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
YARS	8565	broad.mit.edu	37	1	33245096	33245096	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33245096G>C	uc001bvy.1	-	12	2151	c.1363C>G	c.(1363-1365)CTG>GTG	p.L455V	YARS_uc001bvw.1_Missense_Mutation_p.L115V|YARS_uc001bvx.1_Missense_Mutation_p.L106V	NM_003680	NP_003671	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	455	tRNA-binding.				apoptosis|tyrosyl-tRNA aminoacylation	cytosol|extracellular space|nucleus|soluble fraction	ATP binding|interleukin-8 receptor binding|signal transducer activity|tRNA binding|tyrosine-tRNA ligase activity			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	GGAGGGTCCAGAGGTTCAACC	0.537													47	110	---	---	---	---	PASS
KIAA0467	23334	broad.mit.edu	37	1	43868851	43868851	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43868851G>A	uc009vws.1	+	2	115	c.31G>A	c.(31-33)GAA>AAA	p.E11K	C1orf84_uc001cjh.2_Missense_Mutation_p.E11K|C1orf84_uc001cji.1_RNA			Q5T011	SZT2_HUMAN	Homo sapiens mRNA for KIAA0467 protein, partial cds.	11						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTCCCAGGTGGAAGAAGCTGG	0.448													40	116	---	---	---	---	PASS
CCDC24	149473	broad.mit.edu	37	1	44461642	44461642	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44461642T>A	uc001clj.2	+	9	905	c.734T>A	c.(733-735)CTC>CAC	p.L245H	SLC6A9_uc009vxe.2_Intron|SLC6A9_uc010okm.1_Intron|CCDC24_uc001clk.2_Missense_Mutation_p.S199T|CCDC24_uc009vxc.2_Missense_Mutation_p.L209H	NM_152499	NP_689712	Q8N4L8	CCD24_HUMAN	coiled-coil domain containing 24	245											0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				ACACAGGGCCTCAGACCCCCG	0.642													81	228	---	---	---	---	PASS
LRRC42	115353	broad.mit.edu	37	1	54428053	54428053	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54428053A>G	uc001cwj.1	+	6	1098	c.898A>G	c.(898-900)AAC>GAC	p.N300D	LRRC42_uc001cwl.1_Missense_Mutation_p.N300D|LRRC42_uc001cwk.1_Missense_Mutation_p.N300D|LRRC42_uc009vzm.1_Missense_Mutation_p.N300D	NM_052940	NP_443172	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	300											0						TGATCATAGTAACTGCAAGAC	0.463													18	38	---	---	---	---	PASS
DNAJB4	11080	broad.mit.edu	37	1	78470926	78470926	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78470926A>T	uc001dij.2	+	1	291	c.132A>T	c.(130-132)AAA>AAT	p.K44N	DNAJB4_uc010orn.1_Intron	NM_007034	NP_008965	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	44	J.				protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding				0						CAGAGGAAAAATTTAAAGAGG	0.353													37	89	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142803228	142803228	+	Intron	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803228T>C	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		AAGGAATGCTTTGTAACAAAG	0.308													2	3	---	---	---	---	PASS
TARS2	80222	broad.mit.edu	37	1	150459930	150459930	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150459930G>A	uc001euq.2	+	1	11	c.4G>A	c.(4-6)GCC>ACC	p.A2T	TARS2_uc010pcd.1_RNA|TARS2_uc001eur.2_Missense_Mutation_p.A2T|TARS2_uc009wlt.2_5'UTR|TARS2_uc009wls.2_Missense_Mutation_p.A2T	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	2					threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	AAGGAACATGGCCCTGTATCA	0.547													18	62	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155450216	155450216	+	Silent	SNP	G	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155450216G>C	uc009wqq.2	-	3	2925	c.2445C>G	c.(2443-2445)GTC>GTG	p.V815V	ASH1L_uc001fkt.2_Silent_p.V815V|ASH1L_uc009wqr.1_Silent_p.V815V	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	815					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GGTCACTAGAGACACACATAC	0.408													68	203	---	---	---	---	PASS
MEX3A	92312	broad.mit.edu	37	1	156047265	156047265	+	Silent	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156047265G>A	uc001fnd.3	-	2	663	c.663C>T	c.(661-663)CCC>CCT	p.P221P		NM_001093725	NP_001087194	A1L020	MEX3A_HUMAN	MEX3A protein	221						cytoplasmic mRNA processing body|nucleus	RNA binding|zinc ion binding				0	Hepatocellular(266;0.158)|all_neural(408;0.195)					TCACCTGGCCGGGCAGAGCAG	0.652													6	22	---	---	---	---	PASS
MIR199A2	406977	broad.mit.edu	37	1	172113783	172113783	+	RNA	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172113783C>T	hsa-mir-199a-2|MI0000281	-			c.2C>T			DNM3_uc009wwb.2_Intron|DNM3_uc001gie.2_Intron|DNM3_uc001gif.2_Intron																	0						CAGAAGCTTCCTTCTATGTAC	0.532													10	54	---	---	---	---	PASS
FAM5B	57795	broad.mit.edu	37	1	177249921	177249921	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177249921C>T	uc001glf.2	+	8	1921	c.1609C>T	c.(1609-1611)CGG>TGG	p.R537W	FAM5B_uc001glg.2_Missense_Mutation_p.R432W	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	537						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						CAATGACATGCGGCTGGGCAG	0.557													13	32	---	---	---	---	PASS
LHX9	56956	broad.mit.edu	37	1	197898293	197898293	+	Silent	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197898293C>A	uc001guk.1	+	5	1535	c.1098C>A	c.(1096-1098)ACC>ACA	p.T366T	LHX9_uc001gui.1_Silent_p.T357T|LHX9_uc001guj.1_Intron	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1	366					motor axon guidance|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						CAGACCTGACCAATCCCACTA	0.537													4	164	---	---	---	---	PASS
