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	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
RER1	11079	broad.mit.edu	37	1	2333758	2333758	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2333758A>G	uc001aje.1	+	6	669	c.478A>G	c.(478-480)ATC>GTC	p.I160V	RER1_uc001ajf.1_3'UTR	NM_007033	NP_008964	O15258	RER1_HUMAN	RER1 retention in endoplasmic reticulum 1	160	Helical; (Potential).			HAATKGILVAMVCTFFDAFNVPVFWPILVMYFIMLFCITMK RQIKHMIKYRYIPFTHGKRRYRGKEDAGKAFAS -> DASV CGDGRCSCKAGGGRQCPVLAADAALTFSPHLKACGYQGHPC GYGLYFLRRFQRPGVLADSGDVLHHALLYHDEEANQAHD (in Ref. 2; AAC72940).	retrograde vesicle-mediated transport, Golgi to ER	integral to Golgi membrane					0	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.28e-37)|OV - Ovarian serous cystadenocarcinoma(86;8.29e-23)|GBM - Glioblastoma multiforme(42;4.71e-08)|Colorectal(212;4.73e-05)|COAD - Colon adenocarcinoma(227;0.00021)|Kidney(185;0.00116)|BRCA - Breast invasive adenocarcinoma(365;0.00459)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0182)|Lung(427;0.204)		GCTCTTCTGTATCACGATGAA	0.552													28	78	---	---	---	---	PASS
MSH4	4438	broad.mit.edu	37	1	76262748	76262748	+	Silent	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76262748T>C	uc001dhd.1	+	1	119	c.78T>C	c.(76-78)CCT>CCC	p.P26P		NM_002440	NP_002431	O15457	MSH4_HUMAN	mutS homolog 4	26					chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			lung(3)|ovary(2)	5						CCCGCTCACCTCAGGGTCCCC	0.632								MMR					13	38	---	---	---	---	PASS
LPPR4	9890	broad.mit.edu	37	1	99767414	99767414	+	Silent	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99767414T>C	uc001dse.2	+	6	1033	c.927T>C	c.(925-927)TAT>TAC	p.Y309Y	LPPR4_uc010oue.1_Intron	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	309	Helical; (Potential).						phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		TTGATGTCTATTGTGGCTTTT	0.358													9	120	---	---	---	---	PASS
PSMA5	5686	broad.mit.edu	37	1	109969033	109969033	+	5'UTR	SNP	C	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109969033C>G	uc001dxn.2	-	1					PSMA5_uc010ovj.1_5'UTR	NM_002790	NP_002781	P28066	PSA5_HUMAN	proteasome alpha 5 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	protein binding|threonine-type endopeptidase activity				0		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		TCACCGGCAGCCAACTCACCC	0.622													12	24	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144829052	144829052	+	Intron	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144829052C>T	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|uc001elr.3_RNA			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CCACGTATCTCTGGGTAGCTA	0.443													2	4	---	---	---	---	PASS
GPR89A	653519	broad.mit.edu	37	1	145764885	145764885	+	3'UTR	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145764885T>C	uc001eot.2	-	14					NBPF10_uc001emp.3_Intron|GPR89A_uc001eop.2_3'UTR|GPR89A_uc001eoq.2_RNA|GPR89A_uc001eor.2_3'UTR|GPR89A_uc010ozb.1_3'UTR|GPR89A_uc001eos.2_3'UTR|GPR89A_uc010ozc.1_3'UTR|GPR89A_uc010ozd.1_3'UTR	NM_001097612	NP_001091081	B7ZAQ6	GPHRA_HUMAN	G protein-coupled receptor 89A isoform 1						intracellular pH reduction|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein transport	Golgi cisterna membrane|Golgi-associated vesicle membrane|integral to membrane	signal transducer activity|voltage-gated anion channel activity				0	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			GGAAGGAGTATGCTATGAAGG	0.423													4	16	---	---	---	---	PASS
GON4L	54856	broad.mit.edu	37	1	155747557	155747557	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155747557C>A	uc001flz.2	-	15	2044	c.1947G>T	c.(1945-1947)GAG>GAT	p.E649D	GON4L_uc001fly.1_Missense_Mutation_p.E649D|GON4L_uc009wrh.1_Missense_Mutation_p.E649D|GON4L_uc001fma.1_Missense_Mutation_p.E649D|GON4L_uc001fmb.3_5'Flank|GON4L_uc001fmc.2_Missense_Mutation_p.E649D|GON4L_uc001fmd.3_Missense_Mutation_p.E649D|GON4L_uc009wri.2_Missense_Mutation_p.E235D|GON4L_uc009wrj.1_Missense_Mutation_p.E164D|GON4L_uc001fme.2_Missense_Mutation_p.E477D	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	649					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					GTTCAAATAGCTCCTTCACTG	0.443													25	60	---	---	---	---	PASS
LHX9	56956	broad.mit.edu	37	1	197886867	197886867	+	5'UTR	SNP	C	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197886867C>G	uc001guk.1	+	1					LHX9_uc009wzc.1_Intron|LHX9_uc001gui.1_Intron|LHX9_uc001guj.1_Intron	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1						motor axon guidance|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						CCTCCATCCTCGAGCGTCTCT	0.567													22	36	---	---	---	---	PASS
FMOD	2331	broad.mit.edu	37	1	203316461	203316461	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203316461G>T	uc001gzr.2	-	2	1074	c.938C>A	c.(937-939)ACC>AAC	p.T313N	FMOD_uc010pqi.1_RNA	NM_002023	NP_002014	Q06828	FMOD_HUMAN	fibromodulin precursor	313	LRR 9.				transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)			CTCCAGGTTGGTGTTGACTGG	0.522													36	115	---	---	---	---	PASS
RAD51AP2	729475	broad.mit.edu	37	2	17699551	17699551	+	Silent	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17699551G>T	uc002rcl.1	-	1	156	c.132C>A	c.(130-132)GTC>GTA	p.V44V	RAD51AP2_uc010exn.1_Silent_p.V35V	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	44										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CCGCCTTAAAGACACCTCCAG	0.572													47	117	---	---	---	---	PASS
NRBP1	29959	broad.mit.edu	37	2	27656879	27656879	+	Silent	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27656879T>C	uc002rko.2	+	5	1189	c.357T>C	c.(355-357)GAT>GAC	p.D119D	NRBP1_uc002rkq.2_Silent_p.D119D|NRBP1_uc002rkp.2_Silent_p.D119D|NRBP1_uc002rkr.2_5'Flank	NM_013392	NP_037524	Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein	119	Protein kinase.				ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm	ATP binding|protein homodimerization activity|protein kinase activity			ovary(2)|lung(1)	3	Acute lymphoblastic leukemia(172;0.155)					CTGTGTTTGATAATCTGATTC	0.388													92	268	---	---	---	---	PASS
NLRC4	58484	broad.mit.edu	37	2	32481863	32481863	+	5'UTR	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32481863C>T	uc002roi.2	-	2					NLRC4_uc002roj.1_5'UTR|NLRC4_uc010ezt.1_5'UTR	NM_021209	NP_067032	Q9NPP4	NLRC4_HUMAN	caspase recruitment domain protein 12						activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ATGAAAGCTTCCCACCTTTCT	0.333													8	36	---	---	---	---	PASS
PRKD3	23683	broad.mit.edu	37	2	37543392	37543392	+	Silent	SNP	T	A	A	rs62001879	byFrequency	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37543392T>A	uc002rqd.2	-	1	831	c.276A>T	c.(274-276)ATA>ATT	p.I92I	PRKD3_uc002rqf.1_Silent_p.I92I	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3	92					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)				TTTGATAAACTATGGAGCACA	0.373													5	186	---	---	---	---	PASS
PTPN18	26469	broad.mit.edu	37	2	131116984	131116984	+	Silent	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131116984C>T	uc002trc.2	+	4	395	c.294C>T	c.(292-294)AGC>AGT	p.S98S	PTPN18_uc002trd.2_Silent_p.S98S|PTPN18_uc002trb.2_Intron	NM_014369	NP_055184	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type	98	Tyrosine-protein phosphatase.					cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity			ovary(3)|kidney(1)	4	Colorectal(110;0.1)					TGGATGGAAGCCTGGCCTACA	0.617													10	40	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152512437	152512437	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152512437G>A	uc010fnx.2	-	50	6787	c.6596C>T	c.(6595-6597)GCC>GTC	p.A2199V		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	2199	Nebulin 58.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTGATCACTGGCATATTCAGT	0.463													4	93	---	---	---	---	PASS
TMEM169	92691	broad.mit.edu	37	2	216965265	216965265	+	Nonstop_Mutation	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216965265A>T	uc010zjr.1	+	4	1220	c.894A>T	c.(892-894)TAA>TAT	p.*298Y	TMEM169_uc010zjs.1_Nonstop_Mutation_p.*298Y|TMEM169_uc002vfw.2_Nonstop_Mutation_p.*298Y|TMEM169_uc002vfv.3_Nonstop_Mutation_p.*298Y	NM_001142310	NP_001135782	Q96HH4	TM169_HUMAN	transmembrane protein 169	298						integral to membrane				ovary(1)	1		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCACGGTCTAAACTCCCAACA	0.453													20	42	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191469	10191469	+	Splice_Site	SNP	A	G	G	rs5030816		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191469A>G	uc003bvc.2	+	3	677	c.464_splice	c.e3-2	p.V155_splice	VHL_uc003bvd.2_Splice_Site_p.V114_splice	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(3)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTGCCCTTCCAGTGTATACTC	0.498		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				10	10	---	---	---	---	PASS
GPR62	118442	broad.mit.edu	37	3	51990645	51990645	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51990645T>A	uc003dca.3	+	1	1316	c.977T>A	c.(976-978)CTC>CAC	p.L326H		NM_080865	NP_543141	Q9BZJ7	GPR62_HUMAN	G protein-coupled receptor 62	326	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCGCGGGCACTCTTGCAATGC	0.706													14	17	---	---	---	---	PASS
KBTBD8	84541	broad.mit.edu	37	3	67058722	67058722	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67058722G>C	uc003dmy.2	+	4	1772	c.1719G>C	c.(1717-1719)GAG>GAC	p.E573D	KBTBD8_uc011bfv.1_Missense_Mutation_p.E131D	NM_032505	NP_115894	Q8NFY9	KBTB8_HUMAN	T-cell activation kelch repeat protein	573	Kelch 5.									ovary(2)|large_intestine(1)|breast(1)	4		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		AAGTGTATGAGACCCCAGATC	0.448													24	107	---	---	---	---	PASS
HGD	3081	broad.mit.edu	37	3	120369637	120369637	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120369637T>C	uc003edw.2	-	6	788	c.418A>G	c.(418-420)ACC>GCC	p.T140A	HGD_uc003edv.2_Translation_Start_Site	NM_000187	NP_000178	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	140					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)		TCCATGGAGGTATTGCAGAGG	0.493													33	112	---	---	---	---	PASS
ADCY5	111	broad.mit.edu	37	3	123044195	123044195	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123044195G>T	uc003egh.1	-	8	2062	c.2062C>A	c.(2062-2064)CAG>AAG	p.Q688K	ADCY5_uc003egg.1_Missense_Mutation_p.Q321K|ADCY5_uc003egi.1_Missense_Mutation_p.Q247K	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	688	Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		TTGGACACCTGGTTGCCACCC	0.622													32	114	---	---	---	---	PASS
CDV3	55573	broad.mit.edu	37	3	133306950	133306950	+	3'UTR	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133306950C>T	uc003epq.2	+	5					CDV3_uc003epp.3_3'UTR|CDV3_uc003epr.2_3'UTR	NM_017548	NP_060018	Q9UKY7	CDV3_HUMAN	carnitine deficiency-associated gene expressed						cell proliferation	cytoplasm					0						CCACCAACAGCCATTCATCAT	0.458													9	40	---	---	---	---	PASS
