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
WASH7P	653635	broad.mit.edu	37	1	14948	14948	+	Intron	SNP	G	A	A	rs148911281	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14948G>A	uc009vis.2	-						WASH7P_uc009vit.2_Intron|WASH7P_uc001aae.3_Intron|WASH7P_uc009viu.2_Intron|WASH7P_uc001aab.3_Intron|WASH7P_uc001aah.3_Intron|WASH7P_uc009vir.2_Intron|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_Intron|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						GGCCCAGGGCGGGCAGCGGCC	0.597													4	22	---	---	---	---	PASS
DNAJC16	23341	broad.mit.edu	37	1	15893684	15893684	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15893684G>A	uc001aws.2	+	14	1989	c.1869G>A	c.(1867-1869)ATG>ATA	p.M623I	DNAJC16_uc001awt.2_Missense_Mutation_p.M311I|DNAJC16_uc001awu.2_RNA	NM_015291	NP_056106	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	623	Extracellular (Potential).				cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CAGGCCACATGAATGTGGTCC	0.418													28	153	---	---	---	---	PASS
MFSD2A	84879	broad.mit.edu	37	1	40430907	40430907	+	Silent	SNP	C	T	T	rs115805986	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40430907C>T	uc001cev.2	+	4	598	c.417C>T	c.(415-417)GCC>GCT	p.A139A	MFSD2A_uc010ojb.1_Silent_p.A89A|MFSD2A_uc001ceu.2_Silent_p.A126A|MFSD2A_uc010ojc.1_5'UTR|MFSD2A_uc009vvy.2_RNA|MFSD2A_uc001cex.2_5'Flank	NM_001136493	NP_001129965	Q8NA29	MFS2A_HUMAN	major facilitator superfamily domain containing	139	Helical; (Potential).				transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2						CGCCCCTGGCCGTCATTGCCT	0.587													17	85	---	---	---	---	PASS
ECHDC2	55268	broad.mit.edu	37	1	53377478	53377478	+	Intron	SNP	G	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53377478G>C	uc001cup.3	-						ECHDC2_uc001cun.2_5'UTR|ECHDC2_uc001cuo.3_Intron|ECHDC2_uc010onk.1_Intron|ECHDC2_uc010onl.1_Intron|ECHDC2_uc010onm.1_Intron|ECHDC2_uc010onn.1_Intron	NM_018281	NP_060751	Q86YB7	ECHD2_HUMAN	enoyl Coenzyme A hydratase domain containing 2						fatty acid metabolic process	mitochondrion	lyase activity			central_nervous_system(1)	1						AGGAGTCAGGGCAGCCACGGG	0.438													8	64	---	---	---	---	PASS
TSPAN2	10100	broad.mit.edu	37	1	115593075	115593075	+	3'UTR	SNP	A	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115593075A>G	uc001eft.2	-	8						NM_005725	NP_005716	O60636	TSN2_HUMAN	tetraspan 2							integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		ATTTGGTATGAAAGCTTTAGA	0.378													17	62	---	---	---	---	PASS
SELENBP1	8991	broad.mit.edu	37	1	151339307	151339307	+	Silent	SNP	C	T	T	rs146898667	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151339307C>T	uc001exx.2	-	6	602	c.555G>A	c.(553-555)CCG>CCA	p.P185P	SELENBP1_uc010pcy.1_Silent_p.P227P|SELENBP1_uc001exy.2_Silent_p.P82P|SELENBP1_uc001exz.2_Silent_p.P82P|SELENBP1_uc010pcz.1_Silent_p.P123P|SELENBP1_uc009wms.2_Intron|SELENBP1_uc009wmt.2_Silent_p.P82P|SELENBP1_uc001eya.2_Silent_p.P121P|SELENBP1_uc009wmu.2_Silent_p.P82P	NM_003944	NP_003935	Q13228	SBP1_HUMAN	selenium binding protein 1	185					protein transport	cytosol|membrane|nucleolus	protein binding|selenium binding				0	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CATAGCCCAACGGTGCAGCAC	0.577													29	345	---	---	---	---	PASS
AIDA	64853	broad.mit.edu	37	1	222867134	222867134	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222867134G>A	uc001hnn.2	-	4	491	c.286C>T	c.(286-288)CCA>TCA	p.P96S	AIDA_uc001hno.2_RNA|AIDA_uc010pus.1_Missense_Mutation_p.P72S	NM_022831	NP_073742	Q96BJ3	AIDA_HUMAN	axin interactor, dorsalization associated	96					dorsal/ventral pattern formation|negative regulation of JNK cascade|negative regulation of JUN kinase activity|regulation of protein homodimerization activity						0						AACTTACTTGGTTCTAGCTTC	0.279													13	164	---	---	---	---	PASS
KHK	3795	broad.mit.edu	37	2	27320391	27320391	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27320391G>T	uc002ril.2	+	5	955	c.438G>T	c.(436-438)CAG>CAT	p.Q146H	KHK_uc002rim.2_Missense_Mutation_p.Q146H|KHK_uc002rin.2_Missense_Mutation_p.Q147H|KHK_uc002rio.2_Missense_Mutation_p.Q62H	NM_000221	NP_000212	P50053	KHK_HUMAN	ketohexokinase isoform a	146					fructose catabolic process	cytosol	ATP binding|ketohexokinase activity|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATCGGAGCAGGTGAAGATGC	0.622													17	94	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50724674	50724674	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50724674C>G	uc010fbq.2	-	14	4273	c.2796G>C	c.(2794-2796)GAG>GAC	p.E932D	NRXN1_uc002rxb.3_Missense_Mutation_p.E564D|NRXN1_uc002rxe.3_Missense_Mutation_p.E892D|NRXN1_uc002rxc.1_RNA	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	Error:Variant_position_missing_in_P58400_after_alignment					angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TGGCATTAAGCTCACAGTAAT	0.443													15	62	---	---	---	---	PASS
GPR45	11250	broad.mit.edu	37	2	105859013	105859013	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105859013C>T	uc002tco.1	+	1	814	c.698C>T	c.(697-699)TCG>TTG	p.S233L		NM_007227	NP_009158	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	233	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						CACAACCAGTCGGACAGCCTG	0.652													15	112	---	---	---	---	PASS
TFCP2L1	29842	broad.mit.edu	37	2	121981867	121981867	+	3'UTR	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121981867G>A	uc002tmx.2	-	15					TFCP2L1_uc010flr.2_3'UTR|TFCP2L1_uc010flq.2_RNA	NM_014553	NP_055368	Q9NZI6	TF2L1_HUMAN	LBP-9						female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)					CTACATCCACGGGGATCCACA	0.577													4	27	---	---	---	---	PASS
COBLL1	22837	broad.mit.edu	37	2	165551129	165551129	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165551129A>C	uc010zcw.1	-	15	3212	c.3088T>G	c.(3088-3090)TCT>GCT	p.S1030A	COBLL1_uc002ucp.2_Missense_Mutation_p.S963A|COBLL1_uc002ucq.2_Missense_Mutation_p.S925A|COBLL1_uc010zcx.1_Missense_Mutation_p.S971A|COBLL1_uc002ucn.2_Missense_Mutation_p.S391A|COBLL1_uc002uco.2_Missense_Mutation_p.S694A	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	1001										ovary(2)|pancreas(1)	3						TGTGGAACAGAGTGAGGCATT	0.478													9	89	---	---	---	---	PASS
STK17B	9262	broad.mit.edu	37	2	197002269	197002269	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197002269C>A	uc002utk.2	-	8	1345	c.1021G>T	c.(1021-1023)GAG>TAG	p.E341*	STK17B_uc010fsh.2_Nonsense_Mutation_p.E341*	NM_004226	NP_004217	O94768	ST17B_HUMAN	serine/threonine kinase 17B	341					apoptosis|induction of apoptosis|intracellular protein kinase cascade	nucleus	ATP binding|protein serine/threonine kinase activity			lung(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.141)			GGGATATTCTCTTTGTCTTCT	0.418													21	163	---	---	---	---	PASS
IRS1	3667	broad.mit.edu	37	2	227662246	227662246	+	Silent	SNP	G	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227662246G>C	uc002voh.3	-	1	1261	c.1209C>G	c.(1207-1209)ACC>ACG	p.T403T		NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1	403	Ser-rich.				fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GACAATCCGAGGTGGAGCCAT	0.637											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	128	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52437168	52437168	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52437168T>A	uc003ddx.2	-	14	1991	c.1876A>T	c.(1876-1878)AAA>TAA	p.K626*	BAP1_uc003ddw.2_Intron|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_Intron	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	626	Interaction with BRCA1.				monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGTGAGTATTTCTCCCCACTC	0.592			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								10	100	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52582140	52582140	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52582140C>G	uc003des.2	-	30	5021	c.5009G>C	c.(5008-5010)CGA>CCA	p.R1670P	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.R1563P|PBRM1_uc003der.2_Missense_Mutation_p.R1583P|PBRM1_uc003det.2_Missense_Mutation_p.R1578P|PBRM1_uc003deu.2_Missense_Mutation_p.R1633P|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.R1615P|PBRM1_uc010hmk.1_Missense_Mutation_p.R1590P|PBRM1_uc003dey.2_Missense_Mutation_p.R1563P	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1670					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)		CATCAAATCTCGAAGGCGCCA	0.483			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								35	205	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	123987876	123987876	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123987876A>G	uc003ehg.2	+	5	864	c.737A>G	c.(736-738)GAC>GGC	p.D246G	KALRN_uc010hrv.1_Missense_Mutation_p.D246G|KALRN_uc003ehf.1_Missense_Mutation_p.D246G|KALRN_uc011bjy.1_Missense_Mutation_p.D246G	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	246	Spectrin 1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GAGGAGCTGGACCGGGAGGGG	0.632													5	11	---	---	---	---	PASS