NFASC	23114	broad.mit.edu	37	1	204943409	204943409	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204943409C>T	uc001hbj.2	+	13	1710	c.1382C>T	c.(1381-1383)ACA>ATA	p.T461I	NFASC_uc001hbh.2_Missense_Mutation_p.T461I|NFASC_uc010pqz.1_Missense_Mutation_p.T455I|NFASC_uc010pra.1_Missense_Mutation_p.T472I|NFASC_uc001hbi.2_Missense_Mutation_p.T472I|NFASC_uc009xbg.1_Missense_Mutation_p.T545I|NFASC_uc010prb.1_Missense_Mutation_p.T472I|NFASC_uc010prc.1_5'UTR|NFASC_uc001hbk.1_Missense_Mutation_p.T282I	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	461	Extracellular (Potential).|Ig-like C2-type 5.				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCCATCCCCACACTGCGATGG	0.577													9	33	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228459673	228459673	+	Intron	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228459673C>T	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				TGCCAAGGATCAGCCGGTGCA	0.602													8	38	---	---	---	---	PASS
ALLC	55821	broad.mit.edu	37	2	3727534	3727534	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3727534C>T	uc010ewt.2	+	5	409	c.248C>T	c.(247-249)ACG>ATG	p.T83M		NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a	102							allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		TCTTACTTCACGGGAGATTAC	0.532										HNSCC(21;0.051)			36	144	---	---	---	---	PASS
HS1BP3	64342	broad.mit.edu	37	2	20823713	20823713	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20823713T>A	uc002rdw.1	-	6	904	c.863A>T	c.(862-864)GAG>GTG	p.E288V		NM_022460	NP_071905	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	288					cell communication		phosphatidylinositol binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCTCCACTCTCACAGGCGGC	0.652													6	13	---	---	---	---	PASS
AHSA2	130872	broad.mit.edu	37	2	61413601	61413601	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61413601C>G	uc002sbc.1	+	5	1799	c.213C>G	c.(211-213)ATC>ATG	p.I71M	AHSA2_uc002sbb.1_RNA	NM_152392	NP_689605	Q719I0	AHSA2_HUMAN	AHA1, activator of heat shock 90kDa protein	233					response to stress	cytoplasm	ATPase activator activity|chaperone binding			breast(1)	1			Epithelial(17;0.0994)			AGAAGATCATCATGAAATGGA	0.363													29	97	---	---	---	---	PASS
LRRTM1	347730	broad.mit.edu	37	2	80530941	80530941	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80530941C>G	uc002sok.1	-	2	274	c.4G>C	c.(4-6)GAT>CAT	p.D2H	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_RNA	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	2						axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5						AGCAGGAAATCCATTAGCGAG	0.562										HNSCC(69;0.2)			28	63	---	---	---	---	PASS
ZNF2	7549	broad.mit.edu	37	2	95846903	95846903	+	Silent	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95846903A>G	uc002suf.2	+	5	792	c.330A>G	c.(328-330)TCA>TCG	p.S110S	ZNF2_uc002sug.2_Silent_p.S68S|ZNF2_uc010yue.1_Silent_p.S72S|ZNF2_uc010fhs.2_Silent_p.S30S	NM_021088	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2 isoform a	110					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)		CAGAAGGATCATTGAGGGAAT	0.448													11	160	---	---	---	---	PASS
CNNM4	26504	broad.mit.edu	37	2	97475200	97475200	+	Silent	SNP	T	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97475200T>G	uc002swx.2	+	7	2372	c.2274T>G	c.(2272-2274)CTT>CTG	p.L758L	CNNM4_uc010yuy.1_3'UTR	NM_020184	NP_064569	Q6P4Q7	CNNM4_HUMAN	cyclin M4	758					biomineral tissue development|ion transport|response to stimulus|visual perception	integral to membrane|plasma membrane				breast(2)|ovary(1)	3						CCACAACTCTTCTCAACGAGC	0.622													18	61	---	---	---	---	PASS
RNF149	284996	broad.mit.edu	37	2	101889409	101889409	+	Intron	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101889409A>G	uc002tax.1	-						SNORD89_uc002tay.1_RNA	NM_173647		Q8NC42	RN149_HUMAN	ring finger protein 149 precursor							integral to membrane	ligase activity|zinc ion binding			ovary(1)|breast(1)	2						CTGAGGTCAGACTAGTGGTTC	0.443													33	126	---	---	---	---	PASS
TMEM182	130827	broad.mit.edu	37	2	103380788	103380788	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103380788C>T	uc010fjb.2	+	3	420	c.233C>T	c.(232-234)ACC>ATC	p.T78I	TMEM182_uc002tcc.3_Missense_Mutation_p.T35I|TMEM182_uc002tcd.3_5'UTR	NM_144632	NP_653233	Q6ZP80	TM182_HUMAN	transmembrane protein 182 precursor	78	Extracellular (Potential).					integral to membrane					0						TTCTTCCTAGCCAATCAGCCA	0.468													26	100	---	---	---	---	PASS
RAD54L2	23132	broad.mit.edu	37	3	51667705	51667705	+	Nonsense_Mutation	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51667705T>A	uc011bdt.1	+	7	1063	c.938T>A	c.(937-939)TTG>TAG	p.L313*	RAD54L2_uc003dbh.2_5'UTR|RAD54L2_uc011bdu.1_Nonsense_Mutation_p.L7*|RAD54L2_uc003dbj.2_5'UTR	NM_015106	NP_055921	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2	313	Helicase ATP-binding.					nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		GGGAAAACTTTGCAAGTGATC	0.512													37	79	---	---	---	---	PASS
PCCB	5096	broad.mit.edu	37	3	136046479	136046479	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136046479T>C	uc003eqy.1	+	13	1354	c.1303T>C	c.(1303-1305)TAT>CAT	p.Y435H	PCCB_uc003eqz.1_Missense_Mutation_p.Y435H|PCCB_uc011bmc.1_Missense_Mutation_p.Y455H	NM_000532	NP_000523	P05166	PCCB_HUMAN	propionyl Coenzyme A carboxylase, beta	435	Carboxyltransferase.		Y -> C (in PA-2).		fatty acid beta-oxidation	mitochondrial matrix	ATP binding|propionyl-CoA carboxylase activity				0					Biotin(DB00121)|L-Valine(DB00161)	GTTTTAGGCCTATGGAGGTGC	0.493													32	42	---	---	---	---	PASS
SGEF	26084	broad.mit.edu	37	3	153973334	153973334	+	3'UTR	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153973334T>C	uc011bog.1	+	15					SGEF_uc011boh.1_3'UTR|SGEF_uc011boi.1_3'UTR	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TGGGCTAGTTTTATTGTTAAT	0.428													7	17	---	---	---	---	PASS