TOPBP1	11073	broad.mit.edu	37	3	133329915	133329915	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133329915C>A	uc003eps.2	-	25	4238	c.4106G>T	c.(4105-4107)AGA>ATA	p.R1369I		NM_007027	NP_008958	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1369					DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7						AAGTGCTAGTCTTCGTTGCTG	0.368								Other_conserved_DNA_damage_response_genes					11	119	---	---	---	---	PASS
PLD1	5337	broad.mit.edu	37	3	171377081	171377081	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171377081A>T	uc003fhs.2	-	21	2467	c.2351T>A	c.(2350-2352)TTC>TAC	p.F784Y	PLD1_uc003fht.2_Missense_Mutation_p.F746Y|PLD1_uc003fhu.3_Missense_Mutation_p.F78Y|PLD1_uc003fhv.1_Missense_Mutation_p.F109Y	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a	784	Catalytic.				cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ACAGCTTATGAAAAACTGGTT	0.353													56	147	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178952077	178952077	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178952077T>A	uc003fjk.2	+	21	3289	c.3132T>A	c.(3130-3132)AAT>AAA	p.N1044K		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	1044	PI3K/PI4K.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.N1044K(6)|p.N1044D(2)|p.N1044Y(1)|p.N1044S(1)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			AACAAATGAATGATGCACATC	0.368		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			3	89	---	---	---	---	PASS
BCL6	604	broad.mit.edu	37	3	187447399	187447399	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187447399A>T	uc003frp.3	-	5	1251	c.794T>A	c.(793-795)ATC>AAC	p.I265N	BCL6_uc011bsf.1_Missense_Mutation_p.I265N|BCL6_uc010hza.2_Missense_Mutation_p.I163N|BCL6_uc003frq.1_Missense_Mutation_p.I265N	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1	265					negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		CTCTTCTGGGATTGTTTCCTT	0.557			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								27	67	---	---	---	---	PASS
THAP9	79725	broad.mit.edu	37	4	83838698	83838698	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83838698G>A	uc003hnt.2	+	5	1452	c.1333G>A	c.(1333-1335)GTG>ATG	p.V445M	THAP9_uc003hns.1_Missense_Mutation_p.V301M|THAP9_uc003hnu.1_RNA|THAP9_uc003hnv.2_Missense_Mutation_p.V162M	NM_024672	NP_078948	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	445							DNA binding|metal ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	5		Hepatocellular(203;0.114)				GCAGCACCTCGTGGAGTTAGT	0.353													31	72	---	---	---	---	PASS
MAPK10	5602	broad.mit.edu	37	4	87023072	87023072	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87023072A>G	uc003hpq.2	-	6	606	c.539T>C	c.(538-540)CTC>CCC	p.L180P	MAPK10_uc010ikg.2_Missense_Mutation_p.L142P|MAPK10_uc003hpr.2_Missense_Mutation_p.L142P|MAPK10_uc003hps.2_Missense_Mutation_p.L180P|MAPK10_uc003hpt.2_Missense_Mutation_p.L180P|MAPK10_uc003hpu.2_Missense_Mutation_p.L180P|MAPK10_uc003hpv.2_Missense_Mutation_p.L35P|MAPK10_uc010ikh.1_RNA|MAPK10_uc003hpn.2_5'Flank|MAPK10_uc003hpo.2_Missense_Mutation_p.L35P|MAPK10_uc011ccw.1_Missense_Mutation_p.L66P|MAPK10_uc003hpp.2_Missense_Mutation_p.L35P	NM_138982	NP_620448	P53779	MK10_HUMAN	mitogen-activated protein kinase 10 isoform 2	180	Protein kinase.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|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	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		AGCAGAATGGAGGTGCTTAAT	0.383													51	127	---	---	---	---	PASS
NHEDC1	150159	broad.mit.edu	37	4	103822385	103822385	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103822385G>C	uc003hww.2	-	12	1559	c.1437C>G	c.(1435-1437)ATC>ATG	p.I479M	NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Missense_Mutation_p.I252M	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1	479	Helical; (Potential).					integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		TTGGAGCTGTGATCAAGATGG	0.448													5	352	---	---	---	---	PASS
TLL1	7092	broad.mit.edu	37	4	166986847	166986847	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166986847G>C	uc003irh.1	+	16	2667	c.2020G>C	c.(2020-2022)GAT>CAT	p.D674H	TLL1_uc011cjn.1_Missense_Mutation_p.D697H|TLL1_uc011cjo.1_Missense_Mutation_p.D498H	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	674	CUB 3.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TTGCAAATATGATTATGTGGA	0.373													27	74	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187549319	187549319	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187549319G>C	uc003izf.2	-	9	4987	c.4799C>G	c.(4798-4800)TCG>TGG	p.S1600W		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	1600	Extracellular (Potential).|Cadherin 14.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						TGACTCGATCGAGTACAGCAC	0.448										HNSCC(5;0.00058)			10	16	---	---	---	---	PASS
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99715528C>T	uc011cuw.1	-	4		c.382G>A				NR_027503				Homo sapiens glucuronidase, beta pseudogene (LOC100133050), non-coding RNA.												0						AGCGGACAGTCGAAGCCCTTC	0.607													5	17	---	---	---	---	PASS
SLCO4C1	353189	broad.mit.edu	37	5	101597654	101597654	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101597654A>G	uc003knm.2	-	5	1270	c.983T>C	c.(982-984)TTA>TCA	p.L328S		NM_180991	NP_851322	Q6ZQN7	SO4C1_HUMAN	solute carrier organic anion transporter family,	328	Helical; Name=6; (Potential).				cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis	basolateral plasma membrane|integral to membrane	sodium-independent organic anion transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		AGGTATTATTAAAGACCAAGC	0.373													55	71	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170336745	170336745	+	Silent	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170336745G>T	uc003mba.2	+	6	586	c.570G>T	c.(568-570)GTG>GTT	p.V190V	RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA|RANBP17_uc003maw.2_Silent_p.V190V|RANBP17_uc011dew.1_Silent_p.V190V	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	190					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACGTTTTAGTGCTAGCATGCT	0.308			T	TRD@	ALL								16	52	---	---	---	---	PASS
RAB24	53917	broad.mit.edu	37	5	176728925	176728925	+	Splice_Site	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176728925C>T	uc003mfv.2	-	8	916	c.547_splice	c.e8+1	p.E183_splice	RAB24_uc003mfu.2_Splice_Site_p.E154_splice|RAB24_uc003mfw.2_Splice_Site_p.E183_splice|PRELID1_uc003mfx.2_5'Flank|PRELID1_uc003mfy.2_5'Flank	NM_130781	NP_570137	Q969Q5	RAB24_HUMAN	RAB24 gene product						autophagy|protein transport|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|protein binding				0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGCACACACCTGTCATCAC	0.537													38	88	---	---	---	---	PASS
HNRNPH1	3187	broad.mit.edu	37	5	179050064	179050064	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179050064G>A	uc003mkf.3	-	2	177	c.71C>T	c.(70-72)GCC>GTC	p.A24V	HNRNPH1_uc003mkg.3_5'UTR|HNRNPH1_uc003mke.3_Missense_Mutation_p.A24V|HNRNPH1_uc003mkh.3_Missense_Mutation_p.A24V	NM_005520	NP_005511	P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1	24	RRM 1.				regulation of RNA splicing	actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|poly(U) RNA binding|protein binding				0						CACTTCATCGGCCGAGCAAGA	0.458													21	37	---	---	---	---	PASS
LYRM4	57128	broad.mit.edu	37	6	5109597	5109597	+	3'UTR	SNP	A	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5109597A>C	uc003mwp.2	-	3					LYRM4_uc010jnu.2_3'UTR|LYRM4_uc003mwq.2_RNA|uc003mwn.1_Intron	NM_020408	NP_065141	Q9HD34	LYRM4_HUMAN	LYR motif containing 4 isoform 1							mitochondrion|nucleus					0	Ovarian(93;0.11)	all_hematologic(90;0.0901)				CCCCATCTCAAACAGAGAGTG	0.542													30	60	---	---	---	---	PASS
CUL7	9820	broad.mit.edu	37	6	43017376	43017376	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43017376C>T	uc003otq.2	-	7	1897	c.1594G>A	c.(1594-1596)GAA>AAA	p.E532K	CUL7_uc010jyg.2_5'Flank|CUL7_uc011dvb.1_Missense_Mutation_p.E616K|CUL7_uc010jyh.2_Intron|KLC4_uc003otr.1_Intron	NM_014780	NP_055595	Q14999	CUL7_HUMAN	cullin 7	532					interspecies interaction between organisms|ubiquitin-dependent protein catabolic process|vasculogenesis	anaphase-promoting complex|mitochondrion	ubiquitin protein ligase binding			ovary(3)|kidney(1)	4			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			ACGGCCAGTTCAGCTAGGATC	0.577													17	67	---	---	---	---	PASS
CRIP3	401262	broad.mit.edu	37	6	43276136	43276136	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43276136T>C	uc010jyn.1	-	2	55	c.55A>G	c.(55-57)AGC>GGC	p.S19G	CRIP3_uc003ouu.1_Missense_Mutation_p.S19G	NM_206922	NP_996805	Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	19	LIM zinc-binding 1.					cytoplasm	zinc ion binding			skin(1)	1			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			CCCAGGGAGCTCACCTTCTCA	0.612													18	38	---	---	---	---	PASS
PAQR8	85315	broad.mit.edu	37	6	52268836	52268836	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52268836T>A	uc003pao.3	+	2	999	c.825T>A	c.(823-825)TGT>TGA	p.C275*		NM_133367	NP_588608	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member	275	Extracellular (Potential).				cell differentiation|multicellular organismal development|oogenesis	integral to membrane|plasma membrane	receptor activity|steroid binding				0	Lung NSC(77;0.0875)					CGGGTTCCTGTGACATCGTGG	0.577													21	37	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54735119	54735119	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54735119G>C	uc003pck.2	+	2	191	c.75G>C	c.(73-75)AAG>AAC	p.K25N		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	25										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					CTCACTACAAGGAATGGTATC	0.423													51	109	---	---	---	---	PASS
UBE2J1	51465	broad.mit.edu	37	6	90039627	90039627	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90039627G>T	uc010kcb.2	-	9	901	c.728C>A	c.(727-729)CCT>CAT	p.P243H	UBE2J1_uc003pnc.2_Missense_Mutation_p.P243H	NM_016021	NP_057105	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	243	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase activity				0		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		CTTAGCTACAGGTTGGGTAGG	0.473													32	75	---	---	---	---	PASS
MARCKS	4082	broad.mit.edu	37	6	114178975	114178975	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114178975G>C	uc003pvy.3	+	1	449	c.54G>C	c.(52-54)AGG>AGC	p.R18S		NM_002356	NP_002347	P29966	MARCS_HUMAN	myristoylated alanine-rich protein kinase C	18					energy reserve metabolic process|regulation of insulin secretion	actin cytoskeleton|plasma membrane	actin filament binding|calmodulin binding				0		all_cancers(87;7.65e-05)|all_epithelial(87;0.000296)|all_hematologic(75;0.0172)|Colorectal(196;0.0317)|all_lung(197;0.198)		Epithelial(106;1.59e-07)|all cancers(137;9.85e-07)|OV - Ovarian serous cystadenocarcinoma(136;0.000322)		CCGCGGAGAGGCCTGGGGAGG	0.552													5	17	---	---	---	---	PASS