PYDC2	152138	broad.mit.edu	37	3	191179038	191179038	+	Silent	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191179038G>A	uc011bso.1	+	1	87	c.87G>A	c.(85-87)CTG>CTA	p.L29L		NM_001083308	NP_001076777	Q56P42	PYDC2_HUMAN	pyrin domain containing 2	29	DAPIN.					cytoplasm|nucleus					0						TCAAGTCTCTGATCAGAACAA	0.517													24	154	---	---	---	---	PASS
OTOP1	133060	broad.mit.edu	37	4	4190659	4190659	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4190659G>C	uc003ghp.1	-	6	1740	c.1710C>G	c.(1708-1710)GAC>GAG	p.D570E		NM_177998	NP_819056	Q7RTM1	OTOP1_HUMAN	otopetrin 1	570					biomineral tissue development	extracellular space|integral to membrane				ovary(2)|central_nervous_system(1)	3				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CCAATCCATTGTCATACTCAG	0.507													6	108	---	---	---	---	PASS
DCHS2	54798	broad.mit.edu	37	4	155155839	155155839	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155155839T>C	uc003inw.2	-	25	8600	c.8600A>G	c.(8599-8601)GAA>GGA	p.E2867G		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	2867					homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGTCATGCCTTCTGGCAGAGA	0.512													30	202	---	---	---	---	PASS
ZFR	51663	broad.mit.edu	37	5	32404076	32404076	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32404076A>T	uc003jhr.1	-	7	1239	c.1159T>A	c.(1159-1161)TGC>AGC	p.C387S		NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	387					multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)		GACACATCGCAGAGCTCACAA	0.453													36	142	---	---	---	---	PASS
ANKRD34B	340120	broad.mit.edu	37	5	79855842	79855842	+	5'UTR	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79855842C>T	uc010jam.2	-	4					ANKRD34B_uc003kgw.2_5'UTR|ANKRD34B_uc010jan.2_5'UTR	NM_001004441	NP_001004441	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B							cytoplasm|nucleus				pancreas(1)	1		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		CATCCATCTTCGGAGGTTAGA	0.403													4	63	---	---	---	---	PASS
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									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													7	11	---	---	---	---	PASS
PCDH1	5097	broad.mit.edu	37	5	141233715	141233715	+	Silent	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141233715G>A	uc003llp.2	-	5	3723	c.3606C>T	c.(3604-3606)TGC>TGT	p.C1202C		NM_032420	NP_115796	Q08174	PCDH1_HUMAN	protocadherin 1 isoform 2 precursor	Error:Variant_position_missing_in_Q08174_after_alignment					cell-cell signaling|homophilic cell adhesion|nervous system development	cell-cell junction|integral to plasma membrane	calcium ion binding			ovary(5)	5		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		CCGAGTCCTTGCAGGAATCAT	0.662													4	22	---	---	---	---	PASS
E2F3	1871	broad.mit.edu	37	6	20481597	20481597	+	Silent	SNP	C	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20481597C>A	uc003nda.2	+	3	993	c.666C>A	c.(664-666)ACC>ACA	p.T222T	E2F3_uc003ncz.2_Silent_p.T216T	NM_001949	NP_001940	O00716	E2F3_HUMAN	E2F transcription factor 3	222	Leucine-zipper.|Potential.|DEF box.				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			ATGATATCACCAACGTTCTGG	0.483													33	272	---	---	---	---	PASS
ZNF184	7738	broad.mit.edu	37	6	27420046	27420046	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27420046G>C	uc003njj.2	-	5	2103	c.1292C>G	c.(1291-1293)TCA>TGA	p.S431*	ZNF184_uc010jqv.2_Nonsense_Mutation_p.S431*|ZNF184_uc003nji.2_Nonsense_Mutation_p.S431*	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	431	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AGTGAGGTTTGAGTGCTGGCT	0.438													22	224	---	---	---	---	PASS
HLA-H	3136	broad.mit.edu	37	6	29856977	29856977	+	3'UTR	SNP	T	G	G	rs116665472	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29856977T>G	uc010jro.2	+	3					HLA-G_uc011dmb.1_Intron|HLA-H_uc003nod.2_Intron					SubName: Full=cDNA FLJ52667, highly similar to HLA class I histocompatibility antigen, alpha chain H;												0						GTCCAGGCTGTTGTCTGGGTT	0.547													5	25	---	---	---	---	PASS
SYNJ2	8871	broad.mit.edu	37	6	158497795	158497795	+	Silent	SNP	A	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158497795A>G	uc003qqx.1	+	17	2505	c.2430A>G	c.(2428-2430)AAA>AAG	p.K810K	SYNJ2_uc003qqw.1_Silent_p.K810K|SYNJ2_uc003qqy.1_Silent_p.K523K|SYNJ2_uc003qqz.1_Silent_p.K427K|SYNJ2_uc003qra.1_Silent_p.K153K	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	810	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)		GGAGGAAGAAACATCCCTTTG	0.572													9	65	---	---	---	---	PASS
MACC1	346389	broad.mit.edu	37	7	20180449	20180449	+	3'UTR	SNP	G	C	C	rs113534252		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20180449G>C	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						cacacacacagacacacacac	0.164													3	40	---	---	---	---	PASS
MACC1	346389	broad.mit.edu	37	7	20180451	20180451	+	3'UTR	SNP	C	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20180451C>G	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						cacacacagacacacacacac	0.159													3	44	---	---	---	---	PASS
LANCL2	55915	broad.mit.edu	37	7	55479736	55479736	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55479736G>A	uc003tqp.2	+	6	1540	c.962G>A	c.(961-963)TGC>TAC	p.C321Y		NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2	321					negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GTGCACTGGTGCCACGGCGCC	0.562													7	153	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	64531300	64531300	+	RNA	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64531300G>T	uc003ttt.1	+	9		c.1114G>T			uc010kzt.1_RNA					Homo sapiens cDNA clone IMAGE:4215179, partial cds.																		GTGTGGTTCCGGGTGCTGGTG	0.413													3	47	---	---	---	---	PASS
RUNDC3B	154661	broad.mit.edu	37	7	87436831	87436831	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87436831A>G	uc003ujb.2	+	10	1562	c.1151A>G	c.(1150-1152)TAT>TGT	p.Y384C	RUNDC3B_uc011khd.1_Intron|RUNDC3B_uc011khe.1_Missense_Mutation_p.Y367C|RUNDC3B_uc003ujc.2_Intron|RUNDC3B_uc003ujd.2_Intron	NM_138290	NP_612147	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B isoform a	384										skin(1)	1	Esophageal squamous(14;0.00164)					AAACAGTGGTATGAGTAAGTG	0.383													20	94	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136700123	136700123	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136700123G>A	uc003vtf.1	+	4	1134	c.511G>A	c.(511-513)GTG>ATG	p.V171M	CHRM2_uc003vtg.1_Missense_Mutation_p.V171M|CHRM2_uc003vtj.1_Missense_Mutation_p.V171M|CHRM2_uc003vtk.1_Missense_Mutation_p.V171M|CHRM2_uc003vtl.1_Missense_Mutation_p.V171M|CHRM2_uc003vtm.1_Missense_Mutation_p.V171M|CHRM2_uc003vti.1_Missense_Mutation_p.V171M|CHRM2_uc003vto.1_Missense_Mutation_p.V171M|CHRM2_uc003vtn.1_Missense_Mutation_p.V171M|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	171	Extracellular (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	GGTGAGAACTGTGGAGGATGG	0.483													25	224	---	---	---	---	PASS
LUC7L2	51631	broad.mit.edu	37	7	139086943	139086943	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139086943A>T	uc003vux.2	+	4	690	c.316A>T	c.(316-318)AAA>TAA	p.K106*	LUC7L2_uc011kqs.1_Nonsense_Mutation_p.K103*|LUC7L2_uc011kqt.1_Nonsense_Mutation_p.K172*|LUC7L2_uc003vuy.2_Nonsense_Mutation_p.K105*|LUC7L2_uc003vuz.1_Nonsense_Mutation_p.K53*|LUC7L2_uc003vva.2_Nonsense_Mutation_p.K53*	NM_016019	NP_057103	Q9Y383	LC7L2_HUMAN	LUC7-like 2	106	Potential.						enzyme binding|metal ion binding				0	Melanoma(164;0.242)					AGTGGCCAAGAAAAGATTAGC	0.348													8	53	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100148945	100148945	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100148945A>C	uc003yiv.2	+	12	1727	c.1616A>C	c.(1615-1617)GAT>GCT	p.D539A	VPS13B_uc003yiw.2_Missense_Mutation_p.D539A|VPS13B_uc003yit.2_Missense_Mutation_p.D539A|VPS13B_uc003yiu.1_Missense_Mutation_p.D539A|VPS13B_uc003yix.1_Missense_Mutation_p.D10A	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	539					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTTTATATGGATTACCTGTAT	0.383													101	266	---	---	---	---	PASS
