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	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	Algorithm
ATRNL1	26033	hgsc.bcm.edu	37	10	116853707	116853707	+	Silent	SNP	C	C	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	ATRNL1-96	NM_001276282	exon1	c.C198A	p.T66T	GAGGACCGGCTCC	.	75.0	30.0	30.0	0.0	.	Atlas-SNP
SCUBE2	57758	hgsc.bcm.edu	37	11	9101018	9101018	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	SCUBE2-92	NM_020974	exon3	c.G295T	p.V99F	CATGGACACAGCC	.	105.0	9.0	158.0	0.0	.	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	99942451	99942451	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	CNTN5-366	NM_175566	exon9	c.G1092T	p.M364I	TGAGATGGTTAAT	.	84.0	12.0	85.0	0.0	.	Atlas-SNP
SORL1	6653	hgsc.bcm.edu	37	11	121490527	121490527	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	SORL1-228	NM_003105	exon43	c.C5790G	p.D1930E	CCCGGACAGCAGG	.	147.0	40.0	201.0	0.0	.	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123848074	123848074	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	OR10S1-70	NM_001004474	exon1	c.G325C	p.E109Q	AGCCCTCAAAGGA	.	103.0	12.0	140.0	0.0	.	Atlas-SNP
ATG2A	23130	hgsc.bcm.edu	37	11	64673875	64673880	+	In_Frame_Del	DEL	GCCCTT	GCCCTT	-	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	GCCCTT	GCCCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	ATG2A-69	NM_015104	exon21	c.3110_3115del	p.1037_1039del	.	.	30.0	15.0	6.0	0.0	.	Pindel
ACIN1	22985	hgsc.bcm.edu	37	14	23548793	23548793	+	Missense_Mutation	SNP	C	C	T	rs80007670	byfrequency	TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	ACIN1-156	NM_001164814	exon6	c.G1925A	p.R642H	CGTGAACGTGACC	.	148.0	8.0	202.0	0.0	C|0.994;T|0.006	Atlas-SNP
FMN1	342184	hgsc.bcm.edu	37	15	33149251	33149251	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	FMN1-23	NM_001103184	exon13	c.C3224A	p.P1075H	TTGAAAGGCTGGA	.	79.0	15.0	126.0	0.0	.	Atlas-SNP
PATL2	197135	hgsc.bcm.edu	37	15	44964347	44964347	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	.	NM_001145112	exon7	c.G523T	p.A175S	TCTTGGCTGGGGG	.	51.0	7.0	69.0	0.0	.	Atlas-SNP
SLC47A2	146802	hgsc.bcm.edu	37	17	19582079	19582079	+	Missense_Mutation	SNP	G	G	A	rs201004962		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	SLC47A2-90	NM_001256663	exon18	c.C1663T	p.R555C	CACGGCGGATGAC	.	132.0	8.0	139.0	0.0	.	Atlas-SNP
OGFOD3	79701	hgsc.bcm.edu	37	17	80361861	80361861	+	Silent	SNP	C	C	T	rs200973304		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	.	NM_175902	exon7	c.G651A	p.T217T	CGCTTCCGTGCTG	.	105.0	8.0	62.0	0.0	C|0.999;T|0.000	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7013829	7013829	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	LAMA1-149	NM_005559	exon23	c.G3348A	p.G1116G	GCAGGCCCCGGTT	.	174.0	13.0	214.0	0.0	.	Atlas-SNP
XAB2	56949	hgsc.bcm.edu	37	19	7689283	7689283	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	XAB2-272	NM_020196	exon7	c.G871A	p.D291N	TGAAGTCCCGCAC	.	141.0	9.0	109.0	0.0	.	Atlas-SNP
KLF1	10661	hgsc.bcm.edu	37	19	12996235	12996235	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	KLF1-90	NM_006563	exon2	c.C809T	p.S270L	GCCCACGAACGTC	.	142.0	21.0	10.0	0.0	.	Atlas-SNP
LGI4	163175	hgsc.bcm.edu	37	19	35622449	35622449	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	LGI4-91	NM_139284	exon6	c.G469T	p.G157W	GGTTCCCGCGGAG	.	93.0	15.0	7.0	0.0	.	Atlas-SNP
CKM	1158	hgsc.bcm.edu	37	19	45815122	45815122	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	CKM-91	NM_001824	exon5	c.A538G	p.T180A	TCTCCGTCATGCT	.	119.0	19.0	94.0	0.0	.	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49657751	49657751	+	Silent	SNP	A	A	G	rs142699460	byfrequency	TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	HRC-91	NM_002152	exon1	c.T744C	p.D248D	ATCATCATCGTCA	.	96.0	12.0	80.0	0.0	A|0.998;G|0.002	Atlas-SNP