PDGFA	5154	broad.mit.edu	37	7	552066	552066	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:552066G>C	uc003sir.2	-	3	1030	c.187C>G	c.(187-189)CTG>GTG	p.L63V	PDGFA_uc003sis.2_Missense_Mutation_p.L63V|PDGFA_uc003sit.1_Missense_Mutation_p.L77V	NM_002607	NP_002598	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha isoform 1	63					actin cytoskeleton organization|angiogenesis|cell projection assembly|embryo development|hair follicle development|lung alveolus development|negative chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|organ morphogenesis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of DNA replication|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of MAP kinase activity|positive regulation of mesenchymal cell proliferation|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein kinase B signaling cascade|regulation of actin cytoskeleton organization|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling|regulation of peptidyl-tyrosine phosphorylation|regulation of smooth muscle cell migration|skin development	cell surface|endoplasmic reticulum lumen|extracellular space|Golgi membrane|microvillus|platelet alpha granule lumen	collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity				0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		TGAGCTCTCAGGCTGGTGTCC	0.602													5	62	---	---	---	---	PASS
EGFR	1956	broad.mit.edu	37	7	55249116	55249116	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55249116A>G	uc003tqk.2	+	20	2660	c.2414A>G	c.(2413-2415)CAC>CGC	p.H805R	EGFR_uc010kzg.1_Missense_Mutation_p.H760R|EGFR_uc011kco.1_Missense_Mutation_p.H752R|uc003tqo.2_RNA	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	805	Cytoplasmic (Potential).|Protein kinase.				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.H805I(1)		lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	GTCCGGGAACACAAAGACAAT	0.592		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			30	73	---	---	---	---	PASS
LIMK1	3984	broad.mit.edu	37	7	73535222	73535222	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73535222A>C	uc003uaa.1	+	15	1789	c.1624A>C	c.(1624-1626)ATC>CTC	p.I542L	RFC2_uc011kfa.1_Intron|LIMK1_uc010lbl.1_RNA|LIMK1_uc003uab.2_Missense_Mutation_p.I508L	NM_002314	NP_002305	P53667	LIMK1_HUMAN	LIM domain kinase 1	542	Protein kinase.				actin cytoskeleton organization|axon guidance|negative regulation of ubiquitin-protein ligase activity|positive regulation of actin filament bundle assembly|positive regulation of axon extension|Rho protein signal transduction	cytosol|growth cone|nucleus	ATP binding|heat shock protein binding|protein serine/threonine kinase activity|zinc ion binding			stomach(2)|ovary(1)	3		Lung NSC(55;0.137)				TACTGGACAGATCATCGGGCG	0.642													7	87	---	---	---	---	PASS
TAF6	6878	broad.mit.edu	37	7	99705043	99705043	+	Silent	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99705043G>A	uc003uti.2	-	15	1941	c.1860C>T	c.(1858-1860)GGC>GGT	p.G620G	AP4M1_uc003utd.2_Intron|TAF6_uc003utg.2_Silent_p.G542G|TAF6_uc003uth.2_Silent_p.G677G|TAF6_uc003utk.2_Silent_p.G620G|TAF6_uc011kji.1_Silent_p.G657G|TAF6_uc003utj.2_Silent_p.G610G|TAF6_uc003utl.2_Silent_p.G610G|TAF6_uc003utm.2_Silent_p.G620G	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	620					negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGAGGTGGGGCCTCCTTTGC	0.667													4	159	---	---	---	---	PASS
ZNF786	136051	broad.mit.edu	37	7	148769510	148769510	+	Silent	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148769510A>T	uc003wfh.2	-	4	491	c.354T>A	c.(352-354)CCT>CCA	p.P118P	ZNF786_uc011kuk.1_Silent_p.P81P|ZNF786_uc003wfi.2_Silent_p.P32P	NM_152411	NP_689624	Q8N393	ZN786_HUMAN	zinc finger protein 786	118					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			ACTGGCTTTCAGGATCTAATT	0.493													7	15	---	---	---	---	PASS
TNKS	8658	broad.mit.edu	37	8	9588524	9588524	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9588524A>C	uc003wss.2	+	14	2131	c.2126A>C	c.(2125-2127)GAT>GCT	p.D709A	TNKS_uc011kww.1_Missense_Mutation_p.D472A|TNKS_uc010lrs.1_RNA	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related	709	ANK 10.				mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)		CACGGTGCCGATGTCCATGCC	0.448													19	19	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52370154	52370154	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52370154T>C	uc003xqu.3	-	9	987	c.886A>G	c.(886-888)AGA>GGA	p.R296G		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	296	Ig-like C2-type 1.				hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TCTGACTCTCTGGTGTTTCGG	0.448													36	55	---	---	---	---	PASS
NSMAF	8439	broad.mit.edu	37	8	59506790	59506790	+	Splice_Site	SNP	C	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59506790C>G	uc003xtt.2	-	23	2165	c.1951_splice	c.e23+1	p.D651_splice	NSMAF_uc011lee.1_Splice_Site_p.D682_splice	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation						ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)				GGAACACTGACCTTGGGATGT	0.438													12	19	---	---	---	---	PASS
COPS5	10987	broad.mit.edu	37	8	67970384	67970384	+	Silent	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67970384A>G	uc003xxe.2	-	3	772	c.441T>C	c.(439-441)CTT>CTC	p.L147L	COPS5_uc003xxd.2_Silent_p.L83L|COPS5_uc003xxf.2_Silent_p.L192L|COPS5_uc010lyu.1_5'Flank|COPS5_uc010lyv.1_Silent_p.L147L	NM_006837	NP_006828	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	147	JAMM motif.|MPN.				cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			CAATCCCAGAAAGCCAGCAGC	0.418													36	35	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86022019	86022019	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86022019G>T	uc003ycw.2	+	2	448	c.294G>T	c.(292-294)TTG>TTT	p.L98F	LRRCC1_uc010lzz.1_Intron|LRRCC1_uc010maa.1_Intron|LRRCC1_uc003ycx.2_Intron|LRRCC1_uc003ycy.2_Missense_Mutation_p.L78F	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	98	LRR 3.				cell division|mitosis	centriole|nucleus					0						CCTGCAATTTGATTACAAAAG	0.303													16	14	---	---	---	---	PASS
LRP12	29967	broad.mit.edu	37	8	105503616	105503616	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105503616G>A	uc003yma.2	-	7	1960	c.1865C>T	c.(1864-1866)TCA>TTA	p.S622L	LRP12_uc003ymb.2_Missense_Mutation_p.S603L|LRP12_uc003ylz.2_Missense_Mutation_p.S28L	NM_013437	NP_038465	Q9Y561	LRP12_HUMAN	low density lipoprotein-related protein 12	622	Cytoplasmic (Potential).				endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			TCCATCTGCTGAGACCAAAGC	0.438													27	76	---	---	---	---	PASS
KLHL38	340359	broad.mit.edu	37	8	124664213	124664213	+	Silent	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124664213G>C	uc003yqs.1	-	1	978	c.954C>G	c.(952-954)CTC>CTG	p.L318L		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	318	Kelch 1.										0						GCCGTGTCGGGAGTTTGGCAA	0.597													3	68	---	---	---	---	PASS
GSDMD	79792	broad.mit.edu	37	8	144645177	144645177	+	3'UTR	SNP	T	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144645177T>G	uc010mfe.2	+	14					GSDMD_uc003yyf.2_3'UTR|GSDMD_uc003yyg.2_3'UTR|GSDMD_uc003yyh.2_3'UTR	NM_024736	NP_079012	P57764	GSDMD_HUMAN	gasdermin D												0						ATGTGGCCAGTCTACCATGGG	0.597													4	7	---	---	---	---	PASS
NOL6	65083	broad.mit.edu	37	9	33470170	33470170	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33470170A>G	uc003zsz.2	-	4	499	c.398T>C	c.(397-399)CTC>CCC	p.L133P	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zta.2_Missense_Mutation_p.L133P|NOL6_uc010mjv.2_Missense_Mutation_p.L133P|NOL6_uc011lob.1_Intron|NOL6_uc003ztb.1_Missense_Mutation_p.L133P	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	133					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CCCAGCTGGGAGCCATGCCTG	0.468													7	16	---	---	---	---	PASS
TPM2	7169	broad.mit.edu	37	9	35684288	35684288	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35684288C>T	uc003zxq.2	-	8	966	c.727G>A	c.(727-729)GAG>AAG	p.E243K	TPM2_uc003zxr.2_Missense_Mutation_p.E243K|TPM2_uc003zxs.2_Missense_Mutation_p.E243K|TPM2_uc010mkz.2_Missense_Mutation_p.E243K	NM_213674	NP_998839	P07951	TPM2_HUMAN	tropomyosin 2 (beta) isoform 2	243	By similarity.				muscle filament sliding|regulation of ATPase activity	cytosol|muscle thin filament tropomyosin	actin binding|structural constituent of muscle			ovary(1)	1	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACAGACCTCTCGGCAAACTCT	0.498													14	45	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66500841	66500841	+	RNA	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66500841C>T	uc004aed.1	+	3		c.934C>T								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						CCACCTGGTGCCCAGGGCTCC	0.632													3	18	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	88455022	88455022	+	RNA	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88455022G>A	uc004aog.1	+	7		c.1318G>A			uc004aoh.1_5'UTR					Homo sapiens cDNA FLJ42532 fis, clone BRACE3003004.																		ACACAAGTCCGCCTATGTACT	0.398													43	95	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	90746972	90746972	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90746972G>T	uc011lti.1	-	4	1009	c.980C>A	c.(979-981)TCC>TAC	p.S327Y						SubName: Full=cDNA FLJ59639;																		CTCCAGATGGGACAGGGGCTG	0.552													69	154	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113170849	113170849	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113170849A>T	uc010mtz.2	-	38	7368	c.7031T>A	c.(7030-7032)GTT>GAT	p.V2344D	SVEP1_uc010mty.2_Missense_Mutation_p.V270D	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	2344	Sushi 16.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						AAATGTCACAACTCCTACCTC	0.488													14	41	---	---	---	---	PASS
MUSK	4593	broad.mit.edu	37	9	113496565	113496565	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113496565C>A	uc004bey.2	+	6	761	c.663C>A	c.(661-663)CAC>CAA	p.H221Q	MUSK_uc004bex.2_Missense_Mutation_p.H231Q	NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase	221	Ig-like 3.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6						CTGAATCCCACAATGTCACCT	0.473													3	50	---	---	---	---	PASS
CCDC109A	90550	broad.mit.edu	37	10	74619047	74619047	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74619047T>G	uc001jtc.2	+	3	354	c.333T>G	c.(331-333)TTT>TTG	p.F111L	CCDC109A_uc009xqp.1_RNA|CCDC109A_uc009xqq.1_RNA|CCDC109A_uc010qjy.1_RNA|CCDC109A_uc009xqr.2_Missense_Mutation_p.F111L|CCDC109A_uc001jtd.2_Missense_Mutation_p.F62L	NM_138357	NP_612366	Q8NE86	MCU_HUMAN	coiled-coil domain containing 109A	111	Mitochondrial matrix (Potential).				elevation of mitochondrial calcium ion concentration|mitochondrial calcium ion transport|protein complex oligomerization	integral to membrane|mitochondrial inner membrane	protein binding				0	Prostate(51;0.0198)					TTGGTGTATTTTTACGACAAC	0.423													55	135	---	---	---	---	PASS