TBL1XR1	79718	broad.mit.edu	37	3	176769354	176769354	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176769354C>T	uc003fiw.3	-	5	625	c.365G>A	c.(364-366)GGA>GAA	p.G122E	TBL1XR1_uc003fix.3_Missense_Mutation_p.G122E|TBL1XR1_uc011bpz.1_5'UTR|TBL1XR1_uc003fiy.2_Missense_Mutation_p.G122E	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	122					canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTTTGCAGATCCTTGTTGGCT	0.443													43	67	---	---	---	---	PASS
EVC	2121	broad.mit.edu	37	4	5733355	5733355	+	Silent	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5733355C>T	uc003gil.1	+	4	772	c.588C>T	c.(586-588)AAC>AAT	p.N196N	EVC_uc003gim.1_RNA	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	196					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)				TCCGGGTGAACGCCTTCCCTG	0.602													7	50	---	---	---	---	PASS
CC2D2A	57545	broad.mit.edu	37	4	15556749	15556749	+	Silent	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15556749C>T	uc010idv.2	+	21	2786	c.2541C>T	c.(2539-2541)GAC>GAT	p.D847D	CC2D2A_uc003gnx.2_Silent_p.D798D|CC2D2A_uc003gnz.1_RNA|CC2D2A_uc003goa.1_RNA	NM_001080522	NP_001073991	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A isoform	847					cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3						GACTGACAGACATGAAAAAAT	0.473													27	40	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	30724623	30724623	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30724623G>T	uc003gsk.1	+	1	2587	c.1579G>T	c.(1579-1581)GAC>TAC	p.D527Y	PCDH7_uc011bxw.1_Missense_Mutation_p.D480Y|PCDH7_uc011bxx.1_Missense_Mutation_p.D527Y	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	527	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						CAAGGTGGGAGACACCAACGA	0.622													18	60	---	---	---	---	PASS
SEC31A	22872	broad.mit.edu	37	4	83788105	83788105	+	Silent	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83788105T>C	uc003hnf.2	-	10	1217	c.1053A>G	c.(1051-1053)TCA>TCG	p.S351S	SEC31A_uc003hne.2_Silent_p.S123S|SEC31A_uc011ccl.1_Silent_p.S351S|SEC31A_uc003hnl.2_Silent_p.S351S|SEC31A_uc003hng.2_Silent_p.S351S|SEC31A_uc003hnh.2_Silent_p.S351S|SEC31A_uc003hni.2_Silent_p.S351S|SEC31A_uc003hnj.2_Silent_p.S351S|SEC31A_uc011ccm.1_Silent_p.S346S|SEC31A_uc011ccn.1_Silent_p.S351S|SEC31A_uc003hnk.2_Silent_p.S351S|SEC31A_uc003hnm.2_Silent_p.S351S|SEC31A_uc003hnn.1_Silent_p.S351S|SEC31A_uc003hno.2_Silent_p.S351S	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1	351	Interaction with SEC13.				COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				TCCCAAAAGATGATGAAAGCT	0.378													44	137	---	---	---	---	PASS
ARHGAP24	83478	broad.mit.edu	37	4	86893269	86893269	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86893269A>C	uc003hpk.2	+	6	1129	c.680A>C	c.(679-681)AAG>ACG	p.K227T	ARHGAP24_uc003hpj.2_Missense_Mutation_p.K227T|ARHGAP24_uc003hpl.2_Missense_Mutation_p.K132T|ARHGAP24_uc010ikf.2_Missense_Mutation_p.K142T|ARHGAP24_uc003hpm.2_Missense_Mutation_p.K134T	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1	227	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CCTTATGCGAAGTATGAAGAT	0.403													5	177	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114213643	114213643	+	Silent	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114213643T>C	uc003ibe.3	+	21	2449	c.2349T>C	c.(2347-2349)CAT>CAC	p.H783H	ANK2_uc003ibd.3_Silent_p.H762H|ANK2_uc003ibf.3_Silent_p.H783H|ANK2_uc011cgc.1_5'Flank|ANK2_uc003ibc.2_Silent_p.H759H|ANK2_uc011cgb.1_Silent_p.H798H	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	783	ANK 23.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TGCTCCAGCATGGGGCCAAGC	0.617													7	22	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89953850	89953850	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89953850G>A	uc003kju.2	+	21	4603	c.4507G>A	c.(4507-4509)GCA>ACA	p.A1503T	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	1503	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGCCATGCCCGCAAAAAGTGA	0.408													4	180	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90079095	90079095	+	Silent	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90079095G>A	uc003kju.2	+	66	13482	c.13386G>A	c.(13384-13386)GGG>GGA	p.G4462G	GPR98_uc003kjt.2_Silent_p.G2168G|GPR98_uc003kjw.2_Silent_p.G123G	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4462	Extracellular (Potential).|Calx-beta 30.				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTCAGCATGGGCAAAACTTAA	0.388													76	56	---	---	---	---	PASS
RIOK2	55781	broad.mit.edu	37	5	96503556	96503556	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96503556C>T	uc003kmz.2	-	8	1122	c.1012G>A	c.(1012-1014)GAT>AAT	p.D338N	RIOK2_uc003kna.3_Missense_Mutation_p.D338N	NM_018343	NP_060813	Q9BVS4	RIOK2_HUMAN	RIO kinase 2 isoform 1	338	Protein kinase.						ATP binding|protein serine/threonine kinase activity			kidney(1)	1		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		ACTTCTCCATCTGAAAATGAG	0.408													116	364	---	---	---	---	PASS
RGMB	285704	broad.mit.edu	37	5	98115744	98115744	+	Silent	SNP	G	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98115744G>T	uc003knc.2	+	4	1122	c.720G>T	c.(718-720)GTG>GTT	p.V240V	RGMB_uc003knb.2_Silent_p.V240V	NM_001012761	NP_001012779	Q6NW40	RGMB_HUMAN	RGM domain family, member B	199					axon guidance|BMP signaling pathway|cell adhesion|positive regulation of transcription, DNA-dependent	anchored to plasma membrane|ER-Golgi intermediate compartment|membrane raft	identical protein binding				0		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		CAGTTCAAGTGACAAACGTAC	0.413													4	172	---	---	---	---	PASS