NR1H2	7376	hgsc.bcm.edu	37	19	50881825	50881825	+	Silent	SNP	G	G	A	rs55817866	byfrequency	TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	NR1H2-186	NM_001256647	exon5	c.G228A	p.Q76Q	GAAACAGCAGCAG	.	125.0	7.0	64.0	0.0	G|0.903;A|0.097	Atlas-SNP
ZNF761	388561	hgsc.bcm.edu	37	19	53959137	53959137	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	ZNF761-91	NM_001008401	exon7	c.G1376A	p.R459H	GTAGACGTCATAC	.	131.0	24.0	72.0	0.0	.	Atlas-SNP
ZNF628	89887	hgsc.bcm.edu	37	19	55995158	55995158	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	ZNF628-22	NM_033113	exon3	c.G2598A	p.Q866Q	GGTCCAGCTCCAG	.	202.0	68.0	114.0	0.0	.	Atlas-SNP
MUL1	79594	hgsc.bcm.edu	37	1	20828581	20828581	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	MUL1-90	NM_024544	exon3	c.A310G	p.N104D	TTCGATTCCACAC	.	130.0	26.0	168.0	0.0	.	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22182300	22182300	+	Missense_Mutation	SNP	G	G	A	rs151035968	alternate_allele	TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	HSPG2-141	NM_005529	exon45	c.C5681T	p.T1894M	GTGGGCGTGGGGC	.	61.0	42.0	30.0	0.0	G|1.000;T|0.000	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175365862	175365862	+	Missense_Mutation	SNP	G	G	A	rs138654492		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	TNR-324	NM_003285	exon5	c.C1058T	p.T353M	TATTCCGTCACTG	.	100.0	13.0	110.0	0.0	G|1.000;A|0.000	Atlas-SNP
RGSL1	353299	hgsc.bcm.edu	37	1	182499457	182499457	+	Missense_Mutation	SNP	C	C	T	rs202037903		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	RGSL1-226	NM_001137669	exon12	c.C2204T	p.T735M	TGTTAACGCTCCA	.	74.0	38.0	118.0	0.0	.	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186092228	186092228	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	HMCN1-113	NM_031935	exon81	c.G12375C	p.Q4125H	CCGCCAGCGCGTC	.	103.0	33.0	153.0	0.0	.	Atlas-SNP
LIMK2	3985	hgsc.bcm.edu	37	22	31667154	31667154	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	LIMK2-548	NM_005569	exon12	c.G1350A	p.R450R	CCACCGGGATCTG	.	131.0	10.0	152.0	0.0	.	Atlas-SNP
SLC4A10	57282	hgsc.bcm.edu	37	2	162820668	162820668	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	SLC4A10-229	NM_001178016	exon22	c.C2829T	p.F943F	GCTCTTCTGGATG	.	33.0	7.0	42.0	0.0	.	Atlas-SNP
TOPAZ1	375337	hgsc.bcm.edu	37	3	44285176	44285176	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	.	NM_001145030	exon2	c.A1178C	p.D393A	TGATGGATCATTT	.	26.0	8.0	15.0	0.0	.	Atlas-SNP
OR5H14	403273	hgsc.bcm.edu	37	3	97869140	97869140	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	OR5H14-91	NM_001005514	exon1	c.T911C	p.M304T	CAAAAATGTTCAA	.	214.0	19.0	154.0	0.0	.	Atlas-SNP
TRIM42	287015	hgsc.bcm.edu	37	3	140401765	140401765	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	TRIM42-227	NM_152616	exon2	c.C803T	p.S268L	TCCACTCGGATGT	.	244.0	16.0	157.0	0.0	.	Atlas-SNP
PIK3CA	5290	hgsc.bcm.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279	bycluster	TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	PIK3CA,bladder,carcinoma,0	PIK3CA-27752	NM_006218	exon21	c.A3140G	p.H1047R	ATGCACATCATGG	.	179.0	38.0	156.0	0.0	.	Atlas-SNP
SHOX2	6474	hgsc.bcm.edu	37	3	157823581	157823582	+	In_Frame_Ins	INS	-	-	CACCTCCTC	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	SHOX2-90	NM_003030	exon1	c.233_234insGAGGAGGTG	p.V78delinsGGGV	.	.	59.0	12.0	10.0	0.0	.	Atlas-Indel
NPFFR2	10886	hgsc.bcm.edu	37	4	73012700	73012700	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	NPFFR2-92	NM_001144756	exon5	c.A443G	p.Q148R	GGTTCCAGTGTGT	.	79.0	14.0	68.0	0.0	.	Atlas-SNP
