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	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
MIB2	142678	broad.mit.edu	37	1	1562677	1562677	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr1:1562677T>G	uc001agg.2	+	12	1677	c.1550T>G	c.(1549-1551)GTG>GGG	p.V517G	MIB2_uc001agh.2_Missense_Mutation_p.V503G|MIB2_uc001agi.2_Missense_Mutation_p.V513G|MIB2_uc001agj.2_Missense_Mutation_p.V358G|MIB2_uc001agk.2_Missense_Mutation_p.V452G|MIB2_uc001agl.1_Missense_Mutation_p.V473G|MIB2_uc001agm.2_Missense_Mutation_p.V394G|MIB2_uc010nyq.1_Missense_Mutation_p.V473G|MIB2_uc009vkh.2_Missense_Mutation_p.V323G|MIB2_uc001agn.2_Missense_Mutation_p.V149G|MIB2_uc001ago.2_5'Flank	NM_080875	NP_543151	Q96AX9	MIB2_HUMAN	mindbomb homolog 2	517					Notch signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade	endosome	actin binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TCTTGGCAGGTGGACACCAAG	0.647													8	32	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158617396	158617396	+	Missense_Mutation	SNP	G	A	A	rs143642542	by1000genomes	TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr1:158617396G>A	uc001fst.1	-	27	4028	c.3829C>T	c.(3829-3831)CGT>TGT	p.R1277C		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1277	Spectrin 12.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TCCTTTGTACGCCCCTGCAGG	0.562													14	208	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186094769	186094769	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr1:186094769A>G	uc001grq.1	+	82	12762	c.12533A>G	c.(12532-12534)TAC>TGC	p.Y4178C	HMCN1_uc001grs.1_5'Flank	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4178	Ig-like C2-type 41.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						GAAGGACACTACACGGTCAAT	0.388													5	98	---	---	---	---	PASS
UGP2	7360	broad.mit.edu	37	2	64114692	64114692	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr2:64114692A>T	uc002scm.2	+	8	1534	c.1228A>T	c.(1228-1230)AGT>TGT	p.S410C	UGP2_uc002scl.2_Missense_Mutation_p.S399C|UGP2_uc010ypx.1_Missense_Mutation_p.S419C	NM_006759	NP_006750	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2 isoform a	410					glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0						AAACCTCTATAGTCTTAATGC	0.403													8	246	---	---	---	---	PASS
LOXL3	84695	broad.mit.edu	37	2	74763166	74763166	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr2:74763166G>A	uc002smp.1	-	7	1277	c.1205C>T	c.(1204-1206)GCC>GTC	p.A402V	LOXL3_uc002smo.1_Missense_Mutation_p.A41V|LOXL3_uc010ffm.1_Missense_Mutation_p.A402V|LOXL3_uc002smq.1_Missense_Mutation_p.A257V|LOXL3_uc010ffn.1_Missense_Mutation_p.A257V	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor	402	SRCR 3.					extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0						CCGGACCCCGGCATCCTGGCT	0.552													5	162	---	---	---	---	PASS
NCKAP5	344148	broad.mit.edu	37	2	133540002	133540002	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr2:133540002G>A	uc002ttp.2	-	14	4756	c.4382C>T	c.(4381-4383)GCT>GTT	p.A1461V	NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	1461							protein binding				0						TGAACTCACAGCATCAGTCGC	0.502													19	68	---	---	---	---	PASS
PIKFYVE	200576	broad.mit.edu	37	2	209212747	209212747	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr2:209212747G>A	uc002vcz.2	+	35	5532	c.5374G>A	c.(5374-5376)GAT>AAT	p.D1792N		NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	1792	PIPK.				cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						TGAGCCTCAAGGTGTGTTAAA	0.408													5	172	---	---	---	---	PASS
PRR21	643905	broad.mit.edu	37	2	240982173	240982173	+	Missense_Mutation	SNP	A	G	G	rs73107451	by1000genomes	TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr2:240982173A>G	uc010zod.1	-	1	227	c.227T>C	c.(226-228)ATG>ACG	p.M76T		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	proline rich 21	76	Pro-rich.									ovary(1)|skin(1)	2						ATGAAGGGACATGGGTGAAGA	0.612													3	64	---	---	---	---	PASS
