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
SPEN	23013	broad.mit.edu	37	1	16258574	16258574	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16258574A>C	uc001axk.1	+	11	6043	c.5839A>C	c.(5839-5841)ACC>CCC	p.T1947P	SPEN_uc010obp.1_Missense_Mutation_p.T1906P	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1947					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GGTTCCCACCACCCCTCGGAG	0.592													8	85	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974224	16974224	+	RNA	SNP	C	G	G	rs148702086	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974224C>G	uc009vow.2	+	5		c.1034C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						TTGGTCCCAGCCCCAGAGGGA	0.652													5	10	---	---	---	---	PASS
ZDHHC18	84243	broad.mit.edu	37	1	27180348	27180348	+	3'UTR	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27180348C>T	uc001bnb.2	+	8						NM_032283	NP_115659	Q9NUE0	ZDH18_HUMAN	zinc finger, DHHC-type containing 18							integral to membrane	zinc ion binding				0		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)		CGGCTCAGTACTTGCCACCTG	0.597													34	83	---	---	---	---	PASS
IPP	3652	broad.mit.edu	37	1	46212019	46212019	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46212019A>T	uc001cou.2	-	2	332	c.65T>A	c.(64-66)CTC>CAC	p.L22H	IPP_uc001cos.3_Missense_Mutation_p.L22H	NM_005897	NP_005888	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	22						actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					GGCCAAGATGAGTTGGGCATG	0.428													33	87	---	---	---	---	PASS
TDRD5	163589	broad.mit.edu	37	1	179631271	179631271	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179631271G>T	uc001gnf.1	+	14	2443	c.2193G>T	c.(2191-2193)GAG>GAT	p.E731D	TDRD5_uc010pnp.1_Missense_Mutation_p.E785D|TDRD5_uc001gnh.1_Missense_Mutation_p.E286D	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	731					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						CATGCCTGGAGTCAGTGACCA	0.408													5	143	---	---	---	---	PASS
B3GALT2	8707	broad.mit.edu	37	1	193149818	193149818	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193149818T>A	uc001gtc.3	-	2	1590	c.875A>T	c.(874-876)AAA>ATA	p.K292I	CDC73_uc001gtb.2_Intron	NM_003783	NP_003774	O43825	B3GT2_HUMAN	UDP-Gal:betaGlcNAc beta	292	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1						CTTGCTATCTTTGTTTCGATT	0.423													4	88	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214781862	214781862	+	Intron	SNP	T	G	G			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214781862T>G	uc001hkm.2	+						uc001hkn.1_Missense_Mutation_p.T108P	NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CTGGCACCAGTCACGCAGCGA	0.617													3	41	---	---	---	---	PASS
GPR75	10936	broad.mit.edu	37	2	54081819	54081819	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54081819G>C	uc002rxo.3	-	2	346	c.75C>G	c.(73-75)AAC>AAG	p.N25K	ASB3_uc002rxi.3_Intron	NM_006794	NP_006785	O95800	GPR75_HUMAN	G protein-coupled receptor 75	25	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|skin(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GAGAGGTGCTGTTTCCTTCCT	0.532													15	119	---	---	---	---	PASS
ARHGAP25	9938	broad.mit.edu	37	2	69002199	69002199	+	Intron	SNP	A	G	G			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69002199A>G	uc002seu.2	+						ARHGAP25_uc010yqk.1_Intron|ARHGAP25_uc010fdg.2_Intron|ARHGAP25_uc010yql.1_Intron|ARHGAP25_uc002sev.2_5'UTR|ARHGAP25_uc002sew.2_5'UTR|ARHGAP25_uc002sex.2_5'UTR|ARHGAP25_uc010fdh.1_RNA	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4						CTCGGGGGGGACTTTCTCTGG	0.657													5	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89265957	89265957	+	RNA	SNP	G	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89265957G>C	uc010ytr.1	-	95		c.7609C>G			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		GGTTTCTGCTGATACCAGCCT	0.522													62	177	---	---	---	---	PASS
ARHGAP15	55843	broad.mit.edu	37	2	144276874	144276874	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144276874G>A	uc002tvm.3	+	10	1017	c.866G>A	c.(865-867)CGT>CAT	p.R289H	ARHGAP15_uc002tvn.2_Missense_Mutation_p.R55H	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15	289	Rho-GAP.				regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		GTGTGTGAACGTGAAAATTCC	0.408													4	122	---	---	---	---	PASS
COL5A2	1290	broad.mit.edu	37	2	189962055	189962055	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189962055C>T	uc002uqk.2	-	6	679	c.404G>A	c.(403-405)GGA>GAA	p.G135E		NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	135					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TCCTGGAGGTCCCTAAAACAG	0.403													9	47	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215880269	215880269	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215880269T>C	uc002vew.2	-	15	2121	c.1901A>G	c.(1900-1902)TAC>TGC	p.Y634C	ABCA12_uc002vev.2_Missense_Mutation_p.Y316C|ABCA12_uc010zjn.1_5'UTR	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	634					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TCCGATGAGGTAAGACTGCCG	0.393													21	34	---	---	---	---	PASS
WDR48	57599	broad.mit.edu	37	3	39136315	39136315	+	3'UTR	SNP	C	G	G			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39136315C>G	uc003cit.2	+	19					WDR48_uc011ayt.1_3'UTR|WDR48_uc011ayu.1_3'UTR|WDR48_uc011ayv.1_3'UTR|WDR48_uc003ciu.2_RNA	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48						interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CCCACTGATCCCCAACGGGAG	0.473													6	40	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52643898	52643898	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643898A>T	uc003des.2	-	16	2010	c.1998T>A	c.(1996-1998)TAT>TAA	p.Y666*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.Y666*|PBRM1_uc003der.2_Nonsense_Mutation_p.Y634*|PBRM1_uc003det.2_Nonsense_Mutation_p.Y681*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Y681*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Y666*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Y666*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Y666*|PBRM1_uc003dez.1_Nonsense_Mutation_p.Y666*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.Y579*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.Y12*|PBRM1_uc003dfc.2_Nonsense_Mutation_p.Y33*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	666					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			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)		TTACAGCTTCATAGACCTCAT	0.398			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								53	91	---	---	---	---	PASS
