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	TranscriptID	Exon	ChromChange	AAChange	COSMIC_Codon	COSMIC_Gene	Drug_Target
CUL1	8454	hgsc.bcm.edu	36	7	148082047	148082047	+	Nonsense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_003592	exon3	c.C187T	p.R63X	.	.	.
PKD1L1	168507	hgsc.bcm.edu	36	7	47845683	47845683	+	Silent	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_138295	exon36	c.G5655A	p.L1885L	.	.	.
CDH22	64405	hgsc.bcm.edu	36	20	44303275	44303275	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_021248	exon2	c.G284A	p.G95E	.	.	.
CSE1L	1434	hgsc.bcm.edu	36	20	47144892	47144892	+	Silent	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_001316	exon24	c.C2811T	p.T937T	.	.	.
ZNFX1	57169	hgsc.bcm.edu	36	20	47299374	47299374	+	Silent	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_021035	exon14	c.G3594A	p.S1198S	.	.	.
MYT1	4661	hgsc.bcm.edu	36	20	62313092	62313092	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_004535	exon8	c.C1381T	p.R461C	.	.	.
MSR1	4481	hgsc.bcm.edu	36	8	16070656	16070656	+	Silent	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_138716	exon4	c.C312T	p.S104S	.	.	.
ATP6V0D2	245972	hgsc.bcm.edu	36	8	87222870	87222870	+	Missense_Mutation	SNP	A	A	G	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_152565	exon4	c.A557G	p.Y186C	.	.	.
FLG	2312	hgsc.bcm.edu	36	1	150552906	150552906	+	Silent	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_002016	exon3	c.C1080T	p.H360H	.	.	.
TARBP1	6894	hgsc.bcm.edu	36	1	232594035	232594035	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_005646	exon30	c.C4777T	p.R1593C	.	.	.
SLC6A9	6536	hgsc.bcm.edu	36	1	44235835	44235835	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_201649	exon14	c.G2090A	p.G697D	.	.	.
PGM1	5236	hgsc.bcm.edu	36	1	63892634	63892634	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_001172818	exon10	c.G1562A	p.R521Q	.	.	.
SLC5A12	159963	hgsc.bcm.edu	36	11	26699608	26699608	+	Missense_Mutation	SNP	A	A	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_178498	exon1	c.T230G	p.F77C	.	.	.
TMEM14C	51522	hgsc.bcm.edu	36	6	10838838	10838838	+	Silent	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_016462	exon6	c.C292T	p.L98L	.	.	.
PEX3	8504	hgsc.bcm.edu	36	6	143848071	143848071	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_003630	exon11	c.T1031C	p.F344S	.	.	.
SOD2	6648	hgsc.bcm.edu	36	6	160025973	160025973	+	Silent	SNP	G	G	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_001024466	exon3	c.C309A	p.V103V	.	.	.
ME1	4199	hgsc.bcm.edu	36	6	84081818	84081818	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_002395	exon6	c.C634T	p.R212W	.	.	.
MAP2K3	5606	hgsc.bcm.edu	36	17	21144780	21144780	+	Missense_Mutation	SNP	G	G	T	rs56067280	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_002756	exon5	c.G194T	p.R65L	.	.	.
KIF2B	84643	hgsc.bcm.edu	36	17	49256475	49256475	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_032559	exon1	c.G1082A	p.G361E	.	.	.
TP53	7157	hgsc.bcm.edu	36	17	7519200	7519200	+	Missense_Mutation	SNP	G	G	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_001126114	exon5	c.C455G	p.P152R	TP53,thyroid,NS,Substitution - Missense,0	.	.
UQCRC2	7385	hgsc.bcm.edu	36	16	21881632	21881632	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_003366	exon6	c.C439T	p.R147C	.	.	.
RANBP10	57610	hgsc.bcm.edu	36	16	66326440	66326440	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_020850	exon6	c.C598T	p.L200F	.	.	.
CDH2	1000	hgsc.bcm.edu	36	18	23827479	23827479	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_001792	exon8	c.G1141A	p.E381K	.	.	.
DTNA	1837	hgsc.bcm.edu	36	18	30713671	30713671	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_001198938	exon18	c.C1891T	p.R631C	.	.	.
SLC9A9	285195	hgsc.bcm.edu	36	3	144775629	144775629	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_173653	exon8	c.G991A	p.G331S	.	.	.
PLXNB1	5364	hgsc.bcm.edu	36	3	48440396	48440396	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_002673	exon3	c.G629A	p.R210H	.	.	.
KRAS	3845	hgsc.bcm.edu	36	12	25269828	25269828	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_004985	exon4	c.C437T	p.A146V	KRAS,large_intestine,NS,Substitution - Missense,-1	.	.