KCNV2	169522	broad.mit.edu	37	9	2718826	2718826	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2718826G>T	uc003zho.1	+	1	1301	c.1087G>T	c.(1087-1089)GGC>TGC	p.G363C		NM_133497	NP_598004	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	363	Extracellular (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(50;0.0257)		CCACCAACGCGGCCAGACGGT	0.677													11	144	---	---	---	---	PASS
RGS3	5998	broad.mit.edu	37	9	116303649	116303649	+	Intron	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116303649C>T	uc004bhq.2	+						RGS3_uc004bhr.2_Missense_Mutation_p.S584L|RGS3_uc004bhs.2_Intron|RGS3_uc004bht.2_Intron|RGS3_uc010muy.2_Intron|RGS3_uc004bhu.2_Missense_Mutation_p.S322L|RGS3_uc004bhv.2_Intron	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						CCGGTCAACTCAACCAATGCC	0.557													32	485	---	---	---	---	PASS
LOC387646	387646	broad.mit.edu	37	10	27536000	27536000	+	3'UTR	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27536000G>T	uc001its.2	-	1						NR_003525				SubName: Full=cDNA FLJ44924 fis, clone BRAMY3014555;												0						ACGTTCTGAAGGAGCAAATAC	0.383													3	29	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	49239581	49239581	+	5'UTR	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49239581C>T	uc001jgd.2	-	1										RecName: Full=Arf-GAP, GTPase, ANK repeat and PH domain-containing protein 11; AltName: Full=Centaurin-gamma-like protein KIAA1975;																		TCGAGGCTGACGCTAGGGTGC	0.622													7	113	---	---	---	---	PASS
SEC31B	25956	broad.mit.edu	37	10	102257940	102257940	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102257940G>T	uc001krc.1	-	15	1811	c.1709C>A	c.(1708-1710)GCT>GAT	p.A570D	SEC31B_uc010qpo.1_Missense_Mutation_p.A569D|SEC31B_uc001krd.1_Missense_Mutation_p.A107D|SEC31B_uc001krf.1_Missense_Mutation_p.A107D|SEC31B_uc001kre.1_Missense_Mutation_p.A107D|SEC31B_uc001krg.1_Missense_Mutation_p.A139D	NM_015490	NP_056305	Q9NQW1	SC31B_HUMAN	SEC31 homolog B	570					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane				ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		AAGCAGGAGAGCCTGGCTTAG	0.592													7	113	---	---	---	---	PASS
OR4B1	119765	broad.mit.edu	37	11	48238947	48238947	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48238947A>G	uc010rhs.1	+	1	586	c.586A>G	c.(586-588)ATT>GTT	p.I196V		NM_001005470	NP_001005470	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B,	196	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|pancreas(1)	4						GGAGGGGGTTATTGTGTTGGC	0.463													20	184	---	---	---	---	PASS
LTBP3	4054	broad.mit.edu	37	11	65308037	65308037	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65308037T>C	uc001oej.2	-	22	3295	c.3026A>G	c.(3025-3027)AAG>AGG	p.K1009R	LTBP3_uc001oef.2_Missense_Mutation_p.K12R|LTBP3_uc001oeg.2_Missense_Mutation_p.K12R|LTBP3_uc001oeh.2_Missense_Mutation_p.K439R|LTBP3_uc010roi.1_Missense_Mutation_p.K892R|LTBP3_uc001oei.2_Missense_Mutation_p.K1009R|LTBP3_uc010roj.1_Missense_Mutation_p.K710R|LTBP3_uc010rok.1_Missense_Mutation_p.K920R	NM_001130144	NP_001123616	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding	1009	EGF-like 10; calcium-binding (Potential).					extracellular region	calcium ion binding|growth factor binding			central_nervous_system(2)|lung(1)	3						GTTCACGCACTTGCCCTCCTT	0.642											OREG0021080	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	111	---	---	---	---	PASS
GPR152	390212	broad.mit.edu	37	11	67219407	67219407	+	Silent	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67219407G>A	uc001olm.2	-	1	794	c.789C>T	c.(787-789)TTC>TTT	p.F263F	uc009yrw.1_5'Flank|CABP4_uc001oln.2_5'Flank	NM_206997	NP_996880	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	263	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CGTCCCACAGGAAGGCCAGGT	0.632													23	69	---	---	---	---	PASS
NDUFS8	4728	broad.mit.edu	37	11	67799656	67799656	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67799656T>A	uc001onc.2	+	2	145	c.38T>A	c.(37-39)CTG>CAG	p.L13Q	NDUFS8_uc010rpz.1_Missense_Mutation_p.L13Q|NDUFS8_uc009ysb.1_Intron|NDUFS8_uc009ysc.1_Missense_Mutation_p.L13Q	NM_002496	NP_002487	O00217	NDUS8_HUMAN	NADH dehydrogenase ubiquinone Fe-S 8 precursor	13					mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity			skin(1)	1					NADH(DB00157)	CTGCGGGCCCTGGCCCAGGCT	0.602													58	266	---	---	---	---	PASS
BIRC3	330	broad.mit.edu	37	11	102206699	102206699	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102206699G>A	uc001pgx.2	+	8	1549	c.1327G>A	c.(1327-1329)GAT>AAT	p.D443N		NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3	443	CARD.	Breakpoint for translocation to form BIRC3-MALT1.			anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		TTATAAAGATGATTTATTATT	0.303			T	MALT1	MALT								17	192	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103349892	103349892	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103349892C>G	uc001pho.2	+	89	12979	c.12835C>G	c.(12835-12837)CGT>GGT	p.R4279G	DYNC2H1_uc001phn.1_Missense_Mutation_p.R4286G|DYNC2H1_uc009yxe.1_Missense_Mutation_p.R892G	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4279					cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGAAAGGGATCGTGTGGTTAC	0.398													13	127	---	---	---	---	PASS
BSX	390259	broad.mit.edu	37	11	122850082	122850082	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122850082C>T	uc010rzs.1	-	2	346	c.346G>A	c.(346-348)GTT>ATT	p.V116I		NM_001098169	NP_001091639	Q3C1V8	BSH_HUMAN	brain specific homeobox	116	Homeobox.										0		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0361)		TCAGAGAAAACCGTGCGGGCT	0.662													7	115	---	---	---	---	PASS
HEPACAM	220296	broad.mit.edu	37	11	124794752	124794752	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124794752C>T	uc001qbk.2	-	2	705	c.299G>A	c.(298-300)CGA>CAA	p.R100Q	HEPACAM_uc009zbj.2_5'Flank|HEPACAM_uc001qbl.1_Missense_Mutation_p.R100Q	NM_152722	NP_689935	Q14CZ8	HECAM_HUMAN	hepatocyte cell adhesion molecule precursor	100	Extracellular (Potential).|Ig-like V-type.				cell adhesion|cell cycle arrest|regulation of growth	cytoplasm|integral to membrane				pancreas(1)	1	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		TTCAAAGAGTCGGATACGGTC	0.592													7	230	---	---	---	---	PASS
IGSF9B	22997	broad.mit.edu	37	11	133807380	133807380	+	Silent	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133807380G>A	uc001qgx.3	-	5	801	c.570C>T	c.(568-570)GAC>GAT	p.D190D	IGSF9B_uc001qgy.1_Silent_p.D32D	NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	190	Ig-like 2.|Extracellular (Potential).					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		TCAGGCTGCCGTCACTCACCT	0.612													4	38	---	---	---	---	PASS
CHD4	1108	broad.mit.edu	37	12	6704513	6704513	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6704513G>A	uc001qpo.2	-	14	2272	c.2108C>T	c.(2107-2109)ACG>ATG	p.T703M	CHD4_uc001qpn.2_Missense_Mutation_p.T696M|CHD4_uc001qpp.2_Missense_Mutation_p.T700M	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	703					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						AACTGTTGGCGTTTCTGGAGG	0.473													6	246	---	---	---	---	PASS
KRT5	3852	broad.mit.edu	37	12	52908651	52908651	+	3'UTR	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52908651G>T	uc001san.2	-	9						NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5						epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		AACATGGCTTGAGCAACTGCC	0.527													6	41	---	---	---	---	PASS
KRT73	319101	broad.mit.edu	37	12	53001781	53001781	+	3'UTR	SNP	A	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53001781A>C	uc001sas.2	-	9						NM_175068	NP_778238	Q86Y46	K2C73_HUMAN	keratin 73							keratin filament	structural molecule activity			large_intestine(2)|ovary(2)|skin(2)	6				BRCA - Breast invasive adenocarcinoma(357;0.189)		GGAGGCAGAAAGATGGGCTCC	0.502													3	27	---	---	---	---	PASS
ACTR6	64431	broad.mit.edu	37	12	100601498	100601498	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100601498A>G	uc001thb.1	+	4	369	c.313A>G	c.(313-315)ATT>GTT	p.I105V	ACTR6_uc010svh.1_Missense_Mutation_p.I105V|ACTR6_uc001thc.1_5'UTR|ACTR6_uc001thd.1_Missense_Mutation_p.I105V|ACTR6_uc009ztu.1_5'UTR|ACTR6_uc001the.1_Missense_Mutation_p.I23V|ACTR6_uc001thf.1_Missense_Mutation_p.I23V|uc001thg.1_Intron	NM_022496	NP_071941	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog	105						cytoplasm|cytoskeleton				ovary(1)	1						CTTCACTTCAATTCAAGAATC	0.264													23	127	---	---	---	---	PASS