FAS	355	broad.mit.edu	37	10	90774034	90774034	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90774034C>A	uc001kfr.2	+	9	1181	c.835C>A	c.(835-837)CGT>AGT	p.R279S	FAS_uc010qna.1_RNA|FAS_uc001kfs.2_3'UTR|FAS_uc001kft.2_Missense_Mutation_p.R258S|FAS_uc010qnb.1_RNA|FAS_uc010qnc.1_RNA|FAS_uc001kfw.2_3'UTR|FAS_uc010qnd.1_RNA|FAS_uc010qne.1_RNA|FAS_uc009xtp.2_RNA	NM_000043	NP_000034	P25445	TNR6_HUMAN	tumor necrosis factor receptor superfamily,	279	Death.|Interaction with HIPK3 (By similarity).|Cytoplasmic (Potential).				activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death	cytosol|extracellular region|integral to membrane|soluble fraction	identical protein binding|kinase binding			upper_aerodigestive_tract(1)|breast(1)	2		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)		TCAACTGCTTCGTAATTGGCA	0.368									Autoimmune_Lymphoproliferative_syndrome_type_I				4	116	---	---	---	---	PASS
C10orf79	80217	broad.mit.edu	37	10	105922142	105922142	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105922142A>C	uc001kxw.2	-	25	3382	c.3266T>G	c.(3265-3267)ATT>AGT	p.I1089S	C10orf79_uc009xxq.2_Missense_Mutation_p.I397S	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	1089											0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)		CCACGGCTTAATGTGTTTGTG	0.408													40	92	---	---	---	---	PASS
KNDC1	85442	broad.mit.edu	37	10	135024207	135024207	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135024207G>A	uc001llz.1	+	21	3888	c.3887G>A	c.(3886-3888)CGC>CAC	p.R1296H		NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	1296	N-terminal Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CTCCTCGACCGCATCAACAGC	0.622													4	137	---	---	---	---	PASS
CDHR5	53841	broad.mit.edu	37	11	621602	621602	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:621602T>C	uc001lqj.2	-	5	572	c.467A>G	c.(466-468)AAG>AGG	p.K156R	CDHR5_uc001lqk.2_Missense_Mutation_p.K156R|CDHR5_uc009ycc.2_5'UTR|CDHR5_uc009ycd.2_Missense_Mutation_p.K156R|CDHR5_uc001lql.2_Missense_Mutation_p.K156R|CDHR5_uc001lqm.2_5'UTR|CDHR5_uc009yce.1_Missense_Mutation_p.K125R	NM_021924	NP_068743	Q9HBB8	CDHR5_HUMAN	mucin and cadherin-like isoform 1	156	Cadherin 2.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0						AATGTCGTCCTTGTCGCGGTC	0.642													20	60	---	---	---	---	PASS
API5	8539	broad.mit.edu	37	11	43340203	43340203	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43340203A>G	uc010rfh.1	+	2	256	c.83A>G	c.(82-84)TAT>TGT	p.Y28C	API5_uc010rfg.1_Missense_Mutation_p.Y17C|API5_uc001mxf.2_Missense_Mutation_p.Y28C|API5_uc010rfi.1_Intron|API5_uc001mxg.2_5'UTR	NM_001142930	NP_001136402	Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5 isoform a	28					anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3						AAAGATGCCTATCAAGTGATA	0.353													8	109	---	---	---	---	PASS
KIAA0652	9776	broad.mit.edu	37	11	46666953	46666953	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46666953C>A	uc009yld.2	+	4	818	c.134C>A	c.(133-135)CCA>CAA	p.P45Q	KIAA0652_uc001nda.2_Missense_Mutation_p.P45Q|KIAA0652_uc001ndb.2_Missense_Mutation_p.P45Q|KIAA0652_uc001ncz.2_Missense_Mutation_p.P45Q|KIAA0652_uc001ndc.2_Missense_Mutation_p.P45Q|KIAA0652_uc010rgv.1_5'UTR	NM_001142673	NP_001136145	O75143	ATG13_HUMAN	autophagy-related protein 13 isoform 1	45					autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)		TCATCTTCTCCAACGGGTTCA	0.348													16	45	---	---	---	---	PASS
FGF3	2248	broad.mit.edu	37	11	69631129	69631129	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69631129G>A	uc001oph.2	-	2	774	c.283C>T	c.(283-285)CGG>TGG	p.R95W		NM_005247	NP_005238	P11487	FGF3_HUMAN	fibroblast growth factor 3 precursor	95					fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of cardiac muscle tissue development|positive regulation of cell division|positive regulation of cell proliferation	extracellular region	growth factor activity			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			GCCAGGTACCGCCCGGAGAAG	0.607													30	81	---	---	---	---	PASS
CWF19L2	143884	broad.mit.edu	37	11	107197769	107197769	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107197769C>A	uc010rvp.1	-	18	2582	c.2552G>T	c.(2551-2553)GGT>GTT	p.G851V	CWF19L2_uc001pjh.3_RNA|CWF19L2_uc009yxo.2_RNA	NM_152434	NP_689647	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control	851							catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CAGCATCCCACCTATGATTTC	0.358													5	141	---	---	---	---	PASS
REXO2	25996	broad.mit.edu	37	11	114314631	114314631	+	Silent	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114314631T>C	uc001poy.2	+	3	428	c.285T>C	c.(283-285)GAT>GAC	p.D95D	REXO2_uc001poz.2_Intron	NM_015523	NP_056338	Q9Y3B8	ORN_HUMAN	small fragment nuclease precursor	95	Exonuclease.				nucleotide metabolic process	mitochondrion|nucleus	3'-5' exonuclease activity|nucleic acid binding				0		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.65e-06)|Epithelial(105;6.09e-05)|all cancers(92;0.000494)		GCATGTCAGATTGGTGTAAGG	0.453													4	11	---	---	---	---	PASS
TRIM29	23650	broad.mit.edu	37	11	120008528	120008528	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120008528G>A	uc001pwz.2	-	1	336	c.212C>T	c.(211-213)GCG>GTG	p.A71V	TRIM29_uc001pxa.2_RNA	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29	71					transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		CTCATTGCCCGCGAACAGGGC	0.622													5	254	---	---	---	---	PASS
LAG3	3902	broad.mit.edu	37	12	6884470	6884470	+	Silent	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6884470C>T	uc001qqt.3	+	5	1162	c.813C>T	c.(811-813)TAC>TAT	p.Y271Y	LAG3_uc001qqs.2_Silent_p.Y271Y|LAG3_uc001qqu.2_Silent_p.Y101Y	NM_002286	NP_002277	P18627	LAG3_HUMAN	lymphocyte-activation protein 3 precursor	271	Extracellular (Potential).|Ig-like C2-type 2.					integral to membrane	antigen binding|MHC class II protein binding				0						TGACAGTGTACGCTGGAGCAG	0.627													4	166	---	---	---	---	PASS
TAS2R42	353164	broad.mit.edu	37	12	11339532	11339532	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11339532T>G	uc001qzr.1	-	1	12	c.12A>C	c.(10-12)GAA>GAC	p.E4D	PRB4_uc001qzf.1_Intron	NM_181429	NP_852094	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	4	Extracellular (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			TTTTGTCCAATTCGGTGGCCA	0.368													36	68	---	---	---	---	PASS
C12orf77	196415	broad.mit.edu	37	12	25149249	25149249	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25149249C>G	uc001rgf.2	-	2	233	c.28G>C	c.(28-30)GAC>CAC	p.D10H		NM_001101339	NP_001094809	C9JDV5	CL097_HUMAN	hypothetical protein LOC196415	10											0						AGGGAAATGTCTCTGGGTGTT	0.398													6	105	---	---	---	---	PASS
ESPL1	9700	broad.mit.edu	37	12	53670456	53670456	+	Silent	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53670456C>T	uc001sck.2	+	8	1844	c.1753C>T	c.(1753-1755)CTG>TTG	p.L585L	ESPL1_uc001scj.2_Silent_p.L260L	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	585					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						GGCCCTCCTGCTGAGGGAGGA	0.637													3	34	---	---	---	---	PASS
ESPL1	9700	broad.mit.edu	37	12	53685569	53685569	+	Silent	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53685569C>T	uc001sck.2	+	26	5707	c.5616C>T	c.(5614-5616)CTC>CTT	p.L1872L	ESPL1_uc001scj.2_Silent_p.L1547L	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1872					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						CCCAGGAGCTCCTGAATGAGG	0.612													107	162	---	---	---	---	PASS
FGD6	55785	broad.mit.edu	37	12	95546724	95546724	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95546724C>A	uc001tdp.3	-	4	2856	c.2632G>T	c.(2632-2634)GAG>TAG	p.E878*	FGD6_uc009zsx.2_Nonsense_Mutation_p.E11*	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	878	DH.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3						CTCATGATCTCCTTGGCAATA	0.333													26	97	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104056757	104056757	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104056757C>A	uc001tjw.2	+	18	2189	c.2003C>A	c.(2002-2004)ACA>AAA	p.T668K		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	668	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						TGTGATGAAACAAAGAGAGAG	0.458													44	57	---	---	---	---	PASS
HSP90B1	7184	broad.mit.edu	37	12	104341195	104341195	+	Missense_Mutation	SNP	A	C	C	rs3037197		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104341195A>C	uc001tkb.1	+	17	2474	c.2369A>C	c.(2368-2370)GAA>GCA	p.E790A	HSP90B1_uc010swg.1_Missense_Mutation_p.E455A|HSP90B1_uc009zui.1_Missense_Mutation_p.K327Q	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1	790					actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	gatgaagaagaagaaACAGCA	0.184													38	114	---	---	---	---	PASS
STX2	2054	broad.mit.edu	37	12	131276349	131276349	+	3'UTR	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131276349A>T	uc001uio.2	-	11					STX2_uc001uip.2_3'UTR	NM_194356	NP_919337	P32856	STX2_HUMAN	syntaxin 2 isoform 2						acrosome reaction|ectoderm development|intracellular protein transport|organ morphogenesis|signal transduction	basolateral plasma membrane|integral to membrane|microsome|soluble fraction	calcium-dependent protein binding|SNAP receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		ATGCCGGGTTACAGCGTCTGA	0.488													10	15	---	---	---	---	PASS
GPC5	2262	broad.mit.edu	37	13	92346002	92346002	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92346002T>C	uc010tif.1	+	3	1253	c.887T>C	c.(886-888)ATC>ACC	p.I296T		NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor	296						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				CATGCATATATCCGGTCGTTG	0.512													33	75	---	---	---	---	PASS
TM9SF2	9375	broad.mit.edu	37	13	100207857	100207857	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100207857T>A	uc001voj.1	+	15	1841	c.1708T>A	c.(1708-1710)TCT>ACT	p.S570T	TM9SF2_uc010afz.1_Missense_Mutation_p.S405T	NM_004800	NP_004791	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2 precursor	570	Helical; (Potential).				transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					TATTACCTGTTCTGAAGCAAC	0.338													22	71	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101733910	101733910	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101733910C>T	uc001vox.1	-	34	4042	c.3853G>A	c.(3853-3855)GTT>ATT	p.V1285I		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1285	Helical; Name=S3 of repeat IV; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ACCCATACAACGCCAAGCGAC	0.473													5	93	---	---	---	---	PASS
RNASE11	122651	broad.mit.edu	37	14	21058328	21058328	+	5'Flank	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21058328C>T	uc010ahv.2	-						RNASE11_uc010ahx.2_5'Flank|RNASE11_uc010ahw.2_5'Flank|RNASE11_uc001vxs.2_5'UTR|RNASE12_uc001vxt.2_3'UTR|uc001vxu.1_5'Flank	NM_145250	NP_660293	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)							extracellular region	nucleic acid binding|pancreatic ribonuclease activity			ovary(3)	3	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		CCAGTGGCTTCCCCTTCCGCT	0.453													3	8	---	---	---	---	PASS