CHD1	1105	broad.mit.edu	37	5	98228309	98228309	+	Silent	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98228309T>C	uc003knf.2	-	14	2248	c.2100A>G	c.(2098-2100)AAA>AAG	p.K700K		NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	700					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TTTCCACATCTTTCTTAACTC	0.403													121	123	---	---	---	---	PASS
STARD4	134429	broad.mit.edu	37	5	110842074	110842074	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110842074C>A	uc003kph.1	-	3	193	c.109G>T	c.(109-111)GAT>TAT	p.D37Y	STARD4_uc010jbw.1_5'UTR|STARD4_uc010jbx.1_5'UTR|STARD4_uc003kpi.1_RNA|STARD4_uc003kpj.2_Missense_Mutation_p.D37Y	NM_139164	NP_631903	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain	37	START.				lipid transport		lipid binding			ovary(1)	1		all_cancers(142;0.00259)|all_epithelial(76;8.32e-05)|Prostate(80;0.0115)|Colorectal(10;0.0959)|Ovarian(225;0.156)|all_lung(232;0.18)|Lung NSC(167;0.248)		OV - Ovarian serous cystadenocarcinoma(64;4.91e-09)|Epithelial(69;1.39e-08)|all cancers(49;2.34e-06)|COAD - Colon adenocarcinoma(37;0.049)|Colorectal(14;0.138)		ACAGTTACATCTTTCTAGAAA	0.279													3	38	---	---	---	---	PASS
DDX46	9879	broad.mit.edu	37	5	134126192	134126192	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134126192G>T	uc003kzw.2	+	13	1744	c.1576G>T	c.(1576-1578)GTT>TTT	p.V526F	DDX46_uc003kzv.1_RNA	NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	526	Helicase ATP-binding.				mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTGACATATGTTGTTTTAGA	0.274													7	125	---	---	---	---	PASS
RNF14	9604	broad.mit.edu	37	5	141362998	141362998	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141362998A>G	uc003lly.2	+	6	1156	c.1117A>G	c.(1117-1119)AGA>GGA	p.R373G	RNF14_uc003llz.2_Missense_Mutation_p.R373G|RNF14_uc003lma.2_Missense_Mutation_p.R373G|RNF14_uc003lmb.2_Missense_Mutation_p.R247G|RNF14_uc003lmc.2_Missense_Mutation_p.R373G|RNF14_uc011dbg.1_Missense_Mutation_p.R197G|RNF14_uc011dbh.1_Missense_Mutation_p.R70G|RNF14_uc003lmd.2_Missense_Mutation_p.R373G	NM_183399	NP_899646	Q9UBS8	RNF14_HUMAN	ring finger protein 14 isoform 1	373	Potential.|Interaction with androgen receptor.				androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|protein ubiquitination|regulation of androgen receptor signaling pathway|regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|small conjugating protein ligase activity|transcription coactivator activity|zinc ion binding				0		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GGCTAATAAAAGACTTTTGGA	0.373													18	53	---	---	---	---	PASS
RNF14	9604	broad.mit.edu	37	5	141363016	141363016	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141363016T>C	uc003lly.2	+	6	1174	c.1135T>C	c.(1135-1137)TAT>CAT	p.Y379H	RNF14_uc003llz.2_Missense_Mutation_p.Y379H|RNF14_uc003lma.2_Missense_Mutation_p.Y379H|RNF14_uc003lmb.2_Missense_Mutation_p.Y253H|RNF14_uc003lmc.2_Missense_Mutation_p.Y379H|RNF14_uc011dbg.1_Missense_Mutation_p.Y203H|RNF14_uc011dbh.1_Missense_Mutation_p.Y76H|RNF14_uc003lmd.2_Missense_Mutation_p.Y379H	NM_183399	NP_899646	Q9UBS8	RNF14_HUMAN	ring finger protein 14 isoform 1	379	Potential.|Interaction with androgen receptor.				androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|protein ubiquitination|regulation of androgen receptor signaling pathway|regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|small conjugating protein ligase activity|transcription coactivator activity|zinc ion binding				0		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GGATCAAAGGTATGGTAAGAG	0.393													20	52	---	---	---	---	PASS
HIST1H1D	3007	broad.mit.edu	37	6	26235116	26235116	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26235116C>T	uc003nhd.2	-	1	101	c.46G>A	c.(46-48)GAA>AAA	p.E16K		NM_005320	NP_005311	P16402	H13_HUMAN	histone cluster 1, H1d	16					nucleosome assembly	nucleosome|nucleus	DNA binding			skin(1)	1		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GGTGTTTTTTCTGCGGGTGCA	0.488													4	105	---	---	---	---	PASS
PBX2	5089	broad.mit.edu	37	6	32155509	32155509	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32155509T>A	uc003oav.1	-	5	1056	c.785A>T	c.(784-786)TAT>TTT	p.Y262F	PBX2_uc003oaw.2_Missense_Mutation_p.Y262F	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	262	Homeobox; TALE-type.						transcription factor binding			ovary(1)	1						GGAGTAGAAATACTCATTTAG	0.517													3	21	---	---	---	---	PASS
ELMO1	9844	broad.mit.edu	37	7	37262227	37262227	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37262227C>G	uc003tfk.1	-	10	1080	c.773G>C	c.(772-774)AGG>ACG	p.R258T	ELMO1_uc011kbc.1_Missense_Mutation_p.R162T|ELMO1_uc010kxg.1_Missense_Mutation_p.R258T	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	258					actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						TACCTGCCTCCTCTCATCAGG	0.428													55	151	---	---	---	---	PASS
SGK223	157285	broad.mit.edu	37	8	8233967	8233967	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8233967C>G	uc003wsh.3	-	2	1952	c.1952G>C	c.(1951-1953)AGC>ACC	p.S651T		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	651							ATP binding|non-membrane spanning protein tyrosine kinase activity				0						TCTTCCCCAGCTGTGACTCAG	0.597													12	102	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52733161	52733161	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52733161T>A	uc003xqx.3	-	6	1165	c.824A>T	c.(823-825)AAA>ATA	p.K275I	PCMTD1_uc011ldm.1_Missense_Mutation_p.K145I|PCMTD1_uc003xqw.3_Missense_Mutation_p.K275I|PCMTD1_uc011ldn.1_Missense_Mutation_p.K87I|PCMTD1_uc010lya.2_Missense_Mutation_p.K199I	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	275						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				TCTTTTCCTTTTGGGTGGAGC	0.373													5	290	---	---	---	---	PASS