CRY1	1407	broad.mit.edu	37	12	107393578	107393578	+	Silent	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107393578G>A	uc001tmi.3	-	7	1747	c.888C>T	c.(886-888)TTC>TTT	p.F296F		NM_004075	NP_004066	Q16526	CRY1_HUMAN	cryptochrome 1 (photolyase-like)	296	FAD-binding.				DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3						CTGCTGTATAGAAAAATTCAC	0.373													15	97	---	---	---	---	PASS
MMP17	4326	broad.mit.edu	37	12	132325207	132325207	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132325207C>T	uc001ujc.1	+	4	611	c.512C>T	c.(511-513)GCG>GTG	p.A171V	MMP17_uc001ujd.1_Missense_Mutation_p.A87V	NM_016155	NP_057239	Q9ULZ9	MMP17_HUMAN	matrix metalloproteinase 17 preproprotein	171					proteolysis	anchored to membrane|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)		AGCGACATTGCGCCCCTGAAC	0.662													5	195	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109707989	109707989	+	Intron	SNP	T	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109707989T>G	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_3'UTR|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TGCTGTTCAGTGCAGTGTACT	0.403													23	157	---	---	---	---	PASS
EIF2AK4	440275	broad.mit.edu	37	15	40308848	40308848	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40308848T>C	uc001zkm.1	+	28	3955	c.3905T>C	c.(3904-3906)TTG>TCG	p.L1302S	EIF2AK4_uc010bbj.1_Missense_Mutation_p.L1003S|EIF2AK4_uc001zkn.1_Missense_Mutation_p.L402S|EIF2AK4_uc001zko.1_Intron|EIF2AK4_uc010bbk.1_RNA	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	1302	Histidyl-tRNA synthetase-like.				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		GTTGGACTGTTGAAGAAACTC	0.378													23	113	---	---	---	---	PASS
IGDCC3	9543	broad.mit.edu	37	15	65624284	65624284	+	Silent	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65624284G>A	uc002aos.2	-	7	1395	c.1143C>T	c.(1141-1143)AAC>AAT	p.N381N	IGDCC3_uc002aor.1_5'Flank	NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule	381	Extracellular (Potential).|Ig-like C2-type 4.									ovary(3)	3						CATACCTGTTGTTATTCTTGA	0.602													25	123	---	---	---	---	PASS
IL16	3603	broad.mit.edu	37	15	81591913	81591913	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81591913G>A	uc002bgh.3	+	14	2622	c.2246G>A	c.(2245-2247)GGG>GAG	p.G749E	IL16_uc010blq.1_Missense_Mutation_p.G703E|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.G791E|IL16_uc002bgg.2_Missense_Mutation_p.G749E|IL16_uc002bgi.1_Missense_Mutation_p.G139E|IL16_uc002bgj.2_Missense_Mutation_p.G243E|IL16_uc002bgk.2_Missense_Mutation_p.G48E|IL16_uc002bgl.1_Missense_Mutation_p.G48E|IL16_uc010unq.1_Missense_Mutation_p.G48E	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	749					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						GAAGAAGAAGGGACACAGGGC	0.512													13	134	---	---	---	---	PASS
BLM	641	broad.mit.edu	37	15	91292871	91292871	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91292871A>C	uc002bpr.2	+	3	470	c.373A>C	c.(373-375)ACA>CCA	p.T125P	BLM_uc010uqh.1_Missense_Mutation_p.T125P|BLM_uc010uqi.1_5'UTR|BLM_uc010bnx.2_Missense_Mutation_p.T125P	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	125					double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TACCCAAAACACACCAACTGT	0.403			Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				13	98	---	---	---	---	PASS
COG8	84342	broad.mit.edu	37	16	69368915	69368915	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69368915T>C	uc002ewy.2	-	3	993	c.922A>G	c.(922-924)ACT>GCT	p.T308A	COG8_uc002ewz.3_Missense_Mutation_p.T308A	NM_032382	NP_115758	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	308					protein transport	Golgi membrane|Golgi transport complex				ovary(1)	1						TCATTCACAGTGTGCTCACCC	0.577													10	84	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161578	90161578	+	Silent	SNP	G	A	A	rs13337896	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90161578G>A	uc002fqp.2	+	3	931	c.453G>A	c.(451-453)ACG>ACA	p.T151T	uc002fqq.2_Silent_p.T168T					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		GCCAAGGGACGCTACACCGAA	0.587													5	55	---	---	---	---	PASS
PRPF8	10594	broad.mit.edu	37	17	1579248	1579248	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1579248G>A	uc002fte.2	-	18	2767	c.2653C>T	c.(2653-2655)CTC>TTC	p.L885F		NM_006445	NP_006436	Q6P2Q9	PRP8_HUMAN	U5 snRNP-specific protein	885						catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		TGTGTGAGGAGGTGACGCTTG	0.532													11	81	---	---	---	---	PASS
EVI2B	2124	broad.mit.edu	37	17	29632303	29632303	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29632303G>T	uc002hgk.2	-	2	480	c.325C>A	c.(325-327)CCA>ACA	p.P109T	NF1_uc002hgg.2_Intron|NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron|EVI2B_uc010csq.2_Missense_Mutation_p.P124T	NM_006495	NP_006486	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B precursor	109	Extracellular (Potential).					cytoplasm|integral to plasma membrane				ovary(2)	2		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		ATTGGTGTTGGTTGTTTGGTG	0.493													78	416	---	---	---	---	PASS
TUBD1	51174	broad.mit.edu	37	17	57963523	57963523	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57963523C>T	uc002ixw.1	-	3	519	c.241G>A	c.(241-243)GCC>ACC	p.A81T	TUBD1_uc010ddf.1_Missense_Mutation_p.A81T|TUBD1_uc010ddg.1_Missense_Mutation_p.A46T|TUBD1_uc010ddh.1_5'UTR|TUBD1_uc010wok.1_Missense_Mutation_p.A81T|TUBD1_uc002ixx.1_Missense_Mutation_p.A81T|TUBD1_uc010wol.1_Intron|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345	Q9UJT1	TBD_HUMAN	delta-tubulin	81					cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)			CCAGACTGGGCAGCCTTTGAC	0.423													9	185	---	---	---	---	PASS
ABCA8	10351	broad.mit.edu	37	17	66883567	66883567	+	Silent	SNP	G	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66883567G>C	uc002jhp.2	-	23	3284	c.3105C>G	c.(3103-3105)TCC>TCG	p.S1035S	ABCA8_uc002jhq.2_Silent_p.S1075S|ABCA8_uc010wqq.1_Silent_p.S1075S|ABCA8_uc010wqr.1_Silent_p.S1014S	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1035	Helical; (Potential).					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					AGAAGTACAGGGAAACATCCA	0.418													51	294	---	---	---	---	PASS
PNPLA6	10908	broad.mit.edu	37	19	7615512	7615512	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7615512G>A	uc010xjq.1	+	18	2278	c.2083G>A	c.(2083-2085)GAC>AAC	p.D695N	PNPLA6_uc002mgq.1_Missense_Mutation_p.D647N|PNPLA6_uc010xjp.1_Missense_Mutation_p.D621N|PNPLA6_uc002mgr.1_Missense_Mutation_p.D647N|PNPLA6_uc002mgs.2_Missense_Mutation_p.D686N	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b	686	Cytoplasmic (Potential).|cNMP 3.				cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						CGGCCGCGGCGACCTCATCGG	0.642													6	27	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10468521	10468521	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10468521C>T	uc002moc.3	-	17	2763	c.2385G>A	c.(2383-2385)ATG>ATA	p.M795I	TYK2_uc010dxe.2_Missense_Mutation_p.M610I|TYK2_uc002mod.2_Missense_Mutation_p.M795I	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	795	Protein kinase 1.				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity	p.M795V(1)		lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			CCCACTTGTCCATGGCGGTGC	0.642													3	74	---	---	---	---	PASS
ZSWIM4	65249	broad.mit.edu	37	19	13910687	13910687	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13910687G>A	uc002mxh.1	+	2	496	c.307G>A	c.(307-309)GGG>AGG	p.G103R		NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	103							zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			CTTTACCCGCGGGCTGCACCT	0.642													12	83	---	---	---	---	PASS
CPAMD8	27151	broad.mit.edu	37	19	17039855	17039855	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17039855G>T	uc002nfb.2	-	24	3214	c.3182C>A	c.(3181-3183)ACC>AAC	p.T1061N		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1014						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						CATCTTGCTGGTGGAGATCCA	0.582													10	61	---	---	---	---	PASS
RPSAP58	388524	broad.mit.edu	37	19	24010099	24010099	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24010099A>G	uc002nrn.2	+	4	559	c.136A>G	c.(136-138)ATC>GTC	p.I46V		NM_002295	NP_002286			ribosomal protein SA												0						AAGTGATGGCATCTATATCAT	0.448													3	32	---	---	---	---	PASS
