	TATGGTGGCAGGG		51	3	0.06	67	0	0				102	1	0.01			
MSH5	4439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	31725947	31725947	+	Silent	SNP	G	G	C	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_025259	exon13	c.G1071C	p.V357V	GACTGTGTACAGT		70	24	0.34	74	0	0				18	6	0.33			
SOGA3	387104	mdanderson.org	37	6	127796804	127796804	+	Silent	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_001012279	exon6	c.C2367A	p.I789I	GCAGCGGATGTTG		9	2	0.22	14	0	0				0	0				
TBP	6908	hgsc.bcm.edu	37	6	170871004	170871004	+	Silent	SNP	G	G	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_003194	exon3	c.G180A	p.Q60Q	GCAGCAGCAACAA		49	7	0.14	74	0	0				61	0	0.00			
TRA2A	29896	broad.mit.edu	37	7	23545402	23545403	+	Frame_Shift_Del	DEL	TC	TC	-	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	TC	TC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	TRA2A	NM_013293	exon7	c.800_801del	p.267_267del	TCTATATCGACTA		155	9	0.06	166	0	0		29		447	37	0.08			
NOM1	64434	mdanderson.org	37	7	156756636	156756636	+	Missense_Mutation	SNP	G	G	T	rs369881632	alternate_allele	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_138400	exon7	c.G1949T	p.R650M	AGCAGAGGATGAA		56	3	0.05	59	0	0				68	0	0.00			
GLI4	2738	mdanderson.org	37	8	144351632	144351632	+	Silent	SNP	A	A	T	rs6558341	bycluster;byfrequency;byhapmap;by1000genomes;alternate_allele	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_138465	exon2	c.A66T	p.P22P	ATCACCAGGGACA		81	2	0.02	76	0	0				49	0	0.00			
FAM205B	0	broad.mit.edu	37	9	34835480	34835480	+	RNA	SNP	C	C	T	rs75725332	byfrequency	TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	FAM205B	.	.	.	.	GGCCATCGGATGC		65	5	0.08	69	1	0.0144927536		10		0	0				
VCP	7415	mdanderson.org	37	9	35059088	35059088	+	Silent	SNP	T	T	C	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_007126	exon15	c.A2133G	p.R711R	CCTCTCTCGTTCT		53	3	0.06	60	0	0				1518	1	0.00			
.	0	bcgsc.ca	37	9	76264707	76264707	+	RNA	SNP	G	G	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	.	.	.	.	TTGATCGGAAACA		20	7	0.35	20	0	0				0	0				
PHF2	5253	mdanderson.org	37	9	96407931	96407931	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_005392	exon4	c.G320A	p.R107H	TGGCCCGTGTGCC		33	3	0.09	38	0	0				20	0	0.00			
RIBC1	158787	broad.mit.edu	37	X	53457699	53457699	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	RIBC1	NM_001031745	exon7	c.G1019T	p.G340V	GTCTAGGATCCTT		76	3	0.04	57	0	0		20		6	0	0.00			
.	84443	broad.mit.edu	37	X	106846480	106846480	+	Silent	SNP	G	G	A	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	.	.	.	.	ACAACAGCAGCAG		142	6	0.04	122	1	0.0081967213				28	1	0.04			
AFF2	2334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	147891442	147891442	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	NM_002025	exon4	c.C1084T	p.R362W	ATCTTGCGGGTGA		139	48	0.35	113	0	0				0	0				
.	0	broad.mit.edu	37	X	155255062	155255062	+	RNA	SNP	C	C	G	novel		TCGA-YU-A90P-01A-11D-A435-10	TCGA-YU-A90P-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74fe6dad-8904-4817-9bd1-c10506bcf478	9a3ac787-1752-4e74-bb5b-2d9ec803541a	.	.	.	.	.	.	TTCCCCCCCAGAC		123	3	0.02	89	0	0				114	24	0.21	rescued with RNA-seq		