GRID2	2895	hgsc.bcm.edu	37	4	94376818	94376818	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	GRID2-159	NM_001510	exon11	c.C1551T	p.A517A	GAGAGCCGACATA	.	149.0	21.0	123.0	0.0	.	Atlas-SNP
RAPGEF2	9693	hgsc.bcm.edu	37	4	160275135	160275135	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	RAPGEF2-637	NM_014247	exon22	c.A4105G	p.T1369A	GAAGAAACCAAGC	.	131.0	46.0	86.0	0.0	.	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127863580	127863580	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	FBN2-146	NM_001999	exon4	c.A517T	p.T173S	AATAAGTTCCAAT	.	172.0	20.0	131.0	0.0	.	Atlas-SNP
GDF9	2661	hgsc.bcm.edu	37	5	132197395	132197395	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	GDF9-227	NM_005260	exon2	c.G1251A	p.P417P	ACATGACGGTCTT	.	209.0	13.0	133.0	0.0	.	Atlas-SNP
ABLIM3	22885	hgsc.bcm.edu	37	5	148624490	148624490	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	ABLIM3-93	NM_014945	exon16	c.C1398G	p.S466R	CATCAGCCAGACC	.	222.0	81.0	178.0	0.0	.	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65622395	65622395	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	EYS-660	NM_001142800	exon16	c.C2623T	p.H875Y	TACAATGCTGATT	.	171.0	19.0	165.0	0.0	.	Atlas-SNP
PPIL4	85313	hgsc.bcm.edu	37	6	149862718	149862718	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	PPIL4-90	NM_139126	exon2	c.C75A	p.C25X	ATTCAAGCAGGCT	.	77.0	4.0	56.0	0.0	.	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152832157	152832157	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	SYNE1-607	NM_033071	exon7	c.C412A	p.L138I	AATATAGAATAAT	.	190.0	23.0	153.0	0.0	.	Atlas-SNP
CHN2	1124	hgsc.bcm.edu	37	7	29519803	29519803	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	CHN2-229	NM_001039936	exon1	c.G77A	p.R26H	GGAAACGCCAAGA	.	307.0	52.0	220.0	0.0	.	Atlas-SNP
RBM48	84060	hgsc.bcm.edu	37	7	92164285	92164285	+	Splice_Site	SNP	G	G	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	.	NM_032120	exon4	c.1017+1G>T	.	AAAGAGGTAAGGT	.	124.0	13.0	107.0	0.0	.	Atlas-SNP
TRRAP	8295	hgsc.bcm.edu	37	7	98581870	98581870	+	Silent	SNP	G	G	C	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	TRRAP-923	NM_003496	exon59	c.G9102C	p.R3034R	AAGTCGGATTCAT	.	204.0	16.0	151.0	0.0	.	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157333452	157333452	+	Missense_Mutation	SNP	C	C	T	rs138836883		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	PTPRN2-295	NM_130843	exon22	c.G2917A	p.V973M	CAGCCACGGCTGT	.	267.0	20.0	162.0	0.0	C|1.000;T|0.000	Atlas-SNP
ADAM2	2515	hgsc.bcm.edu	37	8	39634610	39634610	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	ADAM2-227	NM_001464	exon11	c.T962A	p.I321N	TAAGTGATCCCCA	.	84.0	7.0	80.0	0.0	.	Atlas-SNP
CHRNB3	1142	hgsc.bcm.edu	37	8	42586825	42586825	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	CHRNB3-91	NM_000749	exon5	c.C375A	p.F125L	CCGCTTCGAAGGC	.	106.0	61.0	112.0	0.0	.	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52321748	52321748	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	PXDNL-70	NM_144651	exon17	c.C2436T	p.H812H	CAAGTCGTGCTCT	.	26.0	5.0	17.0	0.0	.	Atlas-SNP
PPEF1	5475	hgsc.bcm.edu	37	X	18822065	18822065	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	PPEF1-226	NM_006240	exon14	c.C1121T	p.T374M	CAAATACGTGCCG	.	46.0	8.0	43.0	0.0	.	Atlas-SNP
TBL1X	6907	hgsc.bcm.edu	37	X	9656179	9656180	+	In_Frame_Ins	INS	-	-	GCG	novel		TCGA-OR-A5LK-01A-11D-A29I-10	TCGA-OR-A5LK-10A-01D-A29L-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	de28f978-5783-417f-acac-610329360c22	695b49cf-c521-442f-9074-e9b47b7200c9	.	TBL1X-131	NM_001139466	exon7	c.480_481insGCG	p.S160delinsSA	.	.	84.0	28.0	14.0	0.0	.	Atlas-Indel