RPSAP58	388524	broad.mit.edu	37	19	24010116	24010116	+	Silent	SNP	C	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24010116C>G	uc002nrn.2	+	4	576	c.153C>G	c.(151-153)CTC>CTG	p.L51L		NM_002295	NP_002286			ribosomal protein SA												0						TCATAAATCTCAAGAGGACCT	0.458													3	49	---	---	---	---	PASS
RPSAP58	388524	broad.mit.edu	37	19	24010294	24010294	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24010294C>G	uc002nrn.2	+	4	754	c.331C>G	c.(331-333)CAG>GAG	p.Q111E		NM_002295	NP_002286			ribosomal protein SA												0						CTTCACTAACCAGATCCAGGC	0.567													3	53	---	---	---	---	PASS
DLL3	10683	broad.mit.edu	37	19	39998732	39998732	+	3'UTR	SNP	C	G	G			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39998732C>G	uc002olx.2	+	8					DLL3_uc002olw.2_Intron	NM_016941	NP_058637	Q9NYJ7	DLL3_HUMAN	delta-like 3 protein isoform 1 precursor						Notch signaling pathway|skeletal system development	integral to membrane	Notch binding			central_nervous_system(2)|breast(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TCCCTCTTATCGTTTTGAGCT	0.453													6	35	---	---	---	---	PASS
MACROD2	140733	broad.mit.edu	37	20	15412069	15412069	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15412069C>A	uc002wou.2	+	7	824	c.560C>A	c.(559-561)ACA>AAA	p.T187K	MACROD2_uc002wot.2_Missense_Mutation_p.T187K|MACROD2_uc002woz.2_5'UTR	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1	187	Macro.										0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TGCATCTCAACAGGCATTTAT	0.318													30	221	---	---	---	---	PASS
FAM182B	728882	broad.mit.edu	37	20	25848629	25848629	+	RNA	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25848629C>T	uc002wvd.1	-	1		c.158G>A								Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						gctgggatgccgtgctgcttc	0.000													3	10	---	---	---	---	PASS
C20orf191	149934	broad.mit.edu	37	20	26084148	26084148	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26084148T>C	uc002wvj.3	-	2	323	c.268A>G	c.(268-270)ATC>GTC	p.I90V		NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0						AGTTTAAGGATCTGCTGTTCT	0.259													15	92	---	---	---	---	PASS
CBFA2T2	9139	broad.mit.edu	37	20	32232219	32232219	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32232219G>A	uc002wzg.1	+	12	2119	c.1582G>A	c.(1582-1584)GGC>AGC	p.G528S	CBFA2T2_uc010zug.1_Missense_Mutation_p.G302S|CBFA2T2_uc002wze.1_Missense_Mutation_p.G519S|CBFA2T2_uc002wzf.1_RNA|CBFA2T2_uc002wzh.1_Missense_Mutation_p.G499S|CBFA2T2_uc002wzi.1_RNA|CBFA2T2_uc002wzj.1_RNA|CBFA2T2_uc002wzk.1_Missense_Mutation_p.G76S	NM_005093	NP_005084	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit	528	MYND-type.					nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2						GCGATACTGTGGCTCTTTCTG	0.622													5	118	---	---	---	---	PASS
LPIN3	64900	broad.mit.edu	37	20	39984632	39984632	+	Silent	SNP	T	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39984632T>C	uc002xjx.2	+	14	1852	c.1761T>C	c.(1759-1761)ACT>ACC	p.T587T	LPIN3_uc010ggh.2_Silent_p.T588T|LPIN3_uc010zwf.1_RNA	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	587					fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)				caccctccactccTACCTACA	0.478													17	86	---	---	---	---	PASS
C21orf99	149992	broad.mit.edu	37	21	14439197	14439197	+	RNA	SNP	G	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14439197G>C	uc002yja.3	+	10		c.2715G>C				NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						AAGAAGAAGAGAAGAGAAGAA	0.289													9	54	---	---	---	---	PASS
TOP3B	8940	broad.mit.edu	37	22	22317229	22317229	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22317229C>T	uc002zvs.2	-	12	1676	c.1241G>A	c.(1240-1242)AGA>AAA	p.R414K	TOP3B_uc010gtm.1_5'UTR|TOP3B_uc002zvr.2_Missense_Mutation_p.R139K|TOP3B_uc010gtl.2_Missense_Mutation_p.R414K|TOP3B_uc002zvt.3_Missense_Mutation_p.R414K	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	414					DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		GATGAAGTGTCTGGTGATGTA	0.622													14	80	---	---	---	---	PASS
MGAT3	4248	broad.mit.edu	37	22	39884700	39884700	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39884700C>T	uc003axv.3	+	2	1587	c.1348C>T	c.(1348-1350)CGG>TGG	p.R450W	MGAT3_uc010gxy.2_Missense_Mutation_p.R450W	NM_002409	NP_002400	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein	450	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity				0	Melanoma(58;0.04)					CGAGGACAAGCGGGACCTGAA	0.647													4	68	---	---	---	---	PASS
SFRS17A	8227	broad.mit.edu	37	X	1712782	1712782	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1712782G>A	uc004cqa.2	+	2	623	c.427G>A	c.(427-429)GGG>AGG	p.G143R	SFRS17A_uc010ncx.1_Missense_Mutation_p.G143R|SFRS17A_uc004cqb.2_RNA|ASMT_uc004cqd.2_5'Flank	NM_005088	NP_005079	Q02040	AK17A_HUMAN	DNA segment on chromosome X and Y (unique) 155	143					B cell activation|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|signal transduction	nuclear speck|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0		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)				GACCCTGCCGGGGGAGCGGCC	0.667													36	286	---	---	---	---	PASS
TBL1Y	90665	broad.mit.edu	37	Y	6931951	6931951	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:6931951T>C	uc004frb.2	+	8	865	c.218T>C	c.(217-219)TTC>TCC	p.F73S	TBL1Y_uc004frc.2_Missense_Mutation_p.F73S|TBL1Y_uc004frd.2_Missense_Mutation_p.F73S|TBL1Y_uc011nap.1_5'UTR	NM_033284	NP_150600	Q9BQ87	TBL1Y_HUMAN	transducin beta-like 1Y	73	F-box-like.				transcription, DNA-dependent						0						GGCACAGTGTTCGACAGCCGC	0.577													5	58	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974141	16974141	+	RNA	DEL	G	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974141delG	uc009vow.2	+	5		c.951delG			CROCCL1_uc001azg.1_5'Flank|CROCCL1_uc001azi.1_5'Flank|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						TGGCTTGGCCGGGGAGGTCAG	0.667													6	3	---	---	---	---	
PAX7	5081	broad.mit.edu	37	1	18961991	18961991	+	Intron	DEL	G	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18961991delG	uc001bay.2	+						PAX7_uc001baz.2_Intron|PAX7_uc010oct.1_Intron	NM_002584	NP_002575	P23759	PAX7_HUMAN	paired box 7 isoform 1						anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX7/FOXO1(197)	soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1)	203		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		ggaggaagaaggaaggaagga	0.169			T	FOXO1A	alveolar rhabdomyosarcoma								4	2	---	---	---	---	
CEPT1	10390	broad.mit.edu	37	1	111702305	111702316	+	Intron	DEL	TTATTGGTAGTG	-	-	rs78051509		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111702305_111702316delTTATTGGTAGTG	uc001eah.1	+						CEPT1_uc001eag.2_3'UTR|CEPT1_uc001eai.1_Intron|CEPT1_uc001eaj.1_Intron	NM_001007794	NP_001007795	Q9Y6K0	CEPT1_HUMAN	choline/ethanolaminephosphotransferase							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	diacylglycerol cholinephosphotransferase activity|ethanolaminephosphotransferase activity|metal ion binding				0		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	TATTTGTTCATTATTGGTAGTGTTAGGAAATT	0.278													6	5	---	---	---	---	
CELF3	11189	broad.mit.edu	37	1	151677297	151677298	+	Intron	DEL	GA	-	-	rs35738969	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151677297_151677298delGA	uc001eys.1	-						CELF3_uc010pdh.1_Intron|CELF3_uc001eyr.2_Intron|CELF3_uc009wmy.2_Intron|CELF3_uc009wmx.1_Intron	NM_007185	NP_009116	Q5SZQ8	CELF3_HUMAN	trinucleotide repeat containing 4						nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	mRNA binding|nucleotide binding			ovary(1)|central_nervous_system(1)	2						GTGTGTGTGTgagagagagaga	0.475													5	3	---	---	---	---	
C1orf125	126859	broad.mit.edu	37	1	179502762	179502763	+	Intron	DEL	TT	-	-	rs35358411		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179502762_179502763delTT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1												0						AGACAATCCCTTTTTTTTTTTT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	207273434	207273439	+	IGR	DEL	TGTGTA	-	-	rs35665980		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207273434_207273439delTGTGTA								C4BPB (99 upstream) : C4BPA (4072 downstream)																							tgtgtgtgtgtgtgtatgtgtgtgtg	0.257													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12293377	12293378	+	Intron	INS	-	TCCT	TCCT	rs67700339		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12293377_12293378insTCCT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		ccttccttccctccttccttcc	0.000													9	4	---	---	---	---	