MAGI1	9223	broad.mit.edu	37	3	65364846	65364846	+	Intron	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65364846C>T	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmq.1_RNA	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CATTTCTGCACGTGAGGTCTG	0.438													3	3	---	---	---	---	PASS
MBD4	8930	broad.mit.edu	37	3	129150264	129150264	+	3'UTR	SNP	A	G	G			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129150264A>G	uc003emh.1	-	8					uc003emg.2_5'Flank|MBD4_uc003emi.1_3'UTR|MBD4_uc003emj.1_3'UTR|MBD4_uc003emk.1_3'UTR	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4						depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2						CTATGGCTGGAAAGGTGGTTG	0.373								BER_DNA_glycosylases					14	72	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142281238	142281238	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142281238G>A	uc003eux.3	-	4	1128	c.1006C>T	c.(1006-1008)CGG>TGG	p.R336W		NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	336					cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						GACTTAAGCCGCATGAGCACA	0.388								Other_conserved_DNA_damage_response_genes					5	147	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	A	A	rs121913273		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178936082G>A	uc003fjk.2	+	10	1781	c.1624G>A	c.(1624-1626)GAA>AAA	p.E542K		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	542	PI3K helical.		E -> V (in cancer).|E -> K (in KERSEB; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation).|E -> Q (in cancer).		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.E542K(481)|p.E542V(8)|p.E542Q(6)|p.E542G(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)			TCCTCTCTCTGAAATCACTGA	0.333	E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(CAL51_BREAST)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(VMCUB1_URINARY_TRACT)|E542K(BT483_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)	57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			4	74	---	---	---	---	PASS
CCNI	10983	broad.mit.edu	37	4	77977246	77977246	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77977246C>G	uc003hkm.2	-	5	872	c.328G>C	c.(328-330)GTA>CTA	p.V110L	CCNI_uc011ccb.1_Missense_Mutation_p.V96L	NM_006835	NP_006826	Q14094	CCNI_HUMAN	cyclin I	110					spermatogenesis					ovary(1)	1						ACCTTTAGTACTGGAATTCTC	0.368													5	144	---	---	---	---	PASS
FAM13A	10144	broad.mit.edu	37	4	89772247	89772247	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89772247G>A	uc003hse.1	-	7	1139	c.931C>T	c.(931-933)CGG>TGG	p.R311W	FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsh.1_Missense_Mutation_p.R125W	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	311					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						TAACTTAGCCGCAAGCTGAGC	0.453													5	197	---	---	---	---	PASS
NPY2R	4887	broad.mit.edu	37	4	156135237	156135237	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156135237T>C	uc003ioq.2	+	2	641	c.146T>C	c.(145-147)GTA>GCA	p.V49A	NPY2R_uc003ior.2_Missense_Mutation_p.V49A	NM_000910	NP_000901	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	49	Extracellular (Potential).				cardiac left ventricle morphogenesis|inhibition of adenylate cyclase activity by G-protein signaling pathway|locomotory behavior|outflow tract morphogenesis	integral to plasma membrane	calcium channel regulator activity			lung(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0854)				CTGATTGAGGTACAAGTTGTT	0.473													4	62	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187629664	187629664	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187629664T>C	uc003izf.2	-	2	1506	c.1318A>G	c.(1318-1320)ACA>GCA	p.T440A	FAT1_uc010iso.1_Missense_Mutation_p.T440A	NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	440	Extracellular (Potential).|Cadherin 3.				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						CTGTCACTTGTTGTTACTTCA	0.398										HNSCC(5;0.00058)			4	288	---	---	---	---	PASS
KIAA0947	23379	broad.mit.edu	37	5	5462477	5462477	+	Silent	SNP	G	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5462477G>T	uc003jdm.3	+	13	3252	c.3030G>T	c.(3028-3030)GTG>GTT	p.V1010V		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	1010										ovary(1)|central_nervous_system(1)	2						AAGTGACTGTGTCAGGAGGGT	0.542													27	66	---	---	---	---	PASS
FAM71B	153745	broad.mit.edu	37	5	156589921	156589921	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156589921C>T	uc003lwn.2	-	2	1455	c.1355G>A	c.(1354-1356)AGT>AAT	p.S452N		NM_130899	NP_570969	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	452	Bipartite nuclear localization signal (Potential).					nucleus				ovary(4)|pancreas(1)|skin(1)	6	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCTGCGGTGACTTTCACCTGC	0.488													9	298	---	---	---	---	PASS
OR10C1	442194	broad.mit.edu	37	6	29407843	29407843	+	Silent	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29407843C>T	uc011dlp.1	+	1	51	c.51C>T	c.(49-51)TCC>TCT	p.S17S	OR11A1_uc010jrh.1_Intron	NM_013941	NP_039229	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C,	17	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TCGGCTTCTCCCACCTGGCCG	0.507													25	62	---	---	---	---	PASS
ELOVL5	60481	broad.mit.edu	37	6	53135507	53135507	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53135507T>C	uc003pbq.1	-	7	1088	c.640A>G	c.(640-642)ATC>GTC	p.I214V	ELOVL5_uc003pbr.1_Missense_Mutation_p.I214V|ELOVL5_uc011dwx.1_Missense_Mutation_p.I241V|ELOVL5_uc003pbs.1_Missense_Mutation_p.N172S|ELOVL5_uc003pbt.3_RNA	NM_021814	NP_068586	Q9NYP7	ELOV5_HUMAN	elongation of very long chain fatty acids-like	214	Helical; (Potential).			YFGATLNSFIHVLMYSYYGLSSVPSMRPYLWWKKYITQGQL LQFVLTIIQTSCGVIWPCTFPLGWLYFQIGYMISLIALFTN FYIQTYNKKGASRR -> SVCADNHPDQLRGHLAVHIPSWL VVFPDWIHDFPDCSLHKLLHSDLQQERGLPKERPPEGPPEW VHGCCEWTHQQLFTPGKQCEAKEAAEGLKSKN (in Ref. 4; BAD93035).	fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)					GTCTGGATGATTGTCAGCACA	0.522													11	35	---	---	---	---	PASS
KHDRBS2	202559	broad.mit.edu	37	6	62604655	62604655	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62604655G>T	uc003peg.2	-	6	942	c.695C>A	c.(694-696)GCG>GAG	p.A232E		NM_152688	NP_689901	Q5VWX1	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal	232	Pro-rich.			A -> V (in Ref. 1; AAL77219).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)		CACTGGAAGCGCTCCACGGGT	0.632													20	49	---	---	---	---	PASS