LRIG1	26018	broad.mit.edu	37	3	66463350	66463350	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr3:66463350T>G	uc003dmx.2	-	6	750	c.736A>C	c.(736-738)AAC>CAC	p.N246H	LRIG1_uc010hnz.2_5'UTR|LRIG1_uc010hoa.2_Missense_Mutation_p.N246H	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	246	Extracellular (Potential).|LRR 8.					integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TTGCTGATGTTGTTTCGCTGA	0.532													16	60	---	---	---	---	PASS
CHRD	8646	broad.mit.edu	37	3	184104857	184104857	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr3:184104857A>G	uc003fov.2	+	18	2555	c.2309A>G	c.(2308-2310)GAC>GGC	p.D770G	CHRD_uc003fow.2_Missense_Mutation_p.D400G|CHRD_uc003fox.2_Missense_Mutation_p.D770G|CHRD_uc003foy.2_Missense_Mutation_p.D400G|CHRD_uc010hyc.2_Missense_Mutation_p.D360G|CHRD_uc011brr.1_Missense_Mutation_p.D312G	NM_003741	NP_003732	Q9H2X0	CHRD_HUMAN	chordin precursor	770					BMP signaling pathway involved in spinal cord dorsal/ventral patterning|floor plate development|negative regulation of BMP signaling pathway|negative regulation of cell migration|positive regulation of cell adhesion|skeletal system development	extracellular space	cytokine binding			skin(2)|ovary(1)	3	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GATGTCAGAGACTTGCCAGGG	0.592													20	78	---	---	---	---	PASS
FYTTD1	84248	broad.mit.edu	37	3	197497068	197497068	+	Silent	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr3:197497068G>A	uc003fyi.2	+	4	669	c.450G>A	c.(448-450)CAG>CAA	p.Q150Q	FYTTD1_uc011bui.1_Silent_p.Q124Q|FYTTD1_uc011buj.1_Intron|FYTTD1_uc011buk.1_Silent_p.Q83Q	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1	150					mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		ATGAAGGGCAGAGGAAACCAG	0.348													4	21	---	---	---	---	PASS
TDO2	6999	broad.mit.edu	37	4	156835562	156835562	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr4:156835562C>T	uc003ipf.1	+	8	878	c.814C>T	c.(814-816)CGT>TGT	p.R272C		NM_005651	NP_005642	P48775	T23O_HUMAN	tryptophan 2,3-dioxygenase	272					tryptophan catabolic process to kynurenine	cytosol	tryptophan 2,3-dioxygenase activity				0	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)	L-Tryptophan(DB00150)	TGATGAGAAACGTCATGAACA	0.348													17	46	---	---	---	---	PASS
PCDHGA2	56113	broad.mit.edu	37	5	140720334	140720334	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr5:140720334G>T	uc003ljk.1	+	1	1981	c.1796G>T	c.(1795-1797)GGC>GTC	p.G599V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.G599V	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	599	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGACTCGGGCCAGAACGCC	0.697													10	113	---	---	---	---	PASS
TRIM41	90933	broad.mit.edu	37	5	180651243	180651243	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr5:180651243T>G	uc003mne.1	+	1	938	c.244T>G	c.(244-246)TGG>GGG	p.W82G	uc003mnb.1_3'UTR|TRIM41_uc003mnc.1_Missense_Mutation_p.W82G|TRIM41_uc003mnd.1_Missense_Mutation_p.W82G|TRIM41_uc003mnf.1_RNA	NM_033549	NP_291027	Q8WV44	TRI41_HUMAN	tripartite motif-containing 41 isoform 1	82	Glu-rich.					cytoplasm|nucleus	ligase activity|protein binding|zinc ion binding				0	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGCGCGGGGTGGGACACCCC	0.493													8	82	---	---	---	---	PASS
FAM50B	26240	broad.mit.edu	37	6	3850735	3850735	+	Silent	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr6:3850735C>T	uc003mvu.2	+	2	802	c.690C>T	c.(688-690)GCC>GCT	p.A230A		NM_012135	NP_036267	Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	230						nucleus				pancreas(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)				TGCGCTCCGCCGGCGTGGAGC	0.652													3	66	---	---	---	---	PASS