SLC4A5	57835	broad.mit.edu	37	2	74489490	74489490	+	Intron	DEL	C	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74489490delC	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						GGAAGAAATTCtttttttttt	0.284													6	4	---	---	---	---	
NPAS2	4862	broad.mit.edu	37	2	101584655	101584657	+	Intron	DEL	TGA	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101584655_101584657delTGA	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4						TCTTTTTTTTTGAAAGCTTATCT	0.379													23	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134405321	134405322	+	IGR	INS	-	AGG	AGG	rs56187134		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134405321_134405322insAGG								NCKAP5 (79290 upstream) : MGAT5 (606508 downstream)																							ggaaggaaggaaagaaaagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157775775	157775776	+	IGR	INS	-	T	T			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157775775_157775776insT								GPD2 (305528 upstream) : GALNT5 (338564 downstream)																							atttattattatttttttaaca	0.000													1	6	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159954483	159954483	+	Intron	DEL	T	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159954483delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						Gaaataaatcttttttttttt	0.284													6	3	---	---	---	---	
STAC	6769	broad.mit.edu	37	3	36439950	36439951	+	Intron	INS	-	GGAG	GGAG	rs72389687		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36439950_36439951insGGAG	uc003cgh.1	+						STAC_uc010hgd.1_Intron|STAC_uc011aya.1_Intron	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain						intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4						gaaggaaggaaggaaggaagga	0.000													4	2	---	---	---	---	
RBM5	10181	broad.mit.edu	37	3	50142739	50142740	+	Intron	INS	-	A	A	rs77605143		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50142739_50142740insA	uc003cyg.2	+						RBM5_uc011bdj.1_Intron|RBM5_uc011bdk.1_Intron	NM_005778	NP_005769	P52756	RBM5_HUMAN	RNA binding motif protein 5						apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		tactcCGTCTCAAAAAAAAAAA	0.208													4	2	---	---	---	---	
PPM1L	151742	broad.mit.edu	37	3	160672742	160672744	+	Intron	DEL	TCC	-	-	rs72365532	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160672742_160672744delTCC	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338	Q5SGD2	PPM1L_HUMAN	protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			cttccttccttccttcctttcct	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	38387900	38387901	+	IGR	INS	-	AAGGAAGG	AAGGAAGG	rs6812640	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38387900_38387901insAAGGAAGG								TBC1D1 (247107 upstream) : FLJ13197 (226421 downstream)																							aggaaggaagcaaggaaggaag	0.109													4	2	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39279672	39279672	+	Intron	DEL	A	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39279672delA	uc003gtv.2	+						WDR19_uc011byi.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						agattccgtcaaaaaaaaaaa	0.144													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49152026	49152027	+	IGR	INS	-	CCTGTACTCGGGTTG	CCTGTACTCGGGTTG			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49152026_49152027insCCTGTACTCGGGTTG								CWH43 (87933 upstream) : None (None downstream)																							cattccattccattccattcca	0.000													5	3	---	---	---	---	
ART3	419	broad.mit.edu	37	4	77021783	77021783	+	Intron	DEL	A	-	-	rs11289247		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77021783delA	uc003hjo.2	+						ART3_uc003hjk.2_Intron|ART3_uc003hjn.2_Intron|ART3_uc003hjp.2_Intron|ART3_uc010ijb.2_Intron|ART3_uc003hjq.2_Intron|ART3_uc003hjr.2_Intron|ART3_uc010ijc.2_Intron|ART3_uc010ijd.2_Intron	NM_001130016	NP_001123488	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3 isoform a						protein ADP-ribosylation	anchored to membrane|integral to plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity			ovary(2)	2			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			gctccgtctcaaaaaaaaaaa	0.154													12	8	---	---	---	---	
FAM160A1	729830	broad.mit.edu	37	4	152333718	152333730	+	Intron	DEL	CTTTCTTTCTTTC	-	-	rs146973116	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152333718_152333730delCTTTCTTTCTTTC	uc003imj.2	+							NM_001109977	NP_001103447	Q05DH4	F16A1_HUMAN	hypothetical protein LOC729830												0						ttctttctttctttctttctttcctttctttcc	0.108													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185421516	185421519	+	IGR	DEL	TGTG	-	-	rs35039184		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185421516_185421519delTGTG								IRF2 (25790 upstream) : CASP3 (127333 downstream)																							aacATATATAtgtgtgtgtgtgtg	0.098													5	4	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	58511379	58511382	+	Intron	DEL	GTGT	-	-	rs35142413		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58511379_58511382delGTGT	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron|PDE4D_uc003jrv.2_Intron|PDE4D_uc003jrw.2_Intron|PDE4D_uc010iwi.1_Intron	NM_001104631	NP_001098101	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	AAATACAtgcgtgtgtgtgtgtgt	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	85703814	85703815	+	IGR	INS	-	AAGG	AAGG	rs149876942	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85703814_85703815insAAGG								NBPF22P (110452 upstream) : COX7C (209969 downstream)																							ggaaggaaggaaggaaggaagg	0.089													4	4	---	---	---	---	
FBXL17	64839	broad.mit.edu	37	5	107494210	107494211	+	Intron	INS	-	TG	TG	rs140267585	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107494210_107494211insTG	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		gtgtgtgtgtctgtgtgtgtgt	0.307													4	2	---	---	---	---	
IK	3550	broad.mit.edu	37	5	140028326	140028327	+	Intron	INS	-	T	T	rs113938710		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140028326_140028327insT	uc003lgq.2	+						NDUFA2_uc003lgp.2_5'Flank|IK_uc011czk.1_Intron	NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein						cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGGTGTTAAGTTTTTTTTTTT	0.337													4	2	---	---	---	---	
DUSP22	56940	broad.mit.edu	37	6	346430	346431	+	Intron	DEL	AC	-	-	rs35897998		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:346430_346431delAC	uc003msx.2	+						DUSP22_uc011dhn.1_Intron|DUSP22_uc003msy.1_Intron	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22						apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TTTTGTGTAGacacacacacac	0.292													3	3	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51923570	51923573	+	Intron	DEL	TCTA	-	-	rs66624918		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51923570_51923573delTCTA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TCTCCAGCTCtctatctatctatc	0.333													5	3	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70609058	70609058	+	Intron	DEL	T	-	-	rs112888229		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70609058delT	uc003pfc.1	+							NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						ttctttttaattttttttttt	0.124													6	3	---	---	---	---	
ATG5	9474	broad.mit.edu	37	6	106727356	106727357	+	Intron	INS	-	G	G	rs146277372	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106727356_106727357insG	uc003prf.2	-						ATG5_uc010kdb.2_Intron|ATG5_uc003prg.2_Intron|ATG5_uc010kdc.2_Intron	NM_004849	NP_004840	Q9H1Y0	ATG5_HUMAN	APG5 autophagy 5-like						apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		CCATGAACAGAGGACACCAAAA	0.396													3	5	---	---	---	---	
PPIL6	285755	broad.mit.edu	37	6	109740622	109740622	+	Intron	DEL	A	-	-	rs79521587		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109740622delA	uc003ptg.3	-						PPIL6_uc010kdo.2_Intron|PPIL6_uc010kdp.2_Intron	NM_173672	NP_775943	Q8IXY8	PPIL6_HUMAN	peptidylprolyl isomerase-like 6 isoform 1						protein folding		peptidyl-prolyl cis-trans isomerase activity				0		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)		catctcgattaaaaaaaaaaa	0.035													6	4	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155462528	155462529	+	Intron	INS	-	AC	AC	rs143061550	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155462528_155462529insAC	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		CATATATGTGTacacacacaca	0.267													3	3	---	---	---	---	