SYNJ2	8871	broad.mit.edu	37	6	158495714	158495714	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158495714G>T	uc003qqx.1	+	16	2311	c.2236G>T	c.(2236-2238)GAC>TAC	p.D746Y	SYNJ2_uc003qqw.1_Missense_Mutation_p.D746Y|SYNJ2_uc003qqy.1_Missense_Mutation_p.D459Y|SYNJ2_uc003qqz.1_Missense_Mutation_p.D363Y|SYNJ2_uc003qra.1_Missense_Mutation_p.D89Y	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	746	Catalytic (By similarity).						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		TAAACGCCAAGACTGGAAGAA	0.343													21	73	---	---	---	---	PASS
DENND2A	27147	broad.mit.edu	37	7	140301761	140301761	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140301761C>T	uc010lnj.2	-	1	582	c.437G>A	c.(436-438)AGA>AAA	p.R146K	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Missense_Mutation_p.R146K|DENND2A_uc003vvw.2_Missense_Mutation_p.R146K|DENND2A_uc003vvx.2_Missense_Mutation_p.R146K	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	146										ovary(3)|breast(1)	4	Melanoma(164;0.00956)					CTTGCCAAGTCTTGGCTCTCG	0.617													5	167	---	---	---	---	PASS
DLC1	10395	broad.mit.edu	37	8	13251072	13251072	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13251072G>A	uc003wwm.2	-	4	1748	c.1304C>T	c.(1303-1305)CCC>CTC	p.P435L	DLC1_uc003wwn.2_Missense_Mutation_p.P435L|DLC1_uc011kxy.1_Missense_Mutation_p.P435L	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	435					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						CGTAGTCTTGGGTTTGGTTCC	0.393													7	121	---	---	---	---	PASS
HAUS6	54801	broad.mit.edu	37	9	19096686	19096686	+	Silent	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19096686G>A	uc003znk.2	-	2	463	c.210C>T	c.(208-210)ACC>ACT	p.T70T		NM_017645	NP_060115	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	70					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2						AAACTTCTTTGGTGAGAGACT	0.318													4	51	---	---	---	---	PASS
SMC5	23137	broad.mit.edu	37	9	72892386	72892386	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72892386C>T	uc004ahr.2	+	4	658	c.541C>T	c.(541-543)CAG>TAG	p.Q181*		NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein	181					DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						GTTTCTCCCTCAGGTATGAGA	0.338													21	74	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	30987274	30987274	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30987274C>T	uc010qdx.1	+	4	546	c.4C>T	c.(4-6)CTC>TTC	p.L2F						SubName: Full=cDNA FLJ59642, highly similar to Supervillin;																		AAATGTGATGCTCTCCTGTTG	0.403													14	59	---	---	---	---	PASS
TMEM72	643236	broad.mit.edu	37	10	45430236	45430236	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45430236G>C	uc001jbn.2	+	5	679	c.482G>C	c.(481-483)GGC>GCC	p.G161A	uc001jbk.1_Intron|uc001jbl.2_Intron|TMEM72_uc009xmm.1_Missense_Mutation_p.G43A	NM_001123376	NP_001116848	A0PK05	TMM72_HUMAN	transmembrane protein 72	161						integral to membrane					0						AGCACCACCGGCTCTGGGGAC	0.587													5	217	---	---	---	---	PASS
OR2AG1	144125	broad.mit.edu	37	11	6806283	6806283	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6806283C>A	uc001mer.1	+	1	15	c.15C>A	c.(13-15)AAC>AAA	p.N5K		NM_001004489	NP_001004489	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG,	5	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGCTCTGGAACTTCACCTTGG	0.428													31	57	---	---	---	---	PASS
AMBRA1	55626	broad.mit.edu	37	11	46567203	46567203	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46567203G>A	uc010rgu.1	-	5	862	c.502C>T	c.(502-504)CGG>TGG	p.R168W	AMBRA1_uc010rgt.1_5'Flank|AMBRA1_uc009ylc.1_Missense_Mutation_p.R168W|AMBRA1_uc001ncu.1_Missense_Mutation_p.R168W|AMBRA1_uc001ncv.2_Missense_Mutation_p.R168W|AMBRA1_uc001ncw.2_Missense_Mutation_p.R168W|AMBRA1_uc001ncx.2_Missense_Mutation_p.R168W	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	168	WD 3.				autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		AAGGGTTCCCGTCGACTCCAG	0.562													18	106	---	---	---	---	PASS
KIAA1377	57562	broad.mit.edu	37	11	101868446	101868446	+	3'UTR	SNP	A	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101868446A>C	uc001pgm.2	+	11					KIAA1377_uc001pgn.2_3'UTR|KIAA1377_uc010run.1_3'UTR	NM_020802	NP_065853	Q9P2H0	K1377_HUMAN	hypothetical protein LOC57562								protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		TTTTGTGAAAACCAGCCATAG	0.423													9	38	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49424512	49424512	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49424512C>T	uc001rta.3	-	41	13711	c.13711G>A	c.(13711-13713)GCC>ACC	p.A4571T		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4571					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						CTAAAATTGGCGGTGATAGCA	0.597			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			4	88	---	---	---	---	PASS
NAB2	4665	broad.mit.edu	37	12	57485457	57485457	+	Silent	SNP	T	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57485457T>C	uc001smz.2	+	2	1011	c.633T>C	c.(631-633)CCT>CCC	p.P211P		NM_005967	NP_005958	Q15742	NAB2_HUMAN	NGFI-A binding protein 2	211					cell proliferation|negative regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	transcription corepressor activity			upper_aerodigestive_tract(1)|ovary(1)	2						TCTCCCCCCCTGCAGGGGGAG	0.711													6	25	---	---	---	---	PASS
LATS2	26524	broad.mit.edu	37	13	21557681	21557681	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21557681C>A	uc009zzs.2	-	5	2529	c.2164G>T	c.(2164-2166)GAG>TAG	p.E722*	LATS2_uc001unr.3_Nonsense_Mutation_p.E722*	NM_014572	NP_055387	Q9NRM7	LATS2_HUMAN	LATS, large tumor suppressor, homolog 2	722	Protein kinase.|ATP (By similarity).				cell division|G1/S transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|intracellular protein kinase cascade|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity	microtubule organizing center|nucleus|spindle pole	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(3)|ovary(2)|breast(1)|pancreas(1)	10		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		TTGTCTGCCTCGGCCAGGATG	0.542													64	127	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	36841025	36841025	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36841025G>A	uc001wtp.2	+	1	656	c.407G>A	c.(406-408)TGC>TAC	p.C136Y		NM_199286	NP_954980			stella																		TGCAGTTTCTGCGTGTCTAAT	0.428													57	64	---	---	---	---	PASS