MTFR1	9650	broad.mit.edu	37	8	66619369	66619369	+	Silent	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66619369A>G	uc003xvm.2	+	6	854	c.642A>G	c.(640-642)CGA>CGG	p.R214R	MTFR1_uc011lep.1_Silent_p.R214R|MTFR1_uc003xvn.2_Silent_p.R181R|MTFR1_uc003xvo.1_Silent_p.R204R	NM_014637	NP_055452	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1 isoform 1	214						mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			TTAAAGAACGAAGAGAGAAAA	0.483													30	152	---	---	---	---	PASS
HRSP12	10247	broad.mit.edu	37	8	99114990	99114990	+	3'UTR	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99114990T>A	uc003yii.1	-	6						NM_005836	NP_005827	P52758	UK114_HUMAN	heat-responsive protein 12						regulation of translational termination	nucleus	endonuclease activity			ovary(1)	1	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			ATTGTGAAAATTAAAAGGTTA	0.328													60	93	---	---	---	---	PASS
SLC30A8	169026	broad.mit.edu	37	8	118185004	118185004	+	3'UTR	SNP	G	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118185004G>C	uc003yoh.2	+	8					SLC30A8_uc010mcz.2_3'UTR|SLC30A8_uc011lia.1_3'UTR|SLC30A8_uc003yog.2_3'UTR	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			AGAAAATAAGGAACCAAAGGA	0.408													40	54	---	---	---	---	PASS
ACO1	48	broad.mit.edu	37	9	32433772	32433772	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32433772T>A	uc003zqw.3	+	16	2053	c.1898T>A	c.(1897-1899)CTG>CAG	p.L633Q	ACO1_uc010mjh.1_Missense_Mutation_p.L467Q|ACO1_uc003zqx.3_Missense_Mutation_p.L633Q|ACO1_uc003zqy.3_RNA	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1	633					citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TCAGATAAGCTGTTTTTCTGG	0.343													50	84	---	---	---	---	PASS
UNC13B	10497	broad.mit.edu	37	9	35385805	35385805	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35385805A>T	uc003zwq.2	+	22	3005	c.2713A>T	c.(2713-2715)ATG>TTG	p.M905L	UNC13B_uc003zwr.2_Missense_Mutation_p.M905L	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like	905					excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TTTCTTCAGAATGAAGGTAAG	0.483													45	105	---	---	---	---	PASS
PPP6C	5537	broad.mit.edu	37	9	127916187	127916187	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127916187C>A	uc004bpg.3	-	5	678	c.457G>T	c.(457-459)GCT>TCT	p.A153S	PPP6C_uc010mwv.2_Missense_Mutation_p.A190S|PPP6C_uc010mww.2_Missense_Mutation_p.A131S|PPP6C_uc011lzr.1_Missense_Mutation_p.A6S	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform	153					G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						AAACTTACAGCTGCTACTGTG	0.343													3	59	---	---	---	---	PASS
ACBD7	414149	broad.mit.edu	37	10	15121004	15121004	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15121004C>A	uc001inv.2	-	2	96	c.48G>T	c.(46-48)AAG>AAT	p.K16N	ACBD7_uc010qby.1_5'UTR	NM_001039844	NP_001034933	Q8N6N7	ACBD7_HUMAN	acyl-Coenzyme A binding domain containing 7	16	ACB.						fatty-acyl-CoA binding				0						TTGCTTTCAGCTTCCTCACAT	0.363													4	224	---	---	---	---	PASS
TRDMT1	1787	broad.mit.edu	37	10	17195548	17195548	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17195548G>C	uc001iop.2	-	10	1081	c.1033C>G	c.(1033-1035)CCT>GCT	p.P345A	TRDMT1_uc001ioq.2_Missense_Mutation_p.P321A|TRDMT1_uc001ior.2_Missense_Mutation_p.P299A|TRDMT1_uc001ios.2_Missense_Mutation_p.P274A|TRDMT1_uc009xjt.2_Missense_Mutation_p.P264A|TRDMT1_uc010qcc.1_Missense_Mutation_p.P274A|TRDMT1_uc010qcd.1_Missense_Mutation_p.P222A	NM_004412	NP_004403	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1 isoform	345					tRNA processing	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|RNA binding			ovary(1)	1						ATTTCTTTAGGAGTGAAATAT	0.338													17	78	---	---	---	---	PASS
NDST2	8509	broad.mit.edu	37	10	75563696	75563696	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75563696T>C	uc001jvk.2	-	10	2726	c.1922A>G	c.(1921-1923)GAG>GGG	p.E641G	NDST2_uc010qks.1_Missense_Mutation_p.E267G|NDST2_uc010qkt.1_Missense_Mutation_p.E518G|NDST2_uc001jvl.1_Missense_Mutation_p.E48G|NDST2_uc009xro.2_Missense_Mutation_p.E267G|NDST2_uc010qku.1_Missense_Mutation_p.E516G	NM_003635	NP_003626	P52849	NDST2_HUMAN	heparan glucosaminyl	641	Lumenal (Potential).|Heparan sulfate N-sulfotransferase 2.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity	p.E641D(1)		ovary(1)	1	Prostate(51;0.0112)					GAACTGAATCTCCTCAAATGT	0.493													82	189	---	---	---	---	PASS
TMEM180	79847	broad.mit.edu	37	10	104231152	104231152	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104231152A>G	uc001kvt.2	+	6	1046	c.827A>G	c.(826-828)CAG>CGG	p.Q276R	TMEM180_uc001kvs.2_Missense_Mutation_p.Q125R|TMEM180_uc010qql.1_Missense_Mutation_p.Q5R|TMEM180_uc010qqm.1_Missense_Mutation_p.Q125R|TMEM180_uc001kvu.2_Missense_Mutation_p.Q276R	NM_024789	NP_079065	Q14CX5	TM180_HUMAN	transmembrane protein 180	276	Helical; (Potential).					integral to membrane				ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GACCTGGTGCAGGTATGGGGA	0.562													27	91	---	---	---	---	PASS
MRPL23	6150	broad.mit.edu	37	11	1977698	1977698	+	3'UTR	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1977698C>T	uc001lux.2	+	5						NM_021134	NP_066957	Q16540	RM23_HUMAN	mitochondrial ribosomal protein L23						translation	mitochondrial large ribosomal subunit	nucleotide binding|RNA binding|structural constituent of ribosome			large_intestine(2)|ovary(1)	3		all_epithelial(84;6.24e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.0026)|Lung(200;0.0171)|LUSC - Lung squamous cell carcinoma(625;0.0842)		TGTGGCAGAGCAGCGACCCGC	0.776													8	7	---	---	---	---	PASS