MIR550-2	693134	broad.mit.edu	37	7	32772646	32772646	+	RNA	SNP	C	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr7:32772646C>A	hsa-mir-550-2|MI0003601	+			c.54C>A			AVL9_uc011kai.1_Intron|LOC441208_uc003tcy.3_Intron																	0						CTGTTGTTGTCAGATAGTGTC	0.493													4	87	---	---	---	---	PASS
ZC3HAV1	56829	broad.mit.edu	37	7	138764546	138764546	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr7:138764546G>C	uc003vun.2	-	4	1529	c.1141C>G	c.(1141-1143)CTA>GTA	p.L381V	ZC3HAV1_uc003vuo.2_5'Flank|ZC3HAV1_uc003vup.2_Missense_Mutation_p.L381V	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1	381					response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						GCGGCAGGTAGCGTGGGAGAA	0.532													68	201	---	---	---	---	PASS
PLEC	5339	broad.mit.edu	37	8	144995013	144995013	+	Silent	SNP	G	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr8:144995013G>T	uc003zaf.1	-	32	9557	c.9387C>A	c.(9385-9387)ATC>ATA	p.I3129I	PLEC_uc003zab.1_Silent_p.I2992I|PLEC_uc003zac.1_Silent_p.I2996I|PLEC_uc003zad.2_Silent_p.I2992I|PLEC_uc003zae.1_Silent_p.I2960I|PLEC_uc003zag.1_Silent_p.I2970I|PLEC_uc003zah.2_Silent_p.I2978I|PLEC_uc003zaj.2_Silent_p.I3019I	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	3129	Plectin 6.|Globular 2.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9						GCTCGCGGTCGATGACCCTGC	0.672													3	32	---	---	---	---	PASS
ZNF782	158431	broad.mit.edu	37	9	99580381	99580381	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr9:99580381C>T	uc004awp.1	-	6	2205	c.1924G>A	c.(1924-1926)GGG>AGG	p.G642R	ZNF782_uc011lup.1_Missense_Mutation_p.G510R	NM_001001662	NP_001001662	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	642					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				GGTTTCTCCCCGGTGTGAGTT	0.433													7	233	---	---	---	---	PASS
PANK1	53354	broad.mit.edu	37	10	91359112	91359112	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr10:91359112A>T	uc001kgp.1	-	3	1363	c.1207T>A	c.(1207-1209)TGC>AGC	p.C403S	PANK1_uc001kgn.1_Missense_Mutation_p.C178S|PANK1_uc001kgo.1_Missense_Mutation_p.C178S|PANK1_uc009xtu.1_Missense_Mutation_p.C205S	NM_148977	NP_683878	Q8TE04	PANK1_HUMAN	pantothenate kinase 1 isoform alpha	403					coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)	TTATCAAGGCAGTACGGCTTT	0.448													38	338	---	---	---	---	PASS
C10orf81	79949	broad.mit.edu	37	10	115527188	115527188	+	Silent	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr10:115527188C>T	uc001lat.1	+	4	853	c.291C>T	c.(289-291)GTC>GTT	p.V97V	C10orf81_uc001lar.1_Silent_p.V103V|C10orf81_uc009xyc.1_Silent_p.V15V|C10orf81_uc001las.1_Silent_p.V15V	NM_024889	NP_079165	Q5SXH7	CJ081_HUMAN	hypothetical protein LOC79949	97	PH.									central_nervous_system(1)	1		Colorectal(252;0.175)		Epithelial(162;0.0181)|all cancers(201;0.0204)		CTGATGAGGTCATGTCCATCA	0.403													25	73	---	---	---	---	PASS
HBG2	3048	broad.mit.edu	37	11	5275542	5275542	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr11:5275542C>T	uc001mai.1	-	2	732	c.295G>A	c.(295-297)GTG>ATG	p.V99M	HBG2_uc001mak.1_RNA|HBG2_uc001maj.1_Missense_Mutation_p.V99M	NM_000559	NP_000550	P69892	HBG2_HUMAN	A-gamma globin	99					blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCAGGATCCACATGCAGCTTG	0.498													46	276	---	---	---	---	PASS
OR5D16	390144	broad.mit.edu	37	11	55606429	55606429	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr11:55606429C>A	uc010rio.1	+	1	202	c.202C>A	c.(202-204)CTC>ATC	p.L68I		NM_001005496	NP_001005496	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D,	68	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_epithelial(135;0.208)				CCTCAACCACCTCTCCTTTGT	0.433													77	475	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88583140	88583140	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr11:88583140G>A	uc001pcq.2	-	2	1045	c.845C>T	c.(844-846)ACG>ATG	p.T282M	GRM5_uc009yvm.2_Missense_Mutation_p.T282M	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	282	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	ACCTCTCACCGTCATGCCCTC	0.522													53	112	---	---	---	---	PASS