C14orf1	11161	broad.mit.edu	37	14	76118207	76118207	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76118207A>T	uc001xrt.2	-	4	696	c.250T>A	c.(250-252)TTC>ATC	p.F84I	C14orf1_uc001xru.2_RNA	NM_007176	NP_009107	Q9UKR5	ERG28_HUMAN	ergosterol biosynthetic protein 28	84	Helical; (Potential).				sterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|transport vesicle					0		all_epithelial(191;0.125)|all_neural(303;0.13)|Myeloproliferative disorder(585;0.163)		BRCA - Breast invasive adenocarcinoma(234;0.00147)		GCAAGGAGGAAGGTCCAGAGT	0.483													21	35	---	---	---	---	PASS
RTF1	23168	broad.mit.edu	37	15	41763442	41763442	+	Silent	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41763442G>A	uc001zny.2	+	8	1110	c.1098G>A	c.(1096-1098)CGG>CGA	p.R366R		NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component	366	Plus3.				histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		GATTATCACGGCATAAGCTAG	0.458													5	180	---	---	---	---	PASS
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102515299G>A	uc002cdi.2	+	9	1943	c.523G>A	c.(523-525)GGC>AGC	p.G175S	WASH3P_uc002cdl.2_Missense_Mutation_p.G175S|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_Missense_Mutation_p.G175S|WASH3P_uc010bpo.2_RNA|WASH3P_uc002cdq.2_RNA|WASH3P_uc002cdr.2_RNA	NR_003659				RecName: Full=WAS protein family homolog 2; AltName: Full=Protein FAM39B; AltName: Full=CXYorf1-like protein on chromosome 2;												0						TGGGGGCATCGGCAAGGCCAA	0.652													4	14	---	---	---	---	PASS
MEFV	4210	broad.mit.edu	37	16	3293876	3293876	+	Silent	SNP	G	A	A	rs104895161		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3293876G>A	uc002cun.1	-	9	1816	c.1776C>T	c.(1774-1776)GGC>GGT	p.G592G		NM_000243	NP_000234	O15553	MEFV_HUMAN	Mediterranean fever protein	592	B30.2/SPRY.				inflammatory response	cytoplasm|microtubule|microtubule associated complex|nucleus	actin binding|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|lung(1)	6					Colchicine(DB01394)	GTGCCTGAGCGCCAATCAGCT	0.507													7	32	---	---	---	---	PASS
CP110	9738	broad.mit.edu	37	16	19548885	19548885	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19548885A>G	uc002dgl.3	+	4	2141	c.1894A>G	c.(1894-1896)AAA>GAA	p.K632E	CP110_uc002dgk.3_Missense_Mutation_p.K632E			O43303	CP110_HUMAN	RecName: Full=Centrosomal protein of 110 kDa;          Short=Cep110;	632					centriole replication|G2/M transition of mitotic cell cycle|regulation of cytokinesis	centriole|cytosol	protein binding				0						TAACAAGAATAAAATGTTAGG	0.348													3	61	---	---	---	---	PASS
PDXDC2	283970	broad.mit.edu	37	16	70010646	70010646	+	3'UTR	SNP	G	A	A	rs149870591	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70010646G>A	uc010vlq.1	-	6					CLEC18C_uc002exy.2_Intron|PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron					SubName: Full=Putative uncharacterized protein;												0						CTGTAGGGCCGAAGAAGGGAA	0.478													4	67	---	---	---	---	PASS
PDXDC2	283970	broad.mit.edu	37	16	70010650	70010650	+	3'UTR	SNP	A	G	G	rs144900726	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70010650A>G	uc010vlq.1	-	6					CLEC18C_uc002exy.2_Intron|PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron					SubName: Full=Putative uncharacterized protein;												0						AGGGCCGAAGAAGGGAATGTT	0.468													3	59	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161618	90161618	+	Missense_Mutation	SNP	C	T	T	rs13338202	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90161618C>T	uc002fqp.2	+	3	971	c.493C>T	c.(493-495)CGT>TGT	p.R165C	uc002fqq.2_Missense_Mutation_p.R182C					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		CAGTGATGGACGTTGTCAGAA	0.607													4	47	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	21730916	21730916	+	Missense_Mutation	SNP	G	T	T	rs111245273	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21730916G>T	uc002gyy.3	+	2	343	c.218G>T	c.(217-219)CGG>CTG	p.R73L						SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		GTCCTGCGTCGGAGAGGTGGT	0.552													3	68	---	---	---	---	PASS
FLJ36000	284124	broad.mit.edu	37	17	21904125	21904125	+	RNA	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21904125G>A	uc002gza.2	+	1		c.64G>A				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ggagtcgcaaggggccgagca	0.000													5	70	---	---	---	---	PASS
KRTAP4-11	653240	broad.mit.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	C	C	rs149439944	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39274291T>C	uc002hvz.2	-	1	316	c.277A>G	c.(277-279)ATG>GTG	p.M93V		NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	93	14.|27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCAGCACATAGACTGGCAG	0.388													9	43	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630632	44630632	+	3'UTR	SNP	C	T	T	rs142505146	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630632C>T	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						TGTTACACAGCATACAATTCC	0.234													6	30	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630635	44630635	+	3'UTR	SNP	A	G	G	rs150521815	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630635A>G	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						TACACAGCATACAATTCCTGT	0.239													7	33	---	---	---	---	PASS
RNMT	8731	broad.mit.edu	37	18	13737037	13737037	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13737037G>T	uc002ksk.1	+	4	649	c.582G>T	c.(580-582)AAG>AAT	p.K194N	RNMT_uc002ksl.1_Missense_Mutation_p.K194N|RNMT_uc002ksm.1_Missense_Mutation_p.K194N|RNMT_uc010dlk.2_Missense_Mutation_p.K194N|RNMT_uc010xae.1_RNA	NM_003799	NP_003790	O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	194					mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	mRNA (guanine-N7-)-methyltransferase activity|RNA binding				0						TACGACAGAAGAAAAAACGTG	0.348													15	72	---	---	---	---	PASS
MEP1B	4225	broad.mit.edu	37	18	29788192	29788192	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29788192A>T	uc002kxj.3	+	9	924	c.877A>T	c.(877-879)AGG>TGG	p.R293W		NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor	293	Extracellular (Potential).|MAM.				digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2						ACAGGTTCCCAGGGGGCCAGA	0.483													42	67	---	---	---	---	PASS
MYO5B	4645	broad.mit.edu	37	18	47438527	47438527	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47438527A>C	uc002leb.2	-	18	2395	c.2107T>G	c.(2107-2109)TTT>GTT	p.F703V		NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	703	Myosin head-like.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		CGGTTGAAAAAGTCATGGTAG	0.547													57	140	---	---	---	---	PASS