LRP5	4041	broad.mit.edu	37	11	68193567	68193567	+	Silent	SNP	C	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68193567C>G	uc001ont.2	+	16	3624	c.3549C>G	c.(3547-3549)ACC>ACG	p.T1183T	LRP5_uc009ysg.2_Silent_p.T593T	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	1183	LDL-receptor class B 20.|Beta-propeller 4.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						TGGAGAAGACCACCGGGGACA	0.622													30	114	---	---	---	---	PASS
SAPS3	55291	broad.mit.edu	37	11	68355371	68355371	+	Intron	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68355371T>C	uc001onw.2	+						SAPS3_uc001onv.2_Intron|SAPS3_uc001ony.3_Intron|SAPS3_uc001onx.2_Intron|SAPS3_uc009ysh.2_Intron|SAPS3_uc001onu.2_Intron|SAPS3_uc010rqc.1_Intron|SAPS3_uc010rqd.1_Intron|SAPS3_uc001onz.2_Intron|SAPS3_uc001ooa.2_5'UTR	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6						regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)			ATTATATCACTGTCACTGGTC	0.383													38	111	---	---	---	---	PASS
SAPS3	55291	broad.mit.edu	37	11	68355413	68355413	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68355413A>G	uc001onw.2	+	16	1918	c.1651A>G	c.(1651-1653)ATG>GTG	p.M551V	SAPS3_uc001onv.2_Missense_Mutation_p.M551V|SAPS3_uc001ony.3_Missense_Mutation_p.M522V|SAPS3_uc001onx.2_Missense_Mutation_p.M545V|SAPS3_uc009ysh.2_Missense_Mutation_p.M471V|SAPS3_uc001onu.2_Missense_Mutation_p.M471V|SAPS3_uc010rqc.1_Missense_Mutation_p.M319V|SAPS3_uc010rqd.1_Missense_Mutation_p.M234V|SAPS3_uc001onz.2_Intron|SAPS3_uc001ooa.2_Missense_Mutation_p.M1V	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6	551					regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)			TGATTATCAGATGCAACAAAT	0.383													48	167	---	---	---	---	PASS
KRTAP5-10	387273	broad.mit.edu	37	11	71277393	71277393	+	3'UTR	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71277393T>C	uc001oqt.1	+	1						NM_001012710	NP_001012728	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10							keratin filament				skin(1)	1						ATGGCTCAGCTCTCCACTGGG	0.582													7	14	---	---	---	---	PASS
ARAP1	116985	broad.mit.edu	37	11	72398761	72398761	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72398761C>A	uc001osu.2	-	32	4282	c.4093G>T	c.(4093-4095)GAG>TAG	p.E1365*	ARAP1_uc001osv.2_Nonsense_Mutation_p.E1354*|ARAP1_uc001osr.2_Nonsense_Mutation_p.E1125*|ARAP1_uc001oss.2_Nonsense_Mutation_p.E1120*|ARAP1_uc009yth.2_Nonsense_Mutation_p.E1048*|ARAP1_uc010rre.1_Nonsense_Mutation_p.E1109*	NM_001040118	NP_001035207	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1365	PH 4.				actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1						TTCTCTGTCTCATGCACCACT	0.562													5	328	---	---	---	---	PASS
SERPINH1	871	broad.mit.edu	37	11	75280027	75280027	+	Silent	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75280027C>T	uc001owr.2	+	4	994	c.765C>T	c.(763-765)ATC>ATT	p.I255I	SERPINH1_uc009yuf.2_Silent_p.I255I|SERPINH1_uc009yug.2_Silent_p.I255I|SERPINH1_uc001ows.2_Silent_p.I255I|SERPINH1_uc001owt.2_Silent_p.I38I	NM_001235	NP_001226	P50454	SERPH_HUMAN	serine (or cysteine) proteinase inhibitor, clade	255				I -> L (in Ref. 1; CAA43795).	regulation of proteolysis|response to unfolded protein	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	collagen binding|serine-type endopeptidase inhibitor activity			ovary(2)	2	Ovarian(111;0.11)					AGCTGCAAATCGTGGAGATGC	0.582													22	95	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92430597	92430597	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92430597G>C	uc001pdj.3	+	3	3672	c.3655G>C	c.(3655-3657)GAA>CAA	p.E1219Q		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1219	Cadherin 11.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ACAGCAGGCAGAACATTTTCT	0.358										TCGA Ovarian(4;0.039)			4	70	---	---	---	---	PASS
CRYAB	1410	broad.mit.edu	37	11	111779431	111779431	+	3'UTR	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111779431T>C	uc001pmf.1	-	3						NM_001885	NP_001876	P02511	CRYAB_HUMAN	crystallin, alpha B						anti-apoptosis|muscle contraction|negative regulation of intracellular transport|protein folding|protein homooligomerization|response to heat	cytoplasm|nucleus	protein homodimerization activity|structural constituent of eye lens|unfolded protein binding				0		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)		CACAAGACTTTCATTCACTGG	0.408													28	85	---	---	---	---	PASS
ERC1	23085	broad.mit.edu	37	12	1299182	1299182	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1299182A>G	uc001qjb.2	+	12	2556	c.2315A>G	c.(2314-2316)AAG>AGG	p.K772R	ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Missense_Mutation_p.K744R|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_RNA|ERC1_uc001qjf.2_Missense_Mutation_p.K772R|ERC1_uc010sdv.1_Missense_Mutation_p.K520R|ERC1_uc009zdp.2_Missense_Mutation_p.K412R|ERC1_uc001qje.2_RNA	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	772	Potential.				I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			GAAAATGAGAAGAATGACAAA	0.403													18	141	---	---	---	---	PASS
C1S	716	broad.mit.edu	37	12	7174353	7174353	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7174353G>A	uc001qsj.2	+	12	1717	c.998G>A	c.(997-999)GGT>GAT	p.G333D	C1S_uc001qsk.2_Missense_Mutation_p.G333D|C1S_uc001qsl.2_Missense_Mutation_p.G333D|C1S_uc009zfr.2_Missense_Mutation_p.G166D|C1S_uc009zfs.2_RNA	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent	333	Sushi 1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GGACGTGTTGGTGCAACATCT	0.383													61	117	---	---	---	---	PASS