PTPRO	5800	broad.mit.edu	37	12	15731856	15731856	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr12:15731856C>T	uc001rcv.1	+	20	3073	c.2899C>T	c.(2899-2901)CGT>TGT	p.R967C	PTPRO_uc001rcw.1_Missense_Mutation_p.R939C|PTPRO_uc001rcx.1_Missense_Mutation_p.R156C|PTPRO_uc001rcy.1_Missense_Mutation_p.R156C|PTPRO_uc001rcz.1_Missense_Mutation_p.R128C|PTPRO_uc001rda.1_Missense_Mutation_p.R128C	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	967	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				ATGTAAAAACCGTTACACAAA	0.393													21	129	---	---	---	---	PASS
UBC	7316	broad.mit.edu	37	12	125397358	125397358	+	Silent	SNP	T	C	C			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr12:125397358T>C	uc001ugs.3	-	2	1408	c.960A>G	c.(958-960)GAA>GAG	p.E320E	UBC_uc001ugr.2_RNA|UBC_uc001ugu.1_Silent_p.E320E|UBC_uc001ugt.2_Silent_p.E320E|UBC_uc001ugv.2_Intron|UBC_uc001ugw.2_Silent_p.E168E	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	320	Ubiquitin-like 5.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TCGGCTCCACTTCGAGAGTGA	0.522													7	346	---	---	---	---	PASS
CCNA1	8900	broad.mit.edu	37	13	37006834	37006834	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr13:37006834G>A	uc001uvr.3	+	1	426	c.76G>A	c.(76-78)GAA>AAA	p.E26K	CCNA1_uc010teo.1_Intron|CCNA1_uc010abq.2_Intron|CCNA1_uc010abp.2_Intron|CCNA1_uc001uvs.3_Missense_Mutation_p.E26K|CCNA1_uc010abr.2_RNA	NM_003914	NP_003905	P78396	CCNA1_HUMAN	cyclin A1 isoform a	26					cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding			lung(2)|skin(2)|ovary(1)	5		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		TCTCAGCTGGGAAGGACCGGG	0.552													11	41	---	---	---	---	PASS
GOLGA5	9950	broad.mit.edu	37	14	93264023	93264023	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr14:93264023A>C	uc001yaz.1	+	2	423	c.241A>C	c.(241-243)ACT>CCT	p.T81P		NM_005113	NP_005104	Q8TBA6	GOGA5_HUMAN	Golgi autoantigen, golgin subfamily a, 5	81	Cytoplasmic (Potential).				Golgi organization	cis-Golgi network|integral to membrane	ATP binding|protein homodimerization activity|protein tyrosine kinase activity|Rab GTPase binding			ovary(2)|lung(1)	3		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		CTTAGCTGGCACTGCAAATGT	0.413			T	RET	papillary thyroid								10	175	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105411091	105411091	+	Missense_Mutation	SNP	G	A	A	rs143814844	by1000genomes	TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr14:105411091G>A	uc010axc.1	-	7	10817	c.10697C>T	c.(10696-10698)ACG>ATG	p.T3566M	AHNAK2_uc001ypx.2_Missense_Mutation_p.T3466M	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3566						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CACTTTGGGCGTCTTTAAACT	0.612													93	235	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41384239	41384239	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr15:41384239T>G	uc001zni.2	-	5	736	c.523A>C	c.(523-525)AGT>CGT	p.S175R	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	175	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						TTGTCTTTACTATACTTATTT	0.328													57	184	---	---	---	---	PASS
PARP16	54956	broad.mit.edu	37	15	65559013	65559013	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr15:65559013C>T	uc002aoo.2	-	3	660	c.406G>A	c.(406-408)GCC>ACC	p.A136T	PARP16_uc002aop.2_Intron|PARP16_uc002aoq.2_Missense_Mutation_p.A136T	NM_017851	NP_060321	Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	136	PARP catalytic.					integral to membrane	NAD+ ADP-ribosyltransferase activity			lung(2)	2						TAAAATTTGGCGTTGGCTGGG	0.458													4	86	---	---	---	---	PASS