PIN1	5300	broad.mit.edu	37	19	9960334	9960334	+	3'UTR	SNP	A	G	G			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9960334A>G	uc002mml.1	+	4					PIN1_uc002mmm.1_3'UTR|PIN1_uc002mmn.1_RNA	NM_006221	NP_006212	Q13526	PIN1_HUMAN	protein (peptidyl-prolyl cis/trans isomerase)						cell cycle|negative regulation of cell motility|negative regulation of ERK1 and ERK2 cascade|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of type I interferon production|positive regulation of Rho GTPase activity|positive regulation of ubiquitin-protein ligase activity|protein folding|regulation of mitosis|regulation of pathway-restricted SMAD protein phosphorylation	nucleoplasm	GTPase activating protein binding|mitogen-activated protein kinase kinase binding|peptidyl-prolyl cis-trans isomerase activity|phosphoserine binding|phosphothreonine binding			skin(1)	1						GCACCCTTTCACCCCCAATTA	0.547													4	20	---	---	---	---	PASS
ACTN4	81	broad.mit.edu	37	19	39216363	39216363	+	Splice_Site	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39216363G>A	uc002oja.1	+	17	2070	c.2011_splice	c.e17-1	p.E671_splice	ACTN4_uc002ojb.1_5'UTR	NM_004924	NP_004915	O43707	ACTN4_HUMAN	actinin, alpha 4						platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CACCCCCGTAGGAGATCGGGC	0.657													8	10	---	---	---	---	PASS
PAPL	390928	broad.mit.edu	37	19	39597629	39597629	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39597629C>T	uc002oki.2	+	12	1430	c.1156C>T	c.(1156-1158)CCC>TCC	p.P386S	PAPL_uc010egl.2_Intron	NM_001004318	NP_001004318	Q6ZNF0	PAPL_HUMAN	iron/zinc purple acid phosphatase-like protein	386						extracellular region	acid phosphatase activity|metal ion binding				0						CTTCCCGAGGCCCTGGAGTGC	0.647													15	21	---	---	---	---	PASS
LGALS14	56891	broad.mit.edu	37	19	40199946	40199946	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40199946G>A	uc002omg.2	+	4	636	c.413G>A	c.(412-414)AGC>AAC	p.S138N	LGALS14_uc002omf.2_Missense_Mutation_p.S167N	NM_020129	NP_064514	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14 isoform	138	Galectin.					nucleus	sugar binding			ovary(1)|skin(1)	2	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			GTGCTTATCAGCGATTGAGGG	0.483													21	36	---	---	---	---	PASS
LIPE	3991	broad.mit.edu	37	19	42910438	42910438	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42910438T>A	uc002otr.2	-	7	2517	c.2240A>T	c.(2239-2241)GAT>GTT	p.D747V	uc010eif.1_Intron	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	747					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)				CATGATGCCATCTGGCACCCG	0.662													22	36	---	---	---	---	PASS
LILRB5	10990	broad.mit.edu	37	19	54754989	54754989	+	Intron	SNP	T	G	G	rs686335		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54754989T>G	uc002qex.2	-						LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Missense_Mutation_p.E549A|LILRB5_uc002qey.2_Intron|LILRB5_uc002qez.2_Intron|LILRB5_uc002qfa.1_3'UTR	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTGTTTCACCTCGGCATACGT	0.582													4	17	---	---	---	---	PASS
LILRB5	10990	broad.mit.edu	37	19	54754990	54754990	+	Intron	SNP	C	G	G	rs686334		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54754990C>G	uc002qex.2	-						LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Missense_Mutation_p.E549Q|LILRB5_uc002qey.2_Intron|LILRB5_uc002qez.2_Intron|LILRB5_uc002qfa.1_3'UTR	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGTTTCACCTCGGCATACGTC	0.582													5	17	---	---	---	---	PASS
RPL28	6158	broad.mit.edu	37	19	55899351	55899351	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55899351C>A	uc002qkv.2	+	4	301	c.259C>A	c.(259-261)CGC>AGC	p.R87S	RPL28_uc010yga.1_Missense_Mutation_p.R87S|RPL28_uc010ygb.1_Missense_Mutation_p.R87S|RPL28_uc002qkw.1_3'UTR	NM_000991	NP_000982	P46779	RL28_HUMAN	ribosomal protein L28 isoform 2	87					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CAAGAATGCTCGCGCCACGCT	0.617													3	120	---	---	---	---	PASS
SFRS15	57466	broad.mit.edu	37	21	33067196	33067196	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33067196G>A	uc002ypd.2	-	10	1592	c.1166C>T	c.(1165-1167)CCA>CTA	p.P389L	SFRS15_uc002ype.2_Missense_Mutation_p.P389L|SFRS15_uc010glu.2_Missense_Mutation_p.P374L|SFRS15_uc002ypf.1_Missense_Mutation_p.P63L	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	389						nucleus	nucleotide binding|RNA binding				0						CTGCTGCACTGGTGGAGTTGG	0.458													36	82	---	---	---	---	PASS
MCM3AP	8888	broad.mit.edu	37	21	47663535	47663535	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47663535G>T	uc002zir.1	-	24	5176	c.5140C>A	c.(5140-5142)CTC>ATC	p.L1714I	MCM3APAS_uc002zim.2_Intron|MCM3APAS_uc002zin.2_Intron|MCM3AP_uc002zio.1_Missense_Mutation_p.L209I|MCM3AP_uc002zip.1_Missense_Mutation_p.L455I|MCM3AP_uc002ziq.1_Missense_Mutation_p.L641I|MCM3APAS_uc002zis.1_Intron	NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3	1714					DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)					GTTCTGTGGAGCAGGTTCTCC	0.612													25	56	---	---	---	---	PASS
PHF21B	112885	broad.mit.edu	37	22	45291957	45291957	+	Missense_Mutation	SNP	C	T	T	rs114160106	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45291957C>T	uc003bfn.2	-	6	989	c.838G>A	c.(838-840)GCC>ACC	p.A280T	PHF21B_uc003bfm.2_Missense_Mutation_p.A76T|PHF21B_uc011aqk.1_Missense_Mutation_p.A226T|PHF21B_uc011aql.1_Missense_Mutation_p.A238T|PHF21B_uc011aqm.1_Missense_Mutation_p.A226T	NM_138415	NP_612424	Q96EK2	PF21B_HUMAN	PHD finger protein 21B isoform 1	280							zinc ion binding	p.A280T(1)		ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		ACCATGAAGGCGATTTTCTGA	0.522													4	141	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14034	14034	+	RNA	SNP	T	C	C			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14034T>C	uc004cox.3	+	1		c.1698T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCTAAAACAATTTCACAGCAC	0.443													5	3	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	13123162	13123163	+	IGR	INS	-	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13123162_13123163insA								PRAMEF5 (5411 upstream) : LOC440563 (59798 downstream)																							gagactccatcaaaaaaaaaaa	0.233													3	3	---	---	---	---	
DNTTIP2	30836	broad.mit.edu	37	1	94335643	94335644	+	Intron	INS	-	A	A	rs139700012	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94335643_94335644insA	uc001dqf.2	-						DNTTIP2_uc010otm.1_Intron	NM_014597	NP_055412	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal,						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		aatctagggagaaaaaATGGCA	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	94871896	94871897	+	IGR	INS	-	T	T	rs12091363		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94871896_94871897insT								ARHGAP29 (131272 upstream) : ABCD3 (12036 downstream)																							aTTTTGTTTTGTTTTTTTTTTT	0.183													3	4	---	---	---	---	