MAP3K12	7786	hgsc.bcm.edu	36	12	52163995	52163995	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_001193511	exon8	c.A1325G	p.E442G	MAP3K12,breast,NS,Substitution - Missense,-1	.	.
TMTC3	160418	hgsc.bcm.edu	36	12	87066234	87066234	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_181783	exon2	c.T11C	p.I4T	.	.	.
ATP10A	57194	hgsc.bcm.edu	36	15	23479609	23479609	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_024490	exon17	c.G3409A	p.V1137M	.	.	.
PPP3CA	5530	hgsc.bcm.edu	36	4	102166131	102166131	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_001130691	exon13	c.G1450A	p.A484T	.	.	.
GSTCD	79807	hgsc.bcm.edu	36	4	106963597	106963597	+	Silent	SNP	A	A	G	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_024751	exon6	c.A1017G	p.Q339Q	.	.	.
CTSO	1519	hgsc.bcm.edu	36	4	157069006	157069006	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_001334	exon7	c.G863A	p.R288Q	.	.	.
AMOT	154796	hgsc.bcm.edu	36	X	111909460	111909460	+	Nonsense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_133265	exon11	c.C1351T	p.R451X	.	.	.
ZNF645	158506	hgsc.bcm.edu	36	X	22201989	22201989	+	Silent	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_152577	exon1	c.C960T	p.Y320Y	.	.	.
SRPX	8406	hgsc.bcm.edu	36	X	37894044	37894044	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_006307	exon10	c.A1259G	p.D420G	.	.	.
OPHN1	4983	hgsc.bcm.edu	36	X	67200445	67200445	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_002547	exon21	c.C2134T	p.R712W	.	.	.
FAM49A	81553	hgsc.bcm.edu	36	2	16597698	16597698	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_030797	exon12	c.C959A	p.A320E	.	.	.
SLC25A12	8604	hgsc.bcm.edu	36	2	172350094	172350094	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_003705	exon18	c.C1973T	p.P658L	.	.	.
SLC30A3	7781	hgsc.bcm.edu	36	2	27333169	27333169	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_003459	exon6	c.C874T	p.L292F	.	.	.
SPDYA	245711	hgsc.bcm.edu	36	2	28898735	28898735	+	Missense_Mutation	SNP	A	A	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_182756	exon5	c.A335C	p.K112T	.	.	.
COL5A1	1289	hgsc.bcm.edu	36	9	136731576	136731576	+	Missense_Mutation	SNP	C	C	T	rs41306397	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_000093	exon3	c.C278T	p.A93V	.	.	.
FRMPD1	22844	hgsc.bcm.edu	36	9	37730790	37730790	+	Silent	SNP	C	C	G	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_014907	exon15	c.C2265G	p.A755A	.	.	.
PTCH1	5727	hgsc.bcm.edu	36	9	97271088	97271088	+	Silent	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_001083605	exon14	c.G1563A	p.T521T	.	.	.
NALCN	259232	hgsc.bcm.edu	36	13	100560985	100560985	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_052867	exon20	c.A2350G	p.T784A	.	.	.
TMCO3	55002	hgsc.bcm.edu	36	13	113241726	113241726	+	Silent	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_017905	exon10	c.G1593A	p.A531A	.	.	.
GPC5	2262	hgsc.bcm.edu	36	13	91178836	91178836	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_004466	exon4	c.G1070A	p.R357H	.	.	.
TDRD1	56165	hgsc.bcm.edu	36	10	115937726	115937726	+	Missense_Mutation	SNP	A	A	C	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_198795	exon2	c.A146C	p.N49T	.	.	.
BEND7	222389	hgsc.bcm.edu	36	10	13582073	13582073	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_152751	exon3	c.G3A	p.M1I	.	.	.
APC	324	hgsc.bcm.edu	36	5	112192524	112192524	+	Nonsense_Mutation	SNP	G	G	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_001127511	exon12	c.G1645T	p.G549X	.	.	.
NDST1	3340	hgsc.bcm.edu	36	5	149908035	149908035	+	Silent	SNP	C	C	T	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_001543	exon12	c.C2208T	p.A736A	.	.	.
CDH9	1007	hgsc.bcm.edu	36	5	26921868	26921868	+	Missense_Mutation	SNP	T	T	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	NM_016279	exon10	c.A1594T	p.T532S	.	.	.
RAI14	26064	hgsc.bcm.edu	36	5	34860119	34860119	+	Silent	SNP	G	G	A	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	NM_001145522	exon14	c.G2328A	p.S776S	.	.	.
AMY1B	277	hgsc.bcm.edu	36	1	104037558	104037558	+	Missense_Mutation	SNP	T	T	G	novel	unknown	TCGA-AG-3611-01	TCGA-AG-3611-01	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	.	.	.	.	.	.	.