SLCO1B3	28234	broad.mit.edu	37	12	21036504	21036504	+	Silent	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21036504A>G	uc001rek.2	+	12	1776	c.1650A>G	c.(1648-1650)ACA>ACG	p.T550T	SLCO1B3_uc001rel.2_Silent_p.T550T|SLCO1B3_uc010sil.1_Silent_p.T550T|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_Silent_p.T375T	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,	550	Helical; Name=10; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					TCTCTGCAACAGGAGGTACCA	0.348													111	200	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32137779	32137779	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32137779T>G	uc001rks.2	+	4	4304	c.3890T>G	c.(3889-3891)TTG>TGG	p.L1297W	C12orf35_uc001rkt.2_5'Flank	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1297										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			AGAAAAAAATTGAGGTTTCAC	0.358													33	112	---	---	---	---	PASS
LARP4	113251	broad.mit.edu	37	12	50794655	50794655	+	5'UTR	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50794655A>G	uc001rwp.1	+	1					LARP4_uc001rwo.1_5'UTR|LARP4_uc001rwq.1_5'UTR|LARP4_uc001rwr.1_5'UTR|LARP4_uc001rws.1_5'UTR|LARP4_uc001rwm.2_5'UTR|LARP4_uc001rwn.2_5'UTR	NM_052879	NP_443111	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1						GCAGCGGCTGACGGCAGGGGA	0.627													18	80	---	---	---	---	PASS
USP15	9958	broad.mit.edu	37	12	62749239	62749239	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62749239A>C	uc001src.1	+	8	907	c.898A>C	c.(898-900)ATG>CTG	p.M300L	USP15_uc001srb.1_Missense_Mutation_p.M271L	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	300					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TACGTGTTTCATGAACTCAGC	0.373													50	86	---	---	---	---	PASS
B3GALTL	145173	broad.mit.edu	37	13	31903770	31903770	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31903770C>A	uc010aaz.2	+	15	1572	c.1462C>A	c.(1462-1464)CAG>AAG	p.Q488K	B3GALTL_uc001utn.3_RNA|B3GALTL_uc001uto.3_Missense_Mutation_p.Q93K	NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	488	Lumenal (Potential).				fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		CAAAGCCAGGCAGGAGACACA	0.502													26	77	---	---	---	---	PASS
HTR2A	3356	broad.mit.edu	37	13	47408865	47408865	+	3'UTR	SNP	G	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47408865G>T	uc001vbq.2	-	3					HTR2A_uc001vbr.2_3'UTR|HTR2A_uc010acr.2_3'UTR	NM_000621	NP_000612	P28223	5HT2A_HUMAN	5-hydroxytryptamine receptor 2A isoform 1						ERK1 and ERK2 cascade|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	integral to plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|serotonin binding|serotonin receptor activity			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Aripiprazole(DB01238)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Dihydroergotamine(DB00320)|Donepezil(DB00843)|Epinastine(DB00751)|Ergotamine(DB00696)|Fluvoxamine(DB00176)|Mesoridazine(DB00933)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)	TATGATCGTTGGTTCCACTAG	0.388													3	16	---	---	---	---	PASS
ATP7B	540	broad.mit.edu	37	13	52518307	52518307	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52518307C>T	uc001vfw.2	-	14	3338	c.3181G>A	c.(3181-3183)GGG>AGG	p.G1061R	ATP7B_uc010adv.2_Missense_Mutation_p.G631R|ATP7B_uc001vfx.2_Missense_Mutation_p.G854R|ATP7B_uc001vfy.2_Missense_Mutation_p.G950R|ATP7B_uc010tgt.1_Missense_Mutation_p.G996R|ATP7B_uc010tgu.1_Missense_Mutation_p.G1013R|ATP7B_uc010tgv.1_Missense_Mutation_p.G983R|ATP7B_uc001vfv.2_Missense_Mutation_p.G333R|ATP7B_uc010tgs.1_Intron	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1061	Cytoplasmic (Potential).		G -> E (in WD).		ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)		TCCGCAGTCCCCACCACAGCC	0.637									Wilson_disease				18	59	---	---	---	---	PASS
KLF12	11278	broad.mit.edu	37	13	74420129	74420129	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74420129G>T	uc001vjf.2	-	4	727	c.505C>A	c.(505-507)CCT>ACT	p.P169T	KLF12_uc010aeq.2_Missense_Mutation_p.P169T|KLF12_uc001vjg.3_Missense_Mutation_p.P169T	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	169					negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		GGACTTGAAGGCGGTACGGGA	0.512													18	58	---	---	---	---	PASS
RNASE3	6037	broad.mit.edu	37	14	21360444	21360444	+	3'UTR	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21360444C>T	uc001vyj.2	+	2						NM_002935	NP_002926	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3 (eosinophil						defense response to bacterium|RNA catabolic process	extracellular region|soluble fraction	nucleic acid binding|pancreatic ribonuclease activity				0	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	AGTCTCCATACCCCTTCAGCT	0.502													8	57	---	---	---	---	PASS
DIO2	1734	broad.mit.edu	37	14	80669073	80669073	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80669073T>A	uc010tvq.1	-	4	1183	c.781A>T	c.(781-783)AAT>TAT	p.N261Y	DIO2_uc010tvp.1_Missense_Mutation_p.N297Y|DIO2_uc001xut.2_RNA|DIO2_uc010asx.2_3'UTR|DIO2_uc010tvr.1_Missense_Mutation_p.N261Y|DIO2_uc010asy.2_3'UTR	NM_000793	NP_000784	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II isoform a	261					hormone biosynthetic process|selenocysteine incorporation|thyroid hormone generation	integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|ubiquitin protein ligase binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0281)		TTGCTGAAATTCTTCTCCAGC	0.383													18	15	---	---	---	---	PASS
TLE3	7090	broad.mit.edu	37	15	70342426	70342426	+	3'UTR	SNP	G	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70342426G>T	uc002asm.2	-	20					TLE3_uc002ask.2_3'UTR|TLE3_uc002asl.2_3'UTR|TLE3_uc010ukd.1_3'UTR|TLE3_uc010bik.1_3'UTR|TLE3_uc010bil.1_3'UTR|TLE3_uc002asn.2_3'UTR|TLE3_uc002asp.2_3'UTR|TLE3_uc002aso.2_3'UTR	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a						organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						AGCCCTGCTGGAGTTCTTGTT	0.552													4	160	---	---	---	---	PASS