TDRKH	11022	broad.mit.edu	37	1	151752734	151752780	+	Intron	DEL	TACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGT	-	-	rs112300596		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151752734_151752780delTACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGT	uc009wnb.1	-						TDRKH_uc001eyy.2_Intron|TDRKH_uc001ezb.3_Intron|TDRKH_uc001ezc.3_Intron|TDRKH_uc001eza.3_Intron|TDRKH_uc001ezd.3_Intron|TDRKH_uc010pdn.1_Intron	NM_006862	NP_006853	Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing isoform a								RNA binding			ovary(1)|pancreas(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AATTAGCTAATACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGTTACTATCTAT	0.368													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133020743	133020744	+	IGR	INS	-	T	T	rs137914230		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133020743_133020744insT								NCRNA00164 (5201 upstream) : GPR39 (153403 downstream)																							TTAGATAGCTCTTTATTGTCAT	0.327													7	6	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191527	10191527	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191527delA	uc003bvc.2	+	3	733	c.520delA	c.(520-522)AATfs	p.N174fs	VHL_uc003bvd.2_Frame_Shift_Del_p.N133fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	174					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.N174fs*28(2)|p.N174fs*41(1)|p.E173fs*26(1)|p.P172fs*39(1)|p.N174D(1)		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)		CAAGCCTGAGAATTACAGGAG	0.532		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				25	16	---	---	---	---	
ANO10	55129	broad.mit.edu	37	3	43607225	43607225	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43607225delA	uc003cmv.2	-						ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Intron|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Intron	NM_018075	NP_060545	Q9NW15	ANO10_HUMAN	transmembrane protein 16K						cell death	chloride channel complex	chloride channel activity			ovary(2)	2						TTGAACTGCCAAAAAAAAAAA	0.313													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188242759	188242760	+	Intron	INS	-	T	T	rs11393215		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188242759_188242760insT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ctttctttctcttttttttttt	0.035			T	HMGA2|MLL|C12orf9	lipoma|leukemia								5	3	---	---	---	---	
STIM2	57620	broad.mit.edu	37	4	27009063	27009063	+	Intron	DEL	T	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27009063delT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				TTAAAATAGCTTTTTTTTTTT	0.169													6	3	---	---	---	---	
ATP10D	57205	broad.mit.edu	37	4	47492948	47492948	+	Intron	DEL	T	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47492948delT	uc003gxk.1	+						ATP10D_uc003gxj.3_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D						ATP biosynthetic process|cation transport	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(2)|pancreas(1)	3						CAAATACATCTTTTTTTTTTT	0.378													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49506430	49506430	+	IGR	DEL	T	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49506430delT								CWH43 (442337 upstream) : None (None downstream)																							TTCTTCTCTATTTTTTTGTAC	0.279													4	2	---	---	---	---	
TMEM165	55858	broad.mit.edu	37	4	56290940	56290941	+	Intron	INS	-	AATA	AATA	rs140080934	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56290940_56290941insAATA	uc003hax.2	+						TMEM165_uc011bzy.1_Intron	NM_018475	NP_060945	Q9HC07	TM165_HUMAN	transmembrane protein 165							integral to membrane					0	Lung NSC(11;0.00545)|Glioma(25;0.08)|all_neural(26;0.101)|all_epithelial(27;0.135)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0103)			CCATCTCTTATAGAGGTATTAA	0.252													4	4	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79371639	79371640	+	Intron	INS	-	T	T	rs138438777	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79371639_79371640insT	uc003hlb.2	+							NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						ttgttttcttattttttttttc	0.277													6	4	---	---	---	---	
HSPA9	3313	broad.mit.edu	37	5	137909330	137909331	+	Intron	INS	-	AAA	AAA	rs55663873		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137909330_137909331insAAA	uc003ldf.2	-						HSPA9_uc011cyw.1_Intron	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor						anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			agactgtctccaaaaaaaaaaa	0.149													4	2	---	---	---	---	
CLINT1	9685	broad.mit.edu	37	5	157216273	157216277	+	Intron	DEL	TTATG	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157216273_157216277delTTATG	uc003lxj.1	-						CLINT1_uc003lxg.1_Intron|CLINT1_uc003lxh.1_Intron|CLINT1_uc003lxi.1_Intron|CLINT1_uc011ddv.1_Intron	NM_014666	NP_055481	Q14677	EPN4_HUMAN	epsin 4						endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTGTTACAATTTATGTGATATATTT	0.322													27	19	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	33055169	33055170	+	Intron	INS	-	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33055169_33055170insA	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						aggcttgtctcaaaaaaaaaaG	0.139													8	4	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	33066270	33066270	+	Intron	DEL	T	-	-	rs34317509		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33066270delT	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						tgcccggccAttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36007568	36007569	+	IGR	DEL	CA	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36007568_36007569delCA								SEPT7 (62653 upstream) : EEPD1 (185267 downstream)																							GGGCGCCTCCCACCTGGCCCGC	0.634													4	2	---	---	---	---	
SPDYE8P	389517	broad.mit.edu	37	7	74970249	74970249	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74970249delA	uc010lcv.2	+						PMS2L2_uc011kfp.1_Intron|PMS2L2_uc011kfq.1_Intron|PMS2L2_uc003uch.1_Intron|SPDYE8P_uc011kfs.1_Intron|PMS2L2_uc003uco.1_Intron|PMS2L2_uc003ucq.2_Intron					RecName: Full=Putative WBSCR19-like protein 4;												0						TTATAGTCTCaaaaaaaaaaa	0.418													6	3	---	---	---	---	
SEMA3E	9723	broad.mit.edu	37	7	83025865	83025865	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83025865delA	uc003uhy.1	-							NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				CCTGTTAGGGAAAAAAAAATG	0.303													8	4	---	---	---	---	