OXA1L	5018	broad.mit.edu	37	14	23239464	23239464	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23239464C>G	uc001wgn.2	+	5	826	c.826C>G	c.(826-828)CCT>GCT	p.P276A	OXA1L_uc001wgo.2_RNA|OXA1L_uc010akc.2_Missense_Mutation_p.P276A|OXA1L_uc001wgp.2_Missense_Mutation_p.P200A|OXA1L_uc001wgq.2_5'UTR	NM_005015	NP_005006	Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like	216	Helical; (Potential).				aerobic respiration|mitochondrial proton-transporting ATP synthase complex assembly|mitochondrial respiratory chain complex I assembly|negative regulation of ATPase activity|negative regulation of oxidoreductase activity|protein insertion into membrane|protein tetramerization	integral to mitochondrial membrane|mitochondrial respiratory chain|protein complex	protein homodimerization activity|ribosome binding			central_nervous_system(1)	1	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		ACTCTATAAACCTCTCATTCT	0.423													18	38	---	---	---	---	PASS
IRF9	10379	broad.mit.edu	37	14	24633841	24633841	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24633841C>G	uc001wmq.2	+	7	795	c.668C>G	c.(667-669)ACC>AGC	p.T223S	RNF31_uc001wmp.2_RNA|IRF9_uc010alj.2_Intron	NM_006084	NP_006075	Q00978	IRF9_HUMAN	interferon-stimulated transcription factor 3,	223					interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|nucleoplasm	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00853)		CTGCTGCTCACCTTCATCTAC	0.632													30	126	---	---	---	---	PASS
NEDD8	4738	broad.mit.edu	37	14	24687305	24687305	+	Intron	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24687305G>C	uc001wnn.2	-						CHMP4A_uc001wnj.2_5'Flank|MDP1_uc001wnk.1_5'Flank|CHMP4A_uc001wnm.1_5'Flank|MDP1_uc001wnl.1_5'Flank|NEDD8_uc001wno.2_RNA	NM_006156	NP_006147	Q15843	NEDD8_HUMAN	neural precursor cell expressed, developmentally						anatomical structure morphogenesis|protein neddylation|ubiquitin-dependent protein catabolic process	nucleus	ubiquitin protein ligase binding				0				GBM - Glioblastoma multiforme(265;0.0186)		CTTCACATAAGATCGCCATGC	0.383													27	92	---	---	---	---	PASS
FANCM	57697	broad.mit.edu	37	14	45644384	45644384	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45644384T>A	uc001wwd.3	+	14	2526	c.2427T>A	c.(2425-2427)TTT>TTA	p.F809L	FANCM_uc010anf.2_Missense_Mutation_p.F783L|FANCM_uc001wwe.3_Missense_Mutation_p.F345L|FANCM_uc010ang.2_Missense_Mutation_p.F23L	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	809					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						GTGACACCTTTATCACTCACA	0.333								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				5	77	---	---	---	---	PASS
ESR2	2100	broad.mit.edu	37	14	64699828	64699828	+	3'UTR	SNP	T	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64699828T>G	uc001xha.1	-	9					ESR2_uc001xgu.2_Intron|ESR2_uc001xgv.2_Intron|ESR2_uc001xgw.2_Intron|ESR2_uc001xgx.2_Intron|ESR2_uc001xgy.1_Intron|ESR2_uc001xgz.1_3'UTR|ESR2_uc010aqb.1_RNA|ESR2_uc010aqc.1_3'UTR	NM_001437	NP_001428	Q92731	ESR2_HUMAN	estrogen receptor beta isoform 1						cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	GTGACCTCTGTGGGCCAGTTC	0.587													22	52	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72055449	72055449	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72055449A>T	uc001xms.2	+	2	1208	c.860A>T	c.(859-861)AAA>ATA	p.K287I	SIPA1L1_uc001xmt.2_Missense_Mutation_p.K287I|SIPA1L1_uc001xmu.2_Missense_Mutation_p.K287I|SIPA1L1_uc001xmv.2_Missense_Mutation_p.K287I	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	287					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CGACGTTCAAAATCTGAAACT	0.423													31	71	---	---	---	---	PASS
C14orf43	91748	broad.mit.edu	37	14	74205375	74205375	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74205375A>T	uc001xot.2	-	2	2120	c.1337T>A	c.(1336-1338)CTA>CAA	p.L446Q	C14orf43_uc001xou.2_Missense_Mutation_p.L446Q|C14orf43_uc010tud.1_Missense_Mutation_p.L446Q|C14orf43_uc010arw.2_RNA	NM_194278	NP_919254	Q6PJG2	CN043_HUMAN	hypothetical protein LOC91748	446					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115)		TCCGCCCCGTAGCACCTGCCC	0.677													16	49	---	---	---	---	PASS
PTGR2	145482	broad.mit.edu	37	14	74350885	74350885	+	3'UTR	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74350885T>A	uc001xow.2	+	10					PTGR2_uc010tue.1_3'UTR|PTGR2_uc001xox.2_3'UTR|ZNF410_uc001xoy.1_Intron|ZNF410_uc010ary.1_5'Flank|ZNF410_uc010tuf.1_5'Flank|ZNF410_uc010tug.1_5'Flank|ZNF410_uc010tuh.1_5'Flank|ZNF410_uc010tui.1_5'Flank|ZNF410_uc001xoz.1_5'Flank|ZNF410_uc010arz.1_5'Flank|ZNF410_uc001xpa.1_5'Flank|ZNF410_uc001xpb.1_5'Flank	NM_001146154	NP_001139626	Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2						prostaglandin metabolic process		15-oxoprostaglandin 13-oxidase activity|zinc ion binding				0						TTGTAATTGCTGTAAATGTCA	0.323													6	53	---	---	---	---	PASS
OTUB2	78990	broad.mit.edu	37	14	94511094	94511094	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94511094G>A	uc001yci.2	+	5	626	c.466G>A	c.(466-468)GAG>AAG	p.E156K		NM_023112	NP_075601	Q96DC9	OTUB2_HUMAN	OTU domain, ubiquitin aldehyde binding 2	156	OTU.				cellular amino acid metabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination		omega peptidase activity|protein binding|ubiquitin-specific protease activity				0		all_cancers(154;0.12)		Epithelial(152;0.124)|all cancers(159;0.21)|COAD - Colon adenocarcinoma(157;0.215)		CTTCATTGATGAGGAGATGGA	0.592													6	18	---	---	---	---	PASS
SERPINA12	145264	broad.mit.edu	37	14	94964436	94964436	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94964436T>A	uc001ydj.2	-	3	1095	c.299A>T	c.(298-300)CAG>CTG	p.Q100L		NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	100					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)		GTTGAACCCCTGCTTGATCTC	0.527													27	88	---	---	---	---	PASS
BCL11B	64919	broad.mit.edu	37	14	99641322	99641322	+	Silent	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99641322C>T	uc001yga.2	-	4	2118	c.1851G>A	c.(1849-1851)AAG>AAA	p.K617K	BCL11B_uc001ygb.2_Silent_p.K546K	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1	617	Gly-rich.					nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		CGCGCTTCTGCTTGTCGGCCA	0.428			T	TLX3	T-ALL								11	10	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33962623	33962623	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33962623T>G	uc001zhi.2	+	38	5796	c.5726T>G	c.(5725-5727)GTT>GGT	p.V1909G	RYR3_uc010bar.2_Missense_Mutation_p.V1909G	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1909	4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTGCTAGGGGTTCCTTTggaa	0.398													6	15	---	---	---	---	PASS
SPG21	51324	broad.mit.edu	37	15	65273294	65273294	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65273294G>T	uc002aod.2	-	3	226	c.133C>A	c.(133-135)CCT>ACT	p.P45T	SPG21_uc002aoe.2_Missense_Mutation_p.P45T|SPG21_uc010bhb.2_Missense_Mutation_p.P45T|SPG21_uc010bhc.2_5'UTR	NM_001127889	NP_001121361	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 isoform a	45					cell death	cytosol|endosome membrane|trans-Golgi network transport vesicle	CD4 receptor binding				0						AATATGAGAGGACACCTGATA	0.478													19	73	---	---	---	---	PASS
HCN4	10021	broad.mit.edu	37	15	73616205	73616205	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73616205C>A	uc002avp.2	-	8	3223	c.2229G>T	c.(2227-2229)CAG>CAT	p.Q743H		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	743	Cytoplasmic (Potential).				blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6				COAD - Colon adenocarcinoma(1;0.142)		GCACAATCTGCTGGATGATCT	0.617													20	60	---	---	---	---	PASS
CSPG4	1464	broad.mit.edu	37	15	75982732	75982732	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75982732G>T	uc002baw.2	-	3	767	c.674C>A	c.(673-675)ACC>AAC	p.T225N		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	225	Extracellular (Potential).|Neurite growth inhibition (By similarity).|Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2.				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						AAACTCTAGGGTTCCTTCGTC	0.602													4	58	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	76075348	76075348	+	3'UTR	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76075348G>T	uc010umm.1	+	10					uc002bba.1_5'Flank					SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6;																		AGGACGAGAGGCTCCGAGAGC	0.572													24	60	---	---	---	---	PASS
RAB11FIP3	9727	broad.mit.edu	37	16	476674	476674	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:476674G>T	uc002chf.2	+	1	1007	c.668G>T	c.(667-669)CGC>CTC	p.R223L		NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1	223	1 (Potential).|EF-hand 1.				cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)				GGTTTCGTCCGCATCGAGGAC	0.711													7	27	---	---	---	---	PASS
NARFL	64428	broad.mit.edu	37	16	782508	782508	+	Intron	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:782508G>A	uc002cjr.2	-						NARFL_uc002cjp.2_Intron|NARFL_uc002cjq.2_Intron|NARFL_uc002cjs.2_Intron|NARFL_uc010uuq.1_Missense_Mutation_p.H39Y	NM_022493	NP_071938	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like						iron-sulfur cluster assembly|oxygen homeostasis|regulation of transcription, DNA-dependent|response to hypoxia		4 iron, 4 sulfur cluster binding|metal ion binding				0		Hepatocellular(780;0.0218)				CCTAGCCCGTGGTGGGGAGGC	0.647													4	2	---	---	---	---	PASS
CORO7	79585	broad.mit.edu	37	16	4408461	4408461	+	Silent	SNP	C	T	T	rs151072609		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4408461C>T	uc002cwh.3	-	24	2484	c.2364G>A	c.(2362-2364)ACG>ACA	p.T788T	CORO7_uc002cwe.2_RNA|CORO7_uc002cwf.2_Silent_p.T788T|CORO7_uc002cwg.3_Silent_p.T568T|CORO7_uc010uxh.1_Silent_p.T770T|CORO7_uc010uxi.1_Silent_p.T703T|CORO7_uc002cwi.1_Silent_p.T568T	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7	788						cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0						CGTCGCACTCCGTCTTAGGCA	0.697													11	40	---	---	---	---	PASS
TMC5	79838	broad.mit.edu	37	16	19475156	19475156	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19475156A>G	uc002dgc.3	+	8	2044	c.1295A>G	c.(1294-1296)CAG>CGG	p.Q432R	TMC5_uc010vaq.1_Missense_Mutation_p.Q432R|TMC5_uc002dgb.3_Missense_Mutation_p.Q432R|TMC5_uc010var.1_Missense_Mutation_p.Q432R|TMC5_uc002dgd.1_Missense_Mutation_p.Q186R|TMC5_uc002dge.3_Missense_Mutation_p.Q186R|TMC5_uc002dgf.3_Missense_Mutation_p.Q115R|TMC5_uc002dgg.3_Missense_Mutation_p.Q73R	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	432	Extracellular (Potential).					integral to membrane				skin(1)	1						AGCCTGTGGCAGAAGACGCTG	0.458													31	48	---	---	---	---	PASS