TXNDC11	51061	broad.mit.edu	37	16	11785489	11785489	+	Silent	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr16:11785489G>A	uc010buu.1	-	9	1700	c.1638C>T	c.(1636-1638)TTC>TTT	p.F546F	TXNDC11_uc002dbg.1_Silent_p.F519F	NM_015914	NP_056998	Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	546					cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0						CAGAGTCGATGAAGCCTGACA	0.468													98	205	---	---	---	---	PASS
VWA3A	146177	broad.mit.edu	37	16	22120821	22120821	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr16:22120821G>A	uc010vbq.1	+	7	598	c.502G>A	c.(502-504)GGG>AGG	p.G168R	VWA3A_uc010bxc.2_Missense_Mutation_p.G155R	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	168						extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		CCTCATCAAAGGGGCCAGAGT	0.512													9	16	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27782957	27782957	+	Silent	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr16:27782957G>A	uc002dow.2	+	22	4206	c.4182G>A	c.(4180-4182)CCG>CCA	p.P1394P		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	1394										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						ACGAGGCACCGCTGATGCCCT	0.607													7	134	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	74425461	74425461	+	Missense_Mutation	SNP	A	G	G	rs2868593		TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr16:74425461A>G	uc010vmt.1	+	6	633	c.632A>G	c.(631-633)CAT>CGT	p.H211R						RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		TGTCTCCTTCATCCCCTTCCA	0.493													8	244	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161578	90161578	+	Silent	SNP	G	A	A	rs13337896	by1000genomes	TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr16:90161578G>A	uc002fqp.2	+	3	931	c.453G>A	c.(451-453)ACG>ACA	p.T151T	uc002fqq.2_Silent_p.T168T					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		GCCAAGGGACGCTACACCGAA	0.587													5	54	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10430104	10430104	+	Silent	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr17:10430104G>A	uc010coi.2	-	30	4127	c.3999C>T	c.(3997-3999)AAC>AAT	p.N1333N	uc002gml.1_Intron|MYH2_uc002gmp.3_Silent_p.N1333N|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1333	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						GCGCCAGGGCGTTCTTGGCCT	0.498													5	151	---	---	---	---	PASS
PGAP3	93210	broad.mit.edu	37	17	37830251	37830251	+	Silent	SNP	G	A	A	rs147768703	byFrequency	TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr17:37830251G>A	uc002hsj.2	-	5	595	c.552C>T	c.(550-552)TGC>TGT	p.C184C	PGAP3_uc010cvy.2_RNA|PGAP3_uc010wej.1_Silent_p.C163C|PGAP3_uc002hsk.2_Silent_p.C133C|PGAP3_uc010cvz.2_Intron	NM_033419	NP_219487	Q96FM1	PGAP3_HUMAN	per1-like domain containing 1 precursor	184	Helical; (Potential).				GPI anchor biosynthetic process	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	hydrolase activity, acting on ester bonds			upper_aerodigestive_tract(1)	1						CTCACCTGACGCAGCACAGGT	0.587													20	36	---	---	---	---	PASS
WNK4	65266	broad.mit.edu	37	17	40934857	40934857	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr17:40934857G>A	uc002ibj.2	+	2	721	c.700G>A	c.(700-702)GTC>ATC	p.V234I	WNK4_uc010wgx.1_5'UTR|WNK4_uc002ibk.1_5'Flank|WNK4_uc010wgy.1_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	234	Protein kinase.				intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CCCCAACATCGTCCGCTTCTA	0.602													24	60	---	---	---	---	PASS