LPAL2	80350	broad.mit.edu	37	6	160914198	160914198	+	Intron	DEL	T	-	-	rs146778738		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160914198delT	uc003qtj.2	-						LPAL2_uc011efy.1_Intron	NR_028093				Homo sapiens cDNA FLJ43922 fis, clone TESTI4012406.												0		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)		AGATTTTAACTTTTTTTTTTA	0.348													3	3	---	---	---	---	
SBDSP1	155370	broad.mit.edu	37	7	72304629	72304629	+	Intron	DEL	C	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72304629delC	uc003twg.2	+						SBDSP1_uc003twh.2_Intron|SBDSP1_uc003twe.2_Intron	NR_024110				Homo sapiens Shwachman-Bodian-Diamond syndrome pseudogene, mRNA (cDNA clone IMAGE:4329436).												0						ttttttttttctttttttttt	0.109													9	5	---	---	---	---	
GTF2I	2969	broad.mit.edu	37	7	74129040	74129040	+	Intron	DEL	T	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74129040delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|uc003uaz.2_Intron	NM_032999	NP_127492	P78347	GTF2I_HUMAN	general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						CTTGTCAGTCttttttttttt	0.294													6	4	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76796901	76796901	+	Intron	DEL	A	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76796901delA	uc003uga.2	+						CCDC146_uc003ufz.1_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GTTTATTTTTATTATTTTCCA	0.264													4	2	---	---	---	---	
AP4M1	9179	broad.mit.edu	37	7	99701510	99701511	+	Intron	INS	-	AA	AA	rs80333897		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99701510_99701511insAA	uc003utb.3	+						MCM7_uc003usw.1_5'Flank|MCM7_uc003usx.1_5'Flank|AP4M1_uc011kjg.1_Intron|AP4M1_uc010lgl.1_Intron|AP4M1_uc003utc.3_Intron|AP4M1_uc010lgm.2_Intron|AP4M1_uc003utd.2_Intron|AP4M1_uc011kjh.1_Intron|AP4M1_uc003ute.3_Intron|AP4M1_uc003utf.3_Intron	NM_004722	NP_004713	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|coated pit|Golgi trans cisterna	transporter activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					actaaaaatgcaaaaaAAAAAA	0.228													10	5	---	---	---	---	
HBP1	26959	broad.mit.edu	37	7	106836196	106836196	+	Intron	DEL	T	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106836196delT	uc003vdy.2	+						HBP1_uc011klv.1_Intron|HBP1_uc003vdz.2_Intron|HBP1_uc003vea.2_Intron|HBP1_uc003veb.1_Intron	NM_012257	NP_036389	O60381	HBP1_HUMAN	HMG-box transcription factor 1						cell cycle arrest|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	DNA binding			skin(1)	1						AGATGTTTTCTTTTTTTTTTT	0.259													3	4	---	---	---	---	
MYBL1	4603	broad.mit.edu	37	8	67527563	67527574	+	5'Flank	DEL	ACACACACACAC	-	-	rs71561291		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67527563_67527574delACACACACACAC	uc003xwj.2	-						MYBL1_uc003xwl.2_5'Flank|MYBL1_uc003xwk.2_5'Flank|MYBL1_uc003xwm.2_5'Flank	NM_001080416	NP_001073885	P10243	MYBA_HUMAN	v-myb myeloblastosis viral oncogene homolog						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)	3			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			atatatacatacacacacacacacacacacac	0.000													3	3	---	---	---	---	
MATN2	4147	broad.mit.edu	37	8	99006489	99006490	+	Intron	INS	-	GAAGAAGGAGAA	GAAGAAGGAGAA	rs146393102	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99006489_99006490insGAAGAAGGAGAA	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			ggaggaggagggaagaaggaga	0.149													6	3	---	---	---	---	
EPPK1	83481	broad.mit.edu	37	8	144940081	144940082	+	Intron	INS	-	A	A	rs60421625		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144940081_144940082insA	uc003zaa.1	-							NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1							cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			aaaaaaaaaacaaaaaaaaaac	0.337													2	6	---	---	---	---	
AQP7	364	broad.mit.edu	37	9	33386780	33386781	+	Intron	INS	-	A	A	rs144468472	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33386780_33386781insA	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_Intron|AQP7_uc010mjt.2_Intron|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_Intron|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		aatggtaggtcggggggcccag	0.257													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132207762	132207762	+	IGR	DEL	T	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132207762delT								C9orf106 (122880 upstream) : C9orf50 (166744 downstream)																							ccttccttccttccttccttc	0.020													4	2	---	---	---	---	
SFMBT2	57713	broad.mit.edu	37	10	7249383	7249386	+	Intron	DEL	GAAA	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7249383_7249386delGAAA	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						aagaaagaaggaaagaaagaaaga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	16454839	16454840	+	IGR	INS	-	AAGAAAGA	AAGAAAGA	rs34033087		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16454839_16454840insAAGAAAGA								FAM188A (552320 upstream) : PTER (24127 downstream)																							aggaaggaaggaagaaagaaag	0.010													3	3	---	---	---	---	
COL13A1	1305	broad.mit.edu	37	10	71664662	71664664	+	Intron	DEL	TTT	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71664662_71664664delTTT	uc001jpr.1	+						COL13A1_uc001jqj.1_Intron|COL13A1_uc001jps.1_Intron|COL13A1_uc001jpt.1_Intron|COL13A1_uc001jpu.1_Intron|COL13A1_uc001jpv.1_Intron|COL13A1_uc001jpx.1_Intron|COL13A1_uc001jpw.1_Intron|COL13A1_uc001jpy.1_Intron|COL13A1_uc001jpz.1_Intron|COL13A1_uc001jqa.1_Intron|COL13A1_uc001jqc.1_Intron|COL13A1_uc001jqb.1_Intron|COL13A1_uc001jql.2_Intron|COL13A1_uc001jqd.1_Intron|COL13A1_uc001jqe.1_Intron|COL13A1_uc001jqf.1_Intron|COL13A1_uc001jqg.1_Intron|COL13A1_uc001jqh.1_Intron|COL13A1_uc001jqi.1_Intron|COL13A1_uc010qjf.1_Intron|COL13A1_uc001jqk.1_Intron	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1						cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	ttcttttttcttttttttttttt	0.473													5	3	---	---	---	---	
C10orf4	118924	broad.mit.edu	37	10	95445300	95445300	+	Intron	DEL	A	-	-	rs5787072		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95445300delA	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				TACTGTTACCAAAAAAAATCA	0.318													5	3	---	---	---	---	
HRAS	3265	broad.mit.edu	37	11	534404	534415	+	Intron	DEL	CCCAGGCCCAGC	-	-	rs45443193		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:534404_534415delCCCAGGCCCAGC	uc001lpv.2	-						HRAS_uc010qvw.1_Intron|HRAS_uc010qvx.1_Intron|HRAS_uc010qvy.1_Intron	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene						activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding			urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	CTCAGCCAGGCCCAGGCCCAGCCCCAGGCCCC	0.698		6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			9	6	---	---	---	---	
RAB30	27314	broad.mit.edu	37	11	82752238	82752238	+	Intron	DEL	A	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82752238delA	uc001ozu.2	-						RAB30_uc010rst.1_Intron|RAB30_uc001ozv.2_Intron	NM_014488	NP_055303	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0						actctgtctcaaaaaaaaaaa	0.224													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99072082	99072083	+	Intron	INS	-	TCC	TCC	rs151051937	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99072082_99072083insTCC	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		cttcctttcctttccttccttc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127462186	127462187	+	IGR	INS	-	AGG	AGG	rs146290646	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127462186_127462187insAGG								KIRREL3 (588831 upstream) : ETS1 (866469 downstream)																							ggaaggaagaaagggagggaag	0.050													6	3	---	---	---	---	
NTF3	4908	broad.mit.edu	37	12	5596047	5596054	+	Intron	DEL	GTGTGTGT	-	-	rs111941703		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5596047_5596054delGTGTGTGT	uc001qnk.3	+							NM_001102654	NP_001096124	P20783	NTF3_HUMAN	neurotrophin 3 isoform 1 preproprotein						signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding			pancreas(1)	1						TAGTTACGTGgtgtgtgtgtgtgtgtgt	0.288													4	3	---	---	---	---	
ABCC9	10060	broad.mit.edu	37	12	22004837	22004837	+	Intron	DEL	C	-	-	rs4148672		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22004837delC	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	CCAAAGATGGCATTAGAATTT	0.303													4	2	---	---	---	---	
TMTC3	160418	broad.mit.edu	37	12	88582872	88582872	+	Intron	DEL	T	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88582872delT	uc001tau.2	+							NM_181783	NP_861448	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding			skin(1)	1						GCTTACTTAAttttttttttt	0.104													4	2	---	---	---	---	