ITGAL	3683	broad.mit.edu	37	16	30505581	30505581	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30505581C>T	uc002dyi.3	+	12	1438	c.1262C>T	c.(1261-1263)GCC>GTC	p.A421V	ITGAL_uc002dyj.3_Missense_Mutation_p.A338V|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	421	FG-GAP 4.|Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|lung(3)|central_nervous_system(3)|breast(1)	10					Efalizumab(DB00095)	TCGTTGCTGGCCTCGGGAGCC	0.602													13	52	---	---	---	---	PASS
ZFP90	146198	broad.mit.edu	37	16	68598499	68598499	+	Silent	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68598499T>C	uc010cff.2	+	5	2101	c.1809T>C	c.(1807-1809)CAT>CAC	p.H603H	ZFP90_uc002ewb.2_3'UTR|ZFP90_uc002ewc.2_3'UTR|ZFP90_uc002ewd.2_Silent_p.H603H|ZFP90_uc002ewe.2_Silent_p.H603H	NM_133458	NP_597715	Q8TF47	ZFP90_HUMAN	zinc finger protein 90	603	C2H2-type 12.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		AGAGAATTCATACTGGAGAAA	0.398													53	159	---	---	---	---	PASS
MLYCD	23417	broad.mit.edu	37	16	83949048	83949048	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83949048A>G	uc002fgz.2	+	5	1456	c.1436A>G	c.(1435-1437)CAG>CGG	p.Q479R		NM_012213	NP_036345	O95822	DCMC_HUMAN	malonyl-CoA decarboxylase precursor	479					acyl-CoA metabolic process|fatty acid biosynthetic process	mitochondrion|peroxisome	malonyl-CoA decarboxylase activity|methylmalonyl-CoA decarboxylase activity				0						GCCTCTGAGCAGGTCCTCAGC	0.557													4	39	---	---	---	---	PASS
EFTUD2	9343	broad.mit.edu	37	17	42953390	42953390	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42953390C>A	uc002ihn.2	-	10	1042	c.781G>T	c.(781-783)GAC>TAC	p.D261Y	EFTUD2_uc010wje.1_Missense_Mutation_p.D226Y|EFTUD2_uc010wjf.1_Missense_Mutation_p.D251Y	NM_004247	NP_004238	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain	261	GTP (Potential).					Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)				ATCAGCCGGTCAATCTTGTTG	0.502													56	149	---	---	---	---	PASS
C17orf46	124783	broad.mit.edu	37	17	43332848	43332848	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43332848G>T	uc002iis.1	-	4	797	c.701C>A	c.(700-702)CCA>CAA	p.P234Q	LOC100133991_uc010dah.2_Intron|C17orf46_uc010wjk.1_Missense_Mutation_p.P213Q	NM_152343	NP_689556	Q96LK8	CQ046_HUMAN	hypothetical protein LOC124783	234				P -> A (in Ref. 2; AAP97314).						large_intestine(1)|ovary(1)	2						GTCAATGGGTGGCGGGAGATC	0.587													11	22	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630855	44630855	+	3'UTR	SNP	G	C	C	rs144516284	by1000genomes	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630855G>C	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						cttctcttttgagacggagtt	0.139													4	119	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60814731	60814731	+	Intron	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60814731A>G	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron|uc002jaj.1_RNA|uc002jak.2_RNA	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190								ligase activity|zinc ion binding				0						TTCCAGTAAAAGGGCCCATGG	0.428													3	82	---	---	---	---	PASS
CCDC45	90799	broad.mit.edu	37	17	62512942	62512942	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62512942G>C	uc002jem.2	+	5	527	c.469G>C	c.(469-471)GGG>CGG	p.G157R	CCDC45_uc002jen.2_RNA|CCDC45_uc010wqb.1_Intron	NM_138363	NP_612372	Q96GE4	CEP95_HUMAN	coiled-coil domain containing 45	157						centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			AGTTTCTTTTGGGAGGTAGCA	0.343													9	43	---	---	---	---	PASS
SDK2	54549	broad.mit.edu	37	17	71429919	71429919	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71429919C>A	uc010dfm.2	-	10	1264	c.1264G>T	c.(1264-1266)GCA>TCA	p.A422S	SDK2_uc010dfn.2_Missense_Mutation_p.A101S	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2	422	Ig-like C2-type 5.|Extracellular (Potential).				cell adhesion	integral to membrane				ovary(2)	2						GTCTCACATGCTAGCACCACT	0.572													3	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	76535832	76535832	+	IGR	SNP	T	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76535832T>C								DNAH17 (66976 upstream) : CYTH1 (134299 downstream)																							TATAACCATGTTGTCCATTAG	0.348													4	33	---	---	---	---	PASS
SLC26A11	284129	broad.mit.edu	37	17	78196524	78196524	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78196524T>G	uc002jyb.1	+	4	574	c.305T>G	c.(304-306)CTG>CGG	p.L102R	SGSH_uc002jxz.3_5'Flank|SGSH_uc002jya.3_5'Flank|SGSH_uc002jxy.2_5'Flank|SGSH_uc010wue.1_5'Flank|SLC26A11_uc002jyc.1_Missense_Mutation_p.L102R|SLC26A11_uc002jyd.1_Missense_Mutation_p.L102R|SLC26A11_uc010dhv.1_Missense_Mutation_p.L102R	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	102	Helical; (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GATGTGACTCTGGGCCCCACC	0.607													47	152	---	---	---	---	PASS
KIAA1012	22878	broad.mit.edu	37	18	29511372	29511372	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29511372T>A	uc002kxc.3	-	2	636	c.272A>T	c.(271-273)GAT>GTT	p.D91V	KIAA1012_uc002kxb.3_Missense_Mutation_p.D37V|KIAA1012_uc002kxd.3_RNA|KIAA1012_uc002kxe.2_Missense_Mutation_p.D91V	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878	91					ER to Golgi vesicle-mediated transport	cis-Golgi network					0						AGAAACAACATCATTCAAAAG	0.408													52	135	---	---	---	---	PASS
ATP8B1	5205	broad.mit.edu	37	18	55399034	55399034	+	Silent	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55399034A>G	uc002lgw.2	-	1	6	c.6T>C	c.(4-6)AGT>AGC	p.S2S	uc002lgv.1_RNA	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	2	Cytoplasmic (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)				CTCTTTCTGTACTCATTCTGC	0.423									Byler_disease				72	191	---	---	---	---	PASS
TCF3	6929	broad.mit.edu	37	19	1625673	1625673	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1625673C>T	uc002ltr.2	-	7	468	c.401G>A	c.(400-402)AGC>AAC	p.S134N	TCF3_uc002ltt.3_Missense_Mutation_p.S134N|TCF3_uc002ltq.2_Missense_Mutation_p.S83N|TCF3_uc002lts.1_Missense_Mutation_p.S50N	NM_003200	NP_003191	P15923	TFE2_HUMAN	transcription factor 3 isoform E12	134					B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus|protein complex|transcription factor complex	bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding			lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1)	7		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGCCCGGGGCTGTTGAGGGC	0.672			T	PBX1|HLF|TFPT	pre B-ALL								4	6	---	---	---	---	PASS
ZFR2	23217	broad.mit.edu	37	19	3831667	3831667	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3831667C>T	uc002lyw.2	-	4	601	c.589G>A	c.(589-591)GCC>ACC	p.A197T	ZFR2_uc010xhx.1_RNA	NM_015174	NP_055989	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2 isoform 1	197	Pro-rich.					intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		CCCGTGTAGGCGGTGCAGGTG	0.627													3	11	---	---	---	---	PASS
PNPLA6	10908	broad.mit.edu	37	19	7614966	7614966	+	Silent	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7614966C>T	uc010xjq.1	+	16	2004	c.1809C>T	c.(1807-1809)ACC>ACT	p.T603T	PNPLA6_uc002mgq.1_Silent_p.T555T|PNPLA6_uc010xjp.1_Silent_p.T529T|PNPLA6_uc002mgr.1_Silent_p.T555T|PNPLA6_uc002mgs.2_Silent_p.T594T	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b	594	cNMP 2.|Cytoplasmic (Potential).				cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						GCGACTGCACCTTCCTGCGGA	0.622													26	74	---	---	---	---	PASS
ANGPTL6	83854	broad.mit.edu	37	19	10206762	10206762	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10206762G>C	uc002mmx.1	-	2	596	c.478C>G	c.(478-480)CTG>GTG	p.L160V	ANGPTL6_uc002mmy.1_Missense_Mutation_p.L160V	NM_031917	NP_114123	Q8NI99	ANGL6_HUMAN	angiopoietin-like 6 precursor	160					angiogenesis|cell differentiation|signal transduction	extracellular space	receptor binding				0			OV - Ovarian serous cystadenocarcinoma(20;3.58e-08)|Epithelial(33;2.5e-05)|all cancers(31;5.96e-05)			TTGACGTCCAGCTGGTGGAAC	0.741													4	12	---	---	---	---	PASS
IER2	9592	broad.mit.edu	37	19	13263983	13263983	+	5'UTR	SNP	T	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13263983T>A	uc002mwr.2	+	2					STX10_uc010xnb.1_5'Flank|STX10_uc010xnc.1_5'Flank	NM_004907	NP_004898	Q9BTL4	IER2_HUMAN	immediate early response 2											kidney(1)	1			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			CCCCCGCCGCTGTCGCCGTCG	0.637											OREG0025291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	8	---	---	---	---	PASS
ZNF98	148198	broad.mit.edu	37	19	22605147	22605147	+	5'UTR	SNP	A	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22605147A>C	uc002nqt.2	-	1						NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AGAGACAAAGACCCCGCCACA	0.607													4	4	---	---	---	---	PASS
ZNF226	7769	broad.mit.edu	37	19	44681535	44681535	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44681535A>G	uc002oyp.2	+	6	2264	c.2120A>G	c.(2119-2121)TAC>TGC	p.Y707C	ZNF226_uc002oyq.2_Missense_Mutation_p.Y590C|ZNF226_uc002oyr.2_Missense_Mutation_p.Y590C|ZNF226_uc010ejg.2_3'UTR|ZNF226_uc002oys.2_Missense_Mutation_p.Y707C|ZNF226_uc002oyt.2_Missense_Mutation_p.Y707C	NM_001032373	NP_001027545	Q9NYT6	ZN226_HUMAN	zinc finger protein 226 isoform a	707	C2H2-type 17.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)|all_neural(266;0.202)				TGTGGTAAGTACTTCAGTCAG	0.463													6	131	---	---	---	---	PASS
KLK6	5653	broad.mit.edu	37	19	51462529	51462529	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51462529C>T	uc002pui.2	-	7	886	c.626G>A	c.(625-627)GGC>GAC	p.G209D	KLK6_uc010eoj.2_Missense_Mutation_p.A81T|KLK6_uc002puh.2_Missense_Mutation_p.G218D|KLK6_uc002puj.2_Missense_Mutation_p.G102D|KLK6_uc010ycn.1_Missense_Mutation_p.G102D|KLK6_uc002pul.2_Missense_Mutation_p.G209D|KLK6_uc002pum.2_Missense_Mutation_p.G102D	NM_001012964	NP_001012982	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6 isoform A	209	Peptidase S1.				amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		TGACACAAGGCCTCGGAGGTG	0.403													8	91	---	---	---	---	PASS
ZNF587	84914	broad.mit.edu	37	19	58371253	58371253	+	Silent	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58371253G>A	uc002qql.2	+	3	1611	c.1473G>A	c.(1471-1473)CCG>CCA	p.P491P	ZNF587_uc002qqb.2_Silent_p.P448P|ZNF587_uc010yhh.1_Silent_p.P448P|ZNF587_uc002qqi.1_Silent_p.P448P|ZNF587_uc002qqj.1_RNA|ZNF814_uc002qqk.2_Intron|ZNF587_uc010yhk.1_Silent_p.P490P	NM_032828	NP_116217	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	491					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GAGAAAGGCCGTATGAATGCA	0.423													4	191	---	---	---	---	PASS
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58385546G>T	uc002qqo.2	-	3	1484	c.1212C>A	c.(1210-1212)GAC>GAA	p.D404E	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						AATGTTTTTTGTCAGTGTGAA	0.393													6	17	---	---	---	---	PASS
SNRPB	6628	broad.mit.edu	37	20	2442418	2442418	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2442418C>T	uc002wfz.1	-	7	870	c.707G>A	c.(706-708)CGC>CAC	p.R236H	SNRPB_uc002wga.1_3'UTR|SNRPB_uc010zpv.1_3'UTR|SNRPB_uc002wgb.2_3'UTR	NM_198216	NP_937859	P14678	RSMB_HUMAN	small nuclear ribonucleoprotein polypeptide B/B'	236	Repeat-rich region.|				histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|protein binding|RNA binding			ovary(1)	1						CCTTGGTGGGCGCATTCCCGG	0.542													30	70	---	---	---	---	PASS