NMT1	4836	broad.mit.edu	37	17	43138780	43138780	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr17:43138780A>T	uc002ihz.2	+	1	101	c.83A>T	c.(82-84)GAG>GTG	p.E28V	DCAKD_uc010dab.1_5'Flank|NMT1_uc010dac.1_RNA|NMT1_uc002iia.2_RNA	NM_021079	NP_066565	P30419	NMT1_HUMAN	N-myristoyltransferase 1	28					activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|N-terminal protein myristoylation|protein lipoylation	actin cytoskeleton|cell junction|cytosol	glycylpeptide N-tetradecanoyltransferase activity				0		Prostate(33;0.155)				AACGGCCATGAGCACTGCAGC	0.602													3	36	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	76497504	76497504	+	RNA	SNP	C	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr17:76497504C>A	uc002jvt.1	+	2		c.2963C>A								Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		AGCATGCCTCCAAGGCCGGTC	0.612													3	37	---	---	---	---	PASS
SLC1A6	6511	broad.mit.edu	37	19	15067354	15067354	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr19:15067354C>T	uc002naa.1	-	6	1111	c.1103G>A	c.(1102-1104)CGG>CAG	p.R368Q	SLC1A6_uc010dzu.1_Intron|SLC1A6_uc010xod.1_Missense_Mutation_p.R304Q	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity	368					synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)	GAAGGGGTTCCGGTGAGTGAC	0.607													3	59	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	19	23159308	23159308	+	RNA	SNP	A	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr19:23159308A>T	uc002nqy.1	-	3		c.842T>A			uc002nqz.1_Missense_Mutation_p.S213R					Homo sapiens zinc finger protein 117, mRNA (cDNA clone IMAGE:40112371).																		CTCCAGCATGACTTCTCTTAT	0.418													4	131	---	---	---	---	PASS
ZNF814	730051	broad.mit.edu	37	19	58385748	58385748	+	Missense_Mutation	SNP	G	A	A	rs145250945		TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr19:58385748G>A	uc002qqo.2	-	3	1282	c.1010C>T	c.(1009-1011)GCT>GTT	p.A337V	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	337	C2H2-type 5.				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						ACTGAAGCTAGCATATTTGCT	0.353													5	11	---	---	---	---	PASS
BANF2	140836	broad.mit.edu	37	20	17705710	17705710	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr20:17705710G>A	uc002wpz.2	+	3	314	c.40G>A	c.(40-42)GAA>AAA	p.E14K	BANF2_uc010zrs.1_Missense_Mutation_p.E21K|BANF2_uc002wqa.2_Missense_Mutation_p.E14K	NM_178477	NP_848572	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2 isoform 1	14						cytoplasm|nucleus	DNA binding			skin(1)	1						CTTCCTCTCCGAACCCATTGG	0.502													42	161	---	---	---	---	PASS
OGFR	11054	broad.mit.edu	37	20	61444845	61444845	+	Silent	SNP	G	A	A	rs112106909		TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr20:61444845G>A	uc002ydj.2	+	7	1913	c.1878G>A	c.(1876-1878)CCG>CCA	p.P626P	OGFR_uc002ydk.2_Silent_p.P609P|OGFR_uc002ydl.2_Silent_p.P574P|uc011aam.1_Intron	NM_007346	NP_031372	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	626	6.|7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				regulation of cell growth	cytoplasm|membrane|nucleus	opioid receptor activity				0	Breast(26;3.65e-08)					GCCCCCGCCCGGCAGGACCTG	0.746													5	45	---	---	---	---	PASS
TSSK2	23617	broad.mit.edu	37	22	19119550	19119550	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr22:19119550C>A	uc002zow.2	+	1	1230	c.638C>A	c.(637-639)TCC>TAC	p.S213Y	DGCR14_uc002zot.2_3'UTR|DGCR14_uc002zou.2_3'UTR|DGCR14_uc002zov.2_RNA	NM_053006	NP_443732	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	213	Protein kinase.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)	1	Colorectal(54;0.0993)					GTCTGCGGCTCCATGCCCTAT	0.592													87	144	---	---	---	---	PASS
EMID1	129080	broad.mit.edu	37	22	29628247	29628247	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr22:29628247C>A	uc003aen.2	+	8	748	c.673C>A	c.(673-675)CCA>ACA	p.P225T	EMID1_uc003aem.2_Missense_Mutation_p.P227T|EMID1_uc003aeo.2_Missense_Mutation_p.P227T|EMID1_uc003aep.2_Missense_Mutation_p.P227T	NM_133455	NP_597712	Q96A84	EMID1_HUMAN	EMI domain containing 1	225	Collagen-like.					collagen					0						CATTGCAGGTCCACAGGGCCC	0.687													46	94	---	---	---	---	PASS