SPDYE2	441273	broad.mit.edu	37	7	102197784	102197784	+	Intron	DEL	T	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102197784delT	uc011kkx.1	+						UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_Intron|POLR2J3_uc011kkw.1_Intron|SPDYE2_uc003vaa.1_Intron	NM_001031618	NP_001026789	Q495Y8	SPDE2_HUMAN	speedy homolog E2												0						TCCTACAGtcttttttttttt	0.289													4	3	---	---	---	---	
MLL5	55904	broad.mit.edu	37	7	104681592	104681592	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104681592delA	uc003vcm.2	+						MLL5_uc010lja.1_Intron|MLL5_uc010ljb.1_Intron|MLL5_uc003vcl.2_Intron|MLL5_uc010ljc.2_Intron	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5						cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						TTTTTAAAGTAAAAAAAAAAA	0.274													4	2	---	---	---	---	
ELP3	55140	broad.mit.edu	37	8	27964075	27964089	+	Intron	DEL	AAAAAAAAAAGAAAT	-	-	rs71841815		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27964075_27964089delAAAAAAAAAAGAAAT	uc003xgo.3	+						ELP3_uc003xgn.3_Intron|ELP3_uc011laq.1_Intron|ELP3_uc011lar.1_Intron|ELP3_uc011las.1_Intron|ELP3_uc011lat.1_Intron	NM_018091	NP_060561	Q9H9T3	ELP3_HUMAN	elongation protein 3 homolog						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	histone acetyltransferase activity|iron-sulfur cluster binding|metal ion binding|phosphorylase kinase regulator activity|protein binding				0		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		aaaaaaaaaaaaaaaaaaaagaaatacagcctcgt	0.000													4	2	---	---	---	---	
TPD52	7163	broad.mit.edu	37	8	81083599	81083610	+	Intron	DEL	AAGCCCGAGTCC	-	-	rs113293335		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81083599_81083610delAAGCCCGAGTCC	uc003ybs.1	-						TPD52_uc010lzs.1_5'Flank|TPD52_uc003ybt.1_Intron	NM_001025253	NP_001020424	P55327	TPD52_HUMAN	tumor protein D52 isoform 2						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			cgccgagccaaagcccgagtccaagcccgagt	0.514													4	2	---	---	---	---	
PCSK5	5125	broad.mit.edu	37	9	78790207	78790208	+	Intron	INS	-	GAATA	GAATA	rs10124596		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78790207_78790208insGAATA	uc004ajz.2	+						PCSK5_uc004ajy.2_Frame_Shift_Ins_p.R688fs|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						cgaatcgaatcgaatagaatag	0.099													5	4	---	---	---	---	
ZCCHC6	79670	broad.mit.edu	37	9	88943241	88943242	+	Intron	DEL	AA	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88943241_88943242delAA	uc004aoq.2	-						ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						AACTAGAAACAAAAGAGAACAG	0.421													101	44	---	---	---	---	
ALDOB	229	broad.mit.edu	37	9	104187311	104187312	+	Frame_Shift_Ins	INS	-	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104187311_104187312insA	uc004bbk.2	-	8	894_895	c.812_813insT	c.(811-813)TTGfs	p.L271fs		NM_000035	NP_000026	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	271					fructose 1,6-bisphosphate metabolic process|fructose catabolic process|gluconeogenesis|glycolysis|NADH oxidation|positive regulation of ATPase activity|vacuolar proton-transporting V-type ATPase complex assembly	centriolar satellite|cytosol	ATPase binding|cytoskeletal protein binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TGCCACCAGACAAAAAGCAGAT	0.455													52	23	---	---	---	---	
RAD23B	5887	broad.mit.edu	37	9	110081278	110081279	+	Intron	INS	-	T	T			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110081278_110081279insT	uc004bde.2	+						RAD23B_uc011lwa.1_Intron|RAD23B_uc011lwb.1_Intron	NM_002874	NP_002865	P54727	RD23B_HUMAN	UV excision repair protein RAD23 homolog B						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1						ATACATAATGCTTTTTTTTTTC	0.292								Direct_reversal_of_damage|NER					6	3	---	---	---	---	
ANXA7	310	broad.mit.edu	37	10	75155560	75155560	+	Intron	DEL	G	-	-	rs72812299	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75155560delG	uc001jtz.2	-						ANXA7_uc001jua.2_Intron|ANXA7_uc001jub.2_Intron|ANXA7_uc010qki.1_Intron|ANXA7_uc009xre.2_Intron|ANXA7_uc009xrf.1_Intron	NM_004034	NP_004025	P20073	ANXA7_HUMAN	annexin VII isoform 2								calcium ion binding|calcium-dependent phospholipid binding|calcium-dependent protein binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					aaaaaaaaaagaaGCCATACG	0.204													4	2	---	---	---	---	
CCDC83	220047	broad.mit.edu	37	11	85622219	85622219	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85622219delA	uc001pbh.1	+						CCDC83_uc001pbg.1_Intron|CCDC83_uc001pbi.1_Intron|CCDC83_uc001pbj.1_Intron	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83											skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				cgtctcaaataaaaaaaaaaa	0.095													6	3	---	---	---	---	
ADAMTS8	11095	broad.mit.edu	37	11	130287129	130287130	+	Intron	INS	-	TTAAA	TTAAA	rs146577586	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130287129_130287130insTTAAA	uc001qgg.3	-							NM_007037	NP_008968	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1						negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding			central_nervous_system(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		TTATTGAGCTTTTAAATTAAAT	0.297													4	2	---	---	---	---	
A2M	2	broad.mit.edu	37	12	9246251	9246251	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9246251delA	uc001qvk.1	-						A2M_uc009zgk.1_Intron	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor						blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	AGTTGCCACCAAAAAAAAAAA	0.383													9	4	---	---	---	---	
GXYLT1	283464	broad.mit.edu	37	12	42503346	42503346	+	Intron	DEL	G	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42503346delG	uc001rms.3	-						GXYLT1_uc001rmt.3_Intron	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0						aaaaaaaaaaGACACTAGGGG	0.308													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77054687	77054687	+	IGR	DEL	T	-	-	rs2369296	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77054687delT								OSBPL8 (101098 upstream) : ZDHHC17 (103167 downstream)																							aaaaaaaaaataaataaaGGA	0.358													4	3	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129821987	129821988	+	Intron	DEL	CA	-	-	rs34583805		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129821987_129821988delCA	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		Tacacacacgcacacacacaca	0.272													4	4	---	---	---	---	