PRNP	5621	broad.mit.edu	37	20	4680528	4680528	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4680528A>G	uc002wku.2	+	2	1025	c.662A>G	c.(661-663)GAA>GGA	p.E221G	PRNP_uc002wkv.2_Missense_Mutation_p.E221G|PRNP_uc002wkw.2_Missense_Mutation_p.E221G|PRNP_uc002wkx.2_Missense_Mutation_p.E221G|PRNP_uc002wkt.1_Missense_Mutation_p.E191G|PRNP_uc002wky.2_Missense_Mutation_p.E221G|PRNP_uc010gbe.1_Intron	NM_001080122	NP_001073591	P04156	PRIO_HUMAN	prion protein preproprotein	221	Interaction with GRB2, ERI3 and SYN1 (By similarity).				axon guidance|cell cycle arrest|cellular copper ion homeostasis|metabolic process|negative regulation of activated T cell proliferation|negative regulation of calcineurin-NFAT signaling pathway|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-2 production|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T cell receptor signaling pathway|protein homooligomerization|response to oxidative stress	anchored to membrane|endoplasmic reticulum|extrinsic to membrane|Golgi apparatus|membrane raft|nucleus|plasma membrane	copper ion binding|identical protein binding|microtubule binding			central_nervous_system(1)	1					Tetracycline(DB00759)	TACGAGAGGGAATCTCAGGCC	0.527													18	45	---	---	---	---	PASS
BCAS1	8537	broad.mit.edu	37	20	52561451	52561451	+	3'UTR	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52561451G>A	uc002xws.2	-	12					BCAS1_uc010zza.1_3'UTR|BCAS1_uc010zzb.1_3'UTR|BCAS1_uc010gim.2_3'UTR|BCAS1_uc002xwt.2_3'UTR|BCAS1_uc010gil.1_3'UTR	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1							cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			TGGGAACCGTGCTGATTTGTT	0.483													63	143	---	---	---	---	PASS
C21orf99	149992	broad.mit.edu	37	21	14424153	14424153	+	RNA	SNP	C	A	A	rs10439727	by1000genomes	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14424153C>A	uc002yiy.3	+	5		c.2968C>A			C21orf99_uc002yja.3_RNA					Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						GAGGCTGCACCCTTGGCGGAA	0.443													8	15	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587													4	63	---	---	---	---	PASS
MMP11	4320	broad.mit.edu	37	22	24125737	24125737	+	3'UTR	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24125737G>A	uc002zxx.2	+	8					MMP11_uc002zxy.2_RNA|MMP11_uc002zxz.2_RNA	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein						collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|large_intestine(1)	3		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)				TCTGACCATGGCTTGGATGCC	0.597													6	83	---	---	---	---	PASS
EP300	2033	broad.mit.edu	37	22	41513594	41513594	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41513594C>A	uc003azl.3	+	2	893	c.498C>A	c.(496-498)AAC>AAA	p.N166K		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	166					apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						TGGGAATGAACACAGGGATGA	0.507			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				4	45	---	---	---	---	PASS
MAP7D2	256714	broad.mit.edu	37	X	20028912	20028912	+	3'UTR	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20028912C>T	uc004czr.1	-	15					MAP7D2_uc004czq.1_3'UTR|MAP7D2_uc011mji.1_3'UTR|MAP7D2_uc010nfo.1_3'UTR|MAP7D2_uc011mjj.1_3'UTR	NM_152780	NP_689993	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2											ovary(2)|breast(1)	3						TAAAGGGATGCTGTATTTGTC	0.388													7	147	---	---	---	---	PASS
MAGEB10	139422	broad.mit.edu	37	X	27840420	27840420	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27840420G>A	uc004dbw.2	+	3	1224	c.997G>A	c.(997-999)GGT>AGT	p.G333S		NM_182506	NP_872312	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	333										lung(1)|breast(1)|central_nervous_system(1)	3						TGCCACAGCCGGTGCACGTTC	0.483													8	38	---	---	---	---	PASS
GPKOW	27238	broad.mit.edu	37	X	48979947	48979947	+	Silent	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48979947A>T	uc004dmr.2	-	1	133	c.126T>A	c.(124-126)TCT>TCA	p.S42S		NM_015698	NP_056513	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	42						nucleus	nucleic acid binding			ovary(2)	2						TCTCCTCCGGAGATGGCCCCG	0.637													6	13	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76939124	76939124	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76939124C>G	uc004ecp.3	-	9	1856	c.1624G>C	c.(1624-1626)GTT>CTT	p.V542L	ATRX_uc004ecq.3_Missense_Mutation_p.V504L|ATRX_uc004eco.3_Missense_Mutation_p.V327L|ATRX_uc004ecr.2_Missense_Mutation_p.V503L|ATRX_uc010nlx.1_Missense_Mutation_p.V542L|ATRX_uc010nly.1_Missense_Mutation_p.V487L	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	542					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TGATGATCAACTGAACTCTGA	0.383			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						45	418	---	---	---	---	PASS
ATP11C	286410	broad.mit.edu	37	X	138827926	138827926	+	Silent	SNP	C	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138827926C>T	uc004faz.2	-	25	3027	c.2928G>A	c.(2926-2928)GGG>GGA	p.G976G	ATP11C_uc004fax.2_Silent_p.G184G|ATP11C_uc004fay.2_RNA|ATP11C_uc004fba.2_Silent_p.G976G	NM_173694	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C isoform a	976	Helical; (Potential).				ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)					GAAAGTAAGTCCCAAAGAAGA	0.388													33	89	---	---	---	---	PASS
ZNF185	7739	broad.mit.edu	37	X	152132417	152132417	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152132417A>T	uc010ntv.1	+	18	1676	c.1639A>T	c.(1639-1641)ACT>TCT	p.T547S	ZNF185_uc011myg.1_Missense_Mutation_p.T579S|ZNF185_uc011myh.1_Missense_Mutation_p.T550S|ZNF185_uc011myi.1_Missense_Mutation_p.T518S|ZNF185_uc011myj.1_Missense_Mutation_p.T488S|ZNF185_uc011myk.1_Missense_Mutation_p.T548S|ZNF185_uc004fgw.3_Missense_Mutation_p.T326S|ZNF185_uc004fgu.2_Missense_Mutation_p.T176S|ZNF185_uc004fgv.2_Missense_Mutation_p.T244S|ZNF185_uc004fgx.2_Missense_Mutation_p.T185S	NM_007150	NP_009081	O15231	ZN185_HUMAN	zinc finger protein 185	547						cytoplasm|cytoskeleton|focal adhesion	zinc ion binding			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					GGTCACTGTTACTGTCACTGC	0.537													24	50	---	---	---	---	PASS
SLC35D1	23169	broad.mit.edu	37	1	67487400	67487401	+	Intron	DEL	AG	-	-	rs72407410		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67487400_67487401delAG	uc001ddk.2	-						SLC35D1_uc010oph.1_Intron	NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic						chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	acacagacacagacacagacac	0.248													5	3	---	---	---	---	
C1orf14	81626	broad.mit.edu	37	1	182911294	182911294	+	Intron	DEL	T	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182911294delT	uc001gpu.2	-						C1orf14_uc001gpv.2_Intron|C1orf14_uc010pnz.1_Intron|C1orf14_uc001gpw.2_Intron	NM_030933	NP_112195	Q9BZQ2	SHP1L_HUMAN	chromosome 1 open reading frame 14												0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)		CTCTCCTCAGTTTTCGTTTCC	0.443													18	10	---	---	---	---	
PPFIA4	8497	broad.mit.edu	37	1	203024644	203024644	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203024644delA	uc001gyz.2	+	3	989	c.396delA	c.(394-396)CTAfs	p.L132fs	PPFIA4_uc009xaj.2_Frame_Shift_Del_p.L763fs|PPFIA4_uc010pqf.1_Frame_Shift_Del_p.L345fs|PPFIA4_uc001gza.2_Frame_Shift_Del_p.L132fs|PPFIA4_uc001gzb.1_5'Flank	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f	132					cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						TGGAAGCCCTAAACCTGAAGC	0.622													58	25	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242936088	242936089	+	IGR	INS	-	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242936088_242936089insG								PLD5 (248090 upstream) : CEP170 (351642 downstream)																							TAAAGCATTCCGGGAAGCAGCT	0.366													57	27	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65738847	65738847	+	Intron	DEL	T	-	-	rs111377658		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65738847delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		ttttTTGAAATTTTTTTTTTT	0.159													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52678783	52678784	+	Frame_Shift_Ins	INS	-	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52678783_52678784insT	uc003des.2	-	8	847_848	c.835_836insA	c.(835-837)ATAfs	p.I279fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Ins_p.I279fs|PBRM1_uc003der.2_Frame_Shift_Ins_p.I279fs|PBRM1_uc003det.2_Frame_Shift_Ins_p.I279fs|PBRM1_uc003deu.2_Frame_Shift_Ins_p.I279fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Ins_p.I279fs|PBRM1_uc010hmk.1_Frame_Shift_Ins_p.I279fs|PBRM1_uc003dey.2_Frame_Shift_Ins_p.I279fs|PBRM1_uc003dez.1_Frame_Shift_Ins_p.I279fs|PBRM1_uc003dfb.1_Frame_Shift_Ins_p.I177fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	279					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding	p.I279fs*4(2)		kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		Catataaaatatttttttaatt	0.297			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								13	8	---	---	---	---	
DHX36	170506	broad.mit.edu	37	3	154010602	154010602	+	Intron	DEL	T	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154010602delT	uc003ezy.3	-						DHX36_uc010hvq.2_Intron|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTTCAGAGCATTTTTTTTTTA	0.249													6	5	---	---	---	---	
SLC30A5	64924	broad.mit.edu	37	5	68396440	68396440	+	Intron	DEL	A	-	-	rs33982147		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68396440delA	uc003jvh.2	+						SLC30A5_uc003jvg.2_Intron|SLC30A5_uc011crc.1_Intron|SLC30A5_uc003jvi.2_5'Flank	NM_022902	NP_075053	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter),						cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		tctatgagttaaaaaaaaaaa	0.149													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177398373	177398396	+	IGR	DEL	AGGACGAAGAGCTGGAGAGCGCCA	-	-	rs145131557		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177398373_177398396delAGGACGAAGAGCTGGAGAGCGCCA								LOC728554 (87106 upstream) : PROP1 (20840 downstream)																							GTCCCCGGGGAGGACGAAGAGCTGGAGAGCGCCAAGGACGACGA	0.531													2	6	---	---	---	---	
MYO6	4646	broad.mit.edu	37	6	76596477	76596477	+	Intron	DEL	C	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76596477delC	uc003pih.1	+						MYO6_uc003pig.1_Intron|MYO6_uc003pii.1_Intron	NM_004999	NP_004990	Q9UM54	MYO6_HUMAN	myosin VI						actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		AAGTGAAATACCCTGTTTAGC	0.299													30	14	---	---	---	---	
MTHFD1L	25902	broad.mit.edu	37	6	151413789	151413789	+	Intron	DEL	T	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151413789delT	uc003qob.2	+						MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TTTTTTGTCATTTTTTTTTTC	0.388													6	3	---	---	---	---	