MED12	9968	broad.mit.edu	37	X	70344181	70344181	+	Silent	SNP	T	C	C			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chrX:70344181T>C	uc004dyy.2	+	13	2116	c.1917T>C	c.(1915-1917)GAT>GAC	p.D639D	MED12_uc011mpq.1_Silent_p.D639D|MED12_uc004dyz.2_Silent_p.D639D|MED12_uc004dza.2_Silent_p.D486D	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	639					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)					CCTTTGATGATCCTGCCGATG	0.542													4	8	---	---	---	---	PASS
BCORL1	63035	broad.mit.edu	37	X	129155089	129155089	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chrX:129155089C>A	uc004evb.1	+	5	3685	c.3571C>A	c.(3571-3573)CAG>AAG	p.Q1191K	BCORL1_uc010nrd.1_Missense_Mutation_p.Q1093K	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	1191					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						GCCGGAGTCCCAGTCTCCAGG	0.622													3	23	---	---	---	---	PASS
RENBP	5973	broad.mit.edu	37	X	153200994	153200994	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chrX:153200994G>T	uc004fjo.1	-	10	1283	c.1113C>A	c.(1111-1113)TAC>TAA	p.Y371*	NAA10_uc004fjm.1_5'Flank|NAA10_uc004fjn.1_5'Flank|NAA10_uc011mzg.1_5'Flank	NM_002910	NP_002901	P51606	RENBP_HUMAN	renin binding protein	371					mannose metabolic process|regulation of blood pressure		endopeptidase inhibitor activity|mannose-6-phosphate isomerase activity|N-acylglucosamine 2-epimerase activity			ovary(1)|pancreas(1)	2	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	CTCGGCTCAGGTAGCCAAACC	0.542													7	76	---	---	---	---	PASS
HCG22	285834	broad.mit.edu	37	6	31023076	31023078	+	RNA	DEL	GAG	-	-			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr6:31023076_31023078delGAG	uc010jsi.1	+	1		c.1093_1095delGAG			HCG22_uc003nsj.1_Intron	NR_003948				Homo sapiens HLA complex group 22 (HCG22), non-coding RNA.												0						aaaaaaaaaaGAGAGAGAGAGAG	0.177													4	5	---	---	---	---	
NKX3-1	4824	broad.mit.edu	37	8	23539135	23539135	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr8:23539135delA	uc011kzx.1	-	2	352	c.304delT	c.(304-306)TATfs	p.Y102fs	NKX3-1_uc003xdv.1_Intron	NM_006167	NP_006158	Q99801	NKX31_HUMAN	NK3 homeobox 1	102					negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding				0		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		TCCAACAGATAAGACCCCAAG	0.527													178	55	---	---	---	---	
ZNF395	55893	broad.mit.edu	37	8	28209153	28209154	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr8:28209153_28209154insA	uc003xgq.2	-	7	1179_1180	c.1091_1092insT	c.(1090-1092)CTGfs	p.L364fs	ZNF395_uc003xgt.2_Frame_Shift_Ins_p.L364fs|ZNF395_uc003xgr.2_Frame_Shift_Ins_p.L364fs|ZNF395_uc003xgs.2_Frame_Shift_Ins_p.L364fs	NM_018660	NP_061130	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	364					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GAAGAGCAGACAGAGGCAGGCC	0.564													257	13	---	---	---	---	
TCTN2	79867	broad.mit.edu	37	12	124171487	124171488	+	Frame_Shift_Ins	INS	-	ACGAC	ACGAC			TCGA-CH-5745-01A-11D-1576-08	TCGA-CH-5745-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	51db8439-c35f-472e-baf0-8e6e22833c39	e32b30c3-6ed3-42ce-ad17-69b26146f7e4	g.chr12:124171487_124171488insACGAC	uc001ufp.2	+	6	797_798	c.669_670insACGAC	c.(667-672)ACGACGfs	p.T223fs	TCTN2_uc009zya.2_Frame_Shift_Ins_p.T222fs	NM_024809	NP_079085	Q96GX1	TECT2_HUMAN	tectonic family member 2 isoform 1	223_224	Extracellular (Potential).				cilium assembly|smoothened signaling pathway	integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		CTGCTGGGACGACGACACGTGG	0.525													799	7	---	---	---	---	