KDM2B	84678	broad.mit.edu	37	12	121912986	121912989	+	Intron	DEL	TGTG	-	-	rs148404876		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121912986_121912989delTGTG	uc001uat.2	-						KDM2B_uc001uar.2_Intron|KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_Intron	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2						cacatgactCtgtgtgtgtgtgtg	0.113													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79066552	79066554	+	Intron	DEL	AAT	-	-	rs10543814		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79066552_79066554delAAT	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		TGTGAAAAAAAATAATgaaagaa	0.291													2	4	---	---	---	---	
DLGAP5	9787	broad.mit.edu	37	14	55655498	55655501	+	Intron	DEL	AAAA	-	-	rs34953077		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55655498_55655501delAAAA	uc001xbs.2	-						DLGAP5_uc001xbt.2_Intron	NM_014750	NP_055565	Q15398	DLGP5_HUMAN	discs large homolog 7 isoform a						cell proliferation|cell-cell signaling|mitotic chromosome movement towards spindle pole|positive regulation of mitotic metaphase/anaphase transition	nucleus|spindle pole centrosome	phosphoprotein phosphatase activity|protein binding			ovary(1)|skin(1)	2						cttgtaatttaaaaaaaaaaaaaa	0.137													4	2	---	---	---	---	
TMEM63C	57156	broad.mit.edu	37	14	77709044	77709045	+	Intron	INS	-	T	T	rs145534537	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77709044_77709045insT	uc001xtf.2	+						TMEM63C_uc010asq.1_Intron	NM_020431	NP_065164	Q9P1W3	TM63C_HUMAN	transmembrane protein 63C							integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		ACTCAGGTCCATTTTTTTTTGG	0.515													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25276656	25276657	+	IGR	INS	-	T	T	rs146823283	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25276656_25276657insT								ZKSCAN2 (7801 upstream) : HS3ST4 (426690 downstream)																							TTTCTCATTTCTTTTATTTTCT	0.020													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27088704	27088705	+	IGR	INS	-	CTTT	CTTT	rs143025532	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27088704_27088705insCTTT								C16orf82 (8218 upstream) : JMJD5 (126102 downstream)																							ctccttccttccttccttcctt	0.000													11	5	---	---	---	---	
ZCCHC14	23174	broad.mit.edu	37	16	87500652	87500652	+	Intron	DEL	T	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87500652delT	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AAAAAAATTGTtttttttttt	0.229													6	4	---	---	---	---	
ZFP3	124961	broad.mit.edu	37	17	4996471	4996472	+	3'UTR	DEL	TT	-	-	rs72184758		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4996471_4996472delTT	uc002gaq.2	+	2						NM_153018	NP_694563	Q96NJ6	ZFP3_HUMAN	zinc finger protein-3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GATGAGGCACtttttttttttt	0.203													3	3	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58332410	58332410	+	Intron	DEL	T	-	-	rs35284371		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58332410delT	uc002iyo.1	-						USP32_uc002iyn.1_Intron|USP32_uc010wov.1_Intron	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AATGTAGTTCttttttttttt	0.353													9	4	---	---	---	---	
BPTF	2186	broad.mit.edu	37	17	65962538	65962539	+	Intron	INS	-	T	T	rs144411708	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65962538_65962539insT	uc002jgf.2	+						BPTF_uc002jge.2_Intron|BPTF_uc002jgg.2_Intron|BPTF_uc002jgh.2_Intron	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTAGGTAACTATTACTAGAGCA	0.337													7	4	---	---	---	---	
MYO5B	4645	broad.mit.edu	37	18	47352665	47352666	+	3'UTR	INS	-	A	A	rs149289525	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47352665_47352666insA	uc002leb.2	-	40					MYO5B_uc002ldz.2_3'UTR|MYO5B_uc002lea.2_3'UTR	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB						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)		GCAGTAGGTACAAAAAATAATG	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3776194	3776195	+	IGR	INS	-	AAGTG	AAGTG	rs148480350	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3776194_3776195insAAGTG								RAX2 (3975 upstream) : MATK (1773 downstream)																							CTGGCTTTGTTAAGAGGAGAGG	0.332													5	6	---	---	---	---	
ATP5SL	55101	broad.mit.edu	37	19	41938473	41938474	+	Intron	INS	-	GTGT	GTGT	rs149102482	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41938473_41938474insGTGT	uc002oqw.1	-						CYP2F1_uc010xvw.1_Intron|ATP5SL_uc002oqu.1_Intron|ATP5SL_uc002oqv.2_Intron|ATP5SL_uc010xwa.1_Intron|ATP5SL_uc002oqx.1_Intron|ATP5SL_uc002oqy.1_Intron|ATP5SL_uc002oqz.1_Intron|ATP5SL_uc002ora.1_3'UTR|ATP5SL_uc010xwb.1_3'UTR	NM_018035	NP_060505	Q9NW81	AT5SL_HUMAN	ATP5S-like											large_intestine(1)|breast(1)	2						ACAgtgtgtgcgtgtgtgtgtg	0.416													5	3	---	---	---	---	
NPAS1	4861	broad.mit.edu	37	19	47524456	47524457	+	Intron	INS	-	A	A	rs150309227	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47524456_47524457insA	uc002pfw.2	+						NPAS1_uc002pfx.2_Intron|NPAS1_uc002pfy.2_Intron	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1						central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		cctggccgcgggcccccccccg	0.535													6	3	---	---	---	---	
MIR527	574497	broad.mit.edu	37	19	54255879	54255881	+	5'Flank	DEL	TTT	-	-	rs72385066		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54255879_54255881delTTT	hsa-mir-527|MI0003179	+																							0						ttgttttttgttttttttttttt	0.103													10	6	---	---	---	---	
GFRA4	64096	broad.mit.edu	37	20	3641432	3641432	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3641432delG	uc002wio.2	-	2	551	c.551delC	c.(550-552)CCGfs	p.P184fs	GFRA4_uc002win.2_Frame_Shift_Del_p.R158fs|GFRA4_uc002wip.1_Frame_Shift_Del_p.R158fs	NM_145762	NP_665705	Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4 isoform b	184						anchored to membrane|extracellular region|plasma membrane	receptor activity				0						CGCAGGCAGCGGGCGCCCTGG	0.776													4	2	---	---	---	---	
VSTM2L	128434	broad.mit.edu	37	20	36572311	36572312	+	Intron	DEL	CC	-	-	rs33961791		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36572311_36572312delCC	uc002xhk.3	+							NM_080607	NP_542174	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)				GATCTTGGGACCCCCCCCCCCG	0.421													5	3	---	---	---	---	
CCDC117	150275	broad.mit.edu	37	22	29181913	29181913	+	Intron	DEL	A	-	-	rs35631283		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29181913delA	uc003aeb.2	+						CCDC117_uc011aki.1_Intron|CCDC117_uc011akj.1_Intron|CCDC117_uc011akk.1_Intron	NM_173510	NP_775781	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117											breast(1)	1						cccatctcttaaaaaaaaaaa	0.139													6	5	---	---	---	---	
SEC14L3	266629	broad.mit.edu	37	22	30863234	30863235	+	Intron	INS	-	CATCCATCCATC	CATCCATCCATC	rs151165173	by1000genomes	TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30863234_30863235insCATCCATCCATC	uc003ahy.2	-						SEC14L3_uc003ahz.2_Intron|SEC14L3_uc003aia.2_Intron|SEC14L3_uc003aib.2_Intron	NM_174975	NP_777635	Q9UDX4	S14L3_HUMAN	SEC14-like 3							integral to membrane|intracellular	lipid binding|transporter activity			ovary(3)|pancreas(1)|skin(1)	5					Vitamin E(DB00163)	ccatccatccacatccatccat	0.218													5	3	---	---	---	---	
DDX3X	1654	broad.mit.edu	37	X	41196896	41196896	+	Intron	DEL	T	-	-			TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41196896delT	uc004dfe.2	+						DDX3X_uc004dfd.1_Intron|DDX3X_uc010nhf.1_Intron|DDX3X_uc004dff.2_Intron|DDX3X_uc011mkq.1_Intron|DDX3X_uc011mkr.1_Intron|DDX3X_uc011mks.1_Intron|DDX3X_uc004dfg.2_Intron|DDX3X_uc011mkt.1_Intron	NM_001356	NP_001347	O00571	DDX3X_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3						interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6						CATCGTTGCCttttttttttt	0.144										HNSCC(61;0.18)			3	4	---	---	---	---	
XPNPEP2	7512	broad.mit.edu	37	X	128885512	128885519	+	Intron	DEL	AAGAAAGA	-	-	rs67526221		TCGA-CJ-4923-01A-01D-1429-08	TCGA-CJ-4923-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128885512_128885519delAAGAAAGA	uc004eut.1	+							NM_003399	NP_003390	O43895	XPP2_HUMAN	X-prolyl aminopeptidase 2, membrane-bound						cellular process|proteolysis	anchored to membrane|plasma membrane	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0						gaaagaaaggaagaaagaaagaaagaaa	0.000													6	4	---	---	---	---	