CRCP	27297	broad.mit.edu	37	7	65599533	65599533	+	Intron	DEL	T	-	-	rs146459004		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65599533delT	uc003tus.2	+						CRCP_uc003tuv.2_Intron|CRCP_uc011kdw.1_Intron|CRCP_uc003tut.2_Intron|CRCP_uc003tuu.2_Intron	NM_014478	NP_055293	O75575	RPC9_HUMAN	calcitonin gene-related peptide-receptor						acrosome reaction|innate immune response|response to virus|transcription from RNA polymerase III promoter	DNA polymerase III complex|nucleus|plasma membrane	calcitonin receptor activity|DNA-directed RNA polymerase activity|nucleotide binding				0						GGAACAAATCttttttttttt	0.299													4	3	---	---	---	---	
BAIAP2L1	55971	broad.mit.edu	37	7	98015999	98016005	+	Intron	DEL	CCAAAGG	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98015999_98016005delCCAAAGG	uc003upj.2	-							NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			ATTCAACTTTCCAAAGGtttttttttt	0.203													4	3	---	---	---	---	
CPNE3	8895	broad.mit.edu	37	8	87557132	87557132	+	Intron	DEL	T	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87557132delT	uc003ydv.2	+						CPNE3_uc003ydw.1_5'Flank	NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III						lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2						CTGTATTTCATTTTTTTCCCA	0.333													25	11	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	105261141	105261144	+	Intron	DEL	TTCC	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105261141_105261144delTTCC	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			ctctctctctttccctctctctct	0.103										HNSCC(12;0.0054)			4	3	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668387	71668388	+	Intron	INS	-	GATGGATG	GATGGATG	rs73647061	by1000genomes	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668387_71668388insGATGGATG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						actctgtcatagatggatggat	0.069													4	3	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140610840	140610842	+	Intron	DEL	TGT	-	-	rs142045955	by1000genomes	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140610840_140610842delTGT	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		gaggaagttgtgttggtgtcatg	0.000													4	2	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17432798	17432799	+	Intron	INS	-	AAAAA	AAAAA	rs150378097	by1000genomes	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17432798_17432799insAAAAA	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron|uc001ipe.2_Intron|uc001ipf.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						GGGTCTAAATGAAAAAAAAAAC	0.248													4	2	---	---	---	---	
VAX1	11023	broad.mit.edu	37	10	118897631	118897632	+	5'UTR	DEL	GC	-	-	rs71677026		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118897631_118897632delGC	uc009xyx.2	-	1					VAX1_uc001ldb.1_5'UTR	NM_001112704	NP_001106175	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1 isoform a							nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)		AGGGGGGGGGGCGGAGAAGGAA	0.441													7	4	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	2027490	2027490	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2027490delG	uc001qjp.2	-	1	381	c.150delC	c.(148-150)ACCfs	p.T50fs	CACNA2D4_uc009zds.1_RNA|CACNA2D4_uc009zdt.1_Frame_Shift_Del_p.T50fs	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4	50	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GGAGGGCCGAGGTCTTCTGCA	0.622													24	13	---	---	---	---	
HOXC4	3221	broad.mit.edu	37	12	54448167	54448168	+	Intron	INS	-	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54448167_54448168insC	uc001seu.2	+						HOXC4_uc001sex.2_Intron	NM_014620	NP_055435	P09017	HXC4_HUMAN	homeobox C4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TGCTTTTTGctccccccctccc	0.292													10	5	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112685782	112685783	+	Intron	DEL	AC	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112685782_112685783delAC	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						TATTTTACCTacacacacacac	0.277													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125396165	125396166	+	IGR	INS	-	AAAAAAAAA	AAAAAAAAA	rs68000265		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125396165_125396166insAAAAAAAAA								SCARB1 (47646 upstream) : UBC (28 downstream)																							AAAATAAACTTaaaaaaaaaaa	0.361													5	5	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35037841	35037841	+	Intron	DEL	T	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35037841delT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		actcagccTGTTTTTTTTTTT	0.194													4	2	---	---	---	---	
FMN1	342184	broad.mit.edu	37	15	33256125	33256126	+	Intron	DEL	CA	-	-	rs35753530		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33256125_33256126delCA	uc001zhf.3	-							NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TCCTATGAATcacacacacaca	0.302													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	41679506	41679507	+	IGR	INS	-	A	A			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41679506_41679507insA								NUSAP1 (6259 upstream) : NDUFAF1 (46 downstream)																							aactccatctcaaaaaaaaaaa	0.114													5	3	---	---	---	---	
SECISBP2L	9728	broad.mit.edu	37	15	49285288	49285289	+	Intron	INS	-	AGAGAG	AGAGAG	rs140847057	by1000genomes	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49285288_49285289insAGAGAG	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like											breast(1)|skin(1)	2						TAGTTTGAGACAGAGAGAGAgt	0.158													3	3	---	---	---	---	
HN1L	90861	broad.mit.edu	37	16	1741821	1741822	+	Intron	INS	-	TGT	TGT			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1741821_1741822insTGT	uc002cmg.2	+						HN1L_uc010uvi.1_Intron|HN1L_uc010brt.2_Intron|HN1L_uc010bru.2_Intron|HN1L_uc010uvj.1_Intron|HN1L_uc010uvk.1_Intron	NM_144570	NP_653171	Q9H910	HN1L_HUMAN	hematological and neurological expressed 1-like							cytoplasm|nucleus				upper_aerodigestive_tract(1)	1						TGGTTGCTCAGTGTTCTGTGAT	0.520													52	23	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	12021296	12021298	+	IGR	DEL	TGG	-	-	rs60347225		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12021296_12021298delTGG								GSPT1 (10777 upstream) : TNFRSF17 (37666 downstream)																							cgggtgatgatggttccacctca	0.158													4	2	---	---	---	---	
ACD	65057	broad.mit.edu	37	16	67694268	67694269	+	Frame_Shift_Ins	INS	-	G	G			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67694268_67694269insG	uc002etq.3	-	1	450_451	c.113_114insC	c.(112-114)CCTfs	p.P38fs	ACD_uc002etp.3_Frame_Shift_Ins_p.P38fs|ACD_uc002etr.3_Frame_Shift_Ins_p.P38fs|ACD_uc010vjt.1_Frame_Shift_Ins_p.P28fs|PARD6A_uc002ets.2_5'Flank|PARD6A_uc002ett.2_5'Flank|PARD6A_uc002etu.2_5'Flank	NM_001082486	NP_001075955	Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog isoform 1	38					intracellular protein transport|negative regulation of telomere maintenance via telomerase|positive regulation of single-stranded telomeric DNA binding|positive regulation of telomerase activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|telomere assembly	nuclear telomere cap complex|nucleoplasm	DNA binding|DNA polymerase binding			pancreas(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CCTGCGCACGAGGGCGTCCTGC	0.723													18	9	---	---	---	---	
MED31	51003	broad.mit.edu	37	17	6553421	6553422	+	Intron	INS	-	C	C			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6553421_6553422insC	uc002gdg.3	-						MED31_uc002gdh.3_Intron	NM_016060	NP_057144	Q9Y3C7	MED31_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	protein binding				0						AAAAAAAAAAATCTGTAGGTCA	0.342													23	10	---	---	---	---	
LLGL2	3993	broad.mit.edu	37	17	73569776	73569777	+	Intron	INS	-	CT	CT	rs139625742	by1000genomes	TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73569776_73569777insCT	uc002joh.2	+						LLGL2_uc002joi.2_Intron|LLGL2_uc010dgg.1_Intron|LLGL2_uc002joj.2_Intron|LLGL2_uc010wsd.1_Intron	NM_001031803	NP_001026973	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 isoform c						cell cycle|cell division|exocytosis|regulation of establishment or maintenance of cell polarity	cytoplasm|intracellular membrane-bounded organelle	PDZ domain binding			ovary(2)	2	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			TCTGAGATACCGAGGCTCCCAC	0.708													9	5	---	---	---	---	
ABCA7	10347	broad.mit.edu	37	19	1061698	1061699	+	Intron	INS	-	A	A	rs11420923		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1061698_1061699insA	uc002lqw.3	+						ABCA7_uc002lqy.2_Intron|ABCA7_uc010dsc.2_Intron	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7						phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		aacttggtctcaaaaaaaaaaa	0.248													7	6	---	---	---	---	
ITGB1BP3	27231	broad.mit.edu	37	19	3938848	3938848	+	Intron	DEL	T	-	-	rs59201914		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3938848delT	uc002lyz.3	+						ITGB1BP3_uc010xia.1_Intron	NM_170678	NP_733778	Q9NPI5	NRK2_HUMAN	integrin beta 1 binding protein 3						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		ttttgttttgttttttttttt	0.209													3	3	---	---	---	---	
CYP4F12	66002	broad.mit.edu	37	19	15788883	15788883	+	Intron	DEL	C	-	-	rs67197599		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15788883delC	uc002nbl.2	+						CYP4F12_uc010xoo.1_Intron|CYP4F12_uc010xop.1_Intron	NM_023944	NP_076433			cytochrome P450, family 4, subfamily F,											skin(3)|ovary(2)|central_nervous_system(2)	7	Acute lymphoblastic leukemia(2;0.0367)					ttcctttcctcactcactcat	0.020													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	23780500	23780501	+	IGR	INS	-	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23780500_23780501insT								ZNF91 (202231 upstream) : ZNF675 (55208 downstream)																							AAACCTACAAATGTGAAGAATG	0.312													3	3	---	---	---	---	
COX7A1	1346	broad.mit.edu	37	19	36642562	36642563	+	Intron	INS	-	C	C	rs2285599		TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36642562_36642563insC	uc002odm.1	-							NM_001864	NP_001855	P24310	CX7A1_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 1						generation of precursor metabolites and energy	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ACCCCCCCCGACCCCCCACCTG	0.698													10	5	---	---	---	---	
IL3RA	3563	broad.mit.edu	37	X	1501563	1501564	+	3'UTR	INS	-	T	T			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1501563_1501564insT	uc004cps.2	+	12					IL3RA_uc011mhd.1_3'UTR	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TGATAAAGTGATTTTTTTTTTT	0.426													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	48305869	48305869	+	IGR	DEL	T	-	-			TCGA-B0-5713-01A-11D-1669-08	TCGA-B0-5713-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48305869delT								SSX4 (53084 upstream) : SLC38A5 (11059 downstream)																							ATAATACCCATTTTTTTTCTG	0.353													4	2	---	---	---	---	