CDADC1	81602	broad.mit.edu	37	13	49829865	49829865	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49829865delA	uc001vcu.2	+						CDADC1_uc001vcs.1_Intron|CDADC1_uc001vct.1_Intron|CDADC1_uc010tgk.1_Intron|CDADC1_uc001vcv.2_Intron	NM_030911	NP_112173	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1								hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		TTCATCATGGAAAAAAAAATG	0.264													6	3	---	---	---	---	
NARG2	79664	broad.mit.edu	37	15	60728475	60728476	+	Intron	INS	-	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60728475_60728476insA	uc002agp.2	-						NARG2_uc002ago.2_Intron	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2						GCAGTATTTAGAAAAAAAAAAA	0.252													8	5	---	---	---	---	
SMG1	23049	broad.mit.edu	37	16	18883764	18883764	+	Intron	DEL	A	-	-	rs117332168	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18883764delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						TCTATCCATTAAAAAAAAAAA	0.313													6	3	---	---	---	---	
UTP18	51096	broad.mit.edu	37	17	49350959	49350960	+	Intron	INS	-	T	T	rs71355748		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49350959_49350960insT	uc002its.2	+							NM_016001	NP_057085	Q9Y5J1	UTP18_HUMAN	UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			TTATGTTATTGTTTTTTTTTTT	0.238													5	3	---	---	---	---	
SNRPD1	6632	broad.mit.edu	37	18	19202891	19202892	+	Intron	DEL	TT	-	-	rs111943199		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19202891_19202892delTT	uc002ktj.1	+							NM_006938	NP_008869	P62314	SMD1_HUMAN	small nuclear ribonucleoprotein D1 polypeptide						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	catalytic step 2 spliceosome|cytosol|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	protein binding|RNA binding				0						AATTATGTAAtttttttttttt	0.114													4	2	---	---	---	---	
FAM59A	64762	broad.mit.edu	37	18	29973144	29973144	+	Intron	DEL	T	-	-	rs10708225		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29973144delT	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A											ovary(1)|skin(1)	2						CTCTGAATTGttttttttttt	0.308													4	2	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67068606	67068606	+	Intron	DEL	G	-	-	rs34997416		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67068606delG	uc002lkl.2	+							NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				CTGGCTGCCTGGGGGGGGGGC	0.697													4	2	---	---	---	---	
KDM4B	23030	broad.mit.edu	37	19	5144450	5144450	+	Intron	DEL	G	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5144450delG	uc002mbq.3	+						KDM4B_uc010xim.1_Intron|KDM4B_uc002mbr.3_Intron	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1						GGCAGGGGGCGGGGGGAGGCT	0.642													4	2	---	---	---	---	
CC2D1A	54862	broad.mit.edu	37	19	14030491	14030491	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14030491delA	uc002mxo.2	+						CC2D1A_uc002mxn.2_Intron|CC2D1A_uc002mxp.2_Intron|CC2D1A_uc010dzh.2_Intron|CC2D1A_uc002mxq.1_Intron	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			atcctgtctcaaaaaaaaaaa	0.174													4	3	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17750846	17750846	+	Intron	DEL	T	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17750846delT	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						TTCTATGGCAttttttttttt	0.254													5	3	---	---	---	---	
RUVBL2	10856	broad.mit.edu	37	19	49507372	49507373	+	Intron	INS	-	AA	AA	rs74182026		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49507372_49507373insAA	uc002plr.1	+						RUVBL2_uc002plq.1_Intron|RUVBL2_uc010yab.1_Intron|RUVBL2_uc002pls.1_Intron|RUVBL2_uc010emn.1_Intron|RUVBL2_uc010yac.1_Intron	NM_006666	NP_006657	Q9Y230	RUVB2_HUMAN	RuvB-like 2						cellular response to UV|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|protein folding|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|membrane|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|ATP-dependent DNA helicase activity|damaged DNA binding|identical protein binding|unfolded protein binding				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		gatcttgtctcaaaaaaaaaaa	0.173													8	4	---	---	---	---	
NLRP7	199713	broad.mit.edu	37	19	55446085	55446085	+	Intron	DEL	T	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55446085delT	uc002qih.3	-						NLRP7_uc002qig.3_Intron|NLRP7_uc002qii.3_Intron|NLRP7_uc010esk.2_Intron|NLRP7_uc010esl.2_Intron	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7								ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		CCCTATCAGCttttttttttt	0.264													10	5	---	---	---	---	
USP25	29761	broad.mit.edu	37	21	17236478	17236478	+	Intron	DEL	A	-	-	rs72445627		TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17236478delA	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		TTTAAAAGCCAAAAAAAAAAA	0.299													3	4	---	---	---	---	
RNF160	26046	broad.mit.edu	37	21	30332708	30332708	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30332708delA	uc002ymr.2	-							NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294								ligase activity|zinc ion binding				0						aaaagaaaaGAAAAAAAAAAA	0.189													4	2	---	---	---	---	
PCNT	5116	broad.mit.edu	37	21	47754119	47754119	+	Intron	DEL	A	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47754119delA	uc002zji.3	+						PCNT_uc002zjj.2_Intron|PCNT_uc010gqk.1_5'Flank	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					actccgtctcaaaaaaaaaaa	0.184													6	3	---	---	---	---	
GGT1	2678	broad.mit.edu	37	22	25016169	25016170	+	Intron	INS	-	T	T	rs28418841	by1000genomes	TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25016169_25016170insT	uc003aan.1	+						GGT1_uc003aas.1_Intron|GGT1_uc003aat.1_Intron|GGT1_uc003aau.1_Intron|GGT1_uc003aav.1_Intron|GGT1_uc003aaw.1_Intron|GGT1_uc003aax.1_Intron	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	aaaaaaaaaaaaTCTTTCCTCC	0.277													11	5	---	---	---	---	
DGKK	139189	broad.mit.edu	37	X	50127149	50127150	+	Intron	INS	-	A	A			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50127149_50127150insA	uc010njr.1	-							NM_001013742	NP_001013764	Q5KSL6	DGKK_HUMAN	diacylglycerol kinase kappa						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)					TAAAAGGTGATAGAGTTAAATA	0.228													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	97677253	97677253	+	IGR	DEL	C	-	-			TCGA-B0-5711-01A-11D-1669-08	TCGA-B0-5711-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97677253delC								DIAPH2 (821657 upstream) : None (None downstream)																							TTTCAGttttctttttttttt	0.224													6	3	---	---	---	---	