MEX3B	84206	broad.mit.edu	37	15	82336581	82336581	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82336581C>A	uc002bgq.1	-	2	945	c.630G>T	c.(628-630)ATG>ATT	p.M210I		NM_032246	NP_115622	Q6ZN04	MEX3B_HUMAN	mex-3 homolog B	210	KH 2.				protein autophosphorylation	cytoplasmic mRNA processing body|nucleus	calcium ion binding|RNA binding|zinc ion binding			breast(1)|kidney(1)	2						CGTTCTCTGGCATGCCGGTCA	0.612													107	177	---	---	---	---	PASS
WDR90	197335	broad.mit.edu	37	16	706261	706261	+	Intron	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:706261C>T	uc002cii.1	+						WDR90_uc002cig.1_3'UTR|WDR90_uc002cih.1_3'UTR|WDR90_uc002cij.1_Intron|WDR90_uc002cik.1_Intron|WDR90_uc002cil.1_5'Flank|WDR90_uc002cim.1_5'Flank	NM_145294	NP_660337	Q96KV7	WDR90_HUMAN	WD repeat domain 90											ovary(1)	1		Hepatocellular(780;0.0218)				CGGCTCACCCCGGGGTGGCCC	0.677													7	19	---	---	---	---	PASS
ACSM1	116285	broad.mit.edu	37	16	20648507	20648507	+	Intron	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20648507G>A	uc002dhm.1	-						ACSM1_uc002dhn.1_Intron|ACSM1_uc010bwg.1_Intron	NM_052956	NP_443188	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member						benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process	mitochondrial matrix	acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			central_nervous_system(1)|skin(1)	2						CAGGGTCAGCGGTGTTCATGC	0.358													132	180	---	---	---	---	PASS
SLC5A11	115584	broad.mit.edu	37	16	24869990	24869990	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24869990A>G	uc002dmu.2	+	2	258	c.26A>G	c.(25-27)CAG>CGG	p.Q9R	SLC5A11_uc002dms.2_Intron|SLC5A11_uc010vcd.1_Missense_Mutation_p.Q9R|SLC5A11_uc002dmt.2_Intron|SLC5A11_uc010vce.1_Missense_Mutation_p.Q9R|SLC5A11_uc010bxt.2_5'UTR	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	9	Extracellular (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		AGCAGCCCTCAGCCTCCACAG	0.557													32	103	---	---	---	---	PASS
XPO6	23214	broad.mit.edu	37	16	28222834	28222834	+	5'UTR	SNP	G	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28222834G>T	uc002dpa.1	-	1					XPO6_uc002dpb.1_5'UTR|XPO6_uc010vcp.1_5'UTR	NM_015171	NP_055986	Q96QU8	XPO6_HUMAN	exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2						GGCCCCGAGGGGACCCTCTAA	0.652													4	8	---	---	---	---	PASS
CDH11	1009	broad.mit.edu	37	16	65038653	65038653	+	Silent	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65038653C>T	uc002eoi.2	-	3	554	c.120G>A	c.(118-120)GAG>GAA	p.E40E	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Silent_p.E40E|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Silent_p.E40E	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	40					adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CCTTGCCCTTCTCATGGTGCC	0.652			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			8	20	---	---	---	---	PASS
WWP2	11060	broad.mit.edu	37	16	69832593	69832593	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69832593G>A	uc002exu.1	+	4	168	c.79G>A	c.(79-81)GCA>ACA	p.A27T	WWP2_uc002ext.2_Missense_Mutation_p.A27T|WWP2_uc002exv.1_Missense_Mutation_p.A27T	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase	27	C2.				entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6						AGTGGTGTCCGCAAAGCCCAA	0.527											OREG0023909	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	252	---	---	---	---	PASS
TUBB3	10381	broad.mit.edu	37	16	90001521	90001521	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90001521C>T	uc002fph.1	+	4	727	c.662C>T	c.(661-663)ACC>ATC	p.T221I	TUBB3_uc002fpf.2_Missense_Mutation_p.T568I|TUBB3_uc010ciz.1_Missense_Mutation_p.T149I|TUBB3_uc002fpg.1_Missense_Mutation_p.T75I|TUBB3_uc002fpi.1_Missense_Mutation_p.T149I|TUBB3_uc002fpj.1_Missense_Mutation_p.T149I|TUBB3_uc010cjb.1_Missense_Mutation_p.T75I|TUBB3_uc002fpk.1_Missense_Mutation_p.T75I	NM_006086	NP_006077	Q13509	TBB3_HUMAN	tubulin, beta, 4	221					'de novo' posttranslational protein folding|axon guidance|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(2)|pancreas(1)	3		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		GCCACGCCCACCTACGGGGAC	0.632													33	74	---	---	---	---	PASS
TNFRSF13B	23495	broad.mit.edu	37	17	16842795	16842795	+	3'UTR	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16842795C>T	uc002gqs.1	-	5					TNFRSF13B_uc010vwt.1_Intron|TNFRSF13B_uc002gqt.1_3'UTR	NM_012452	NP_036584	O14836	TR13B_HUMAN	tumor necrosis factor receptor 13B						cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding|receptor activity			kidney(2)	2						cccctctccccacctctcttt	0.149									IgA_Deficiency_Selective				4	13	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18062259	18062259	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18062259C>T	uc010vxh.1	+	52	9442	c.9104C>T	c.(9103-9105)TCC>TTC	p.S3035F	MYO15A_uc010vxi.1_Missense_Mutation_p.S299F|MYO15A_uc010vxk.1_Intron|MYO15A_uc010vxl.1_Missense_Mutation_p.S24F|MYO15A_uc002gsl.2_5'UTR|MYO15A_uc010vxm.1_5'Flank|MYO15A_uc002gsm.1_5'Flank|MYO15A_uc010cpv.2_5'Flank	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	3035	Tail.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					AGGCTGAAATCCAAGGAGCCT	0.473													25	97	---	---	---	---	PASS
CYTSB	92521	broad.mit.edu	37	17	20000054	20000054	+	Silent	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20000054C>T	uc002gwq.2	+	2	235	c.90C>T	c.(88-90)TCC>TCT	p.S30S	CYTSB_uc010cqx.2_Silent_p.S30S|CYTSB_uc002gwr.2_Silent_p.S30S|CYTSB_uc002gws.2_Silent_p.S30S	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b	30						nucleus					0						CAGCCTCTTCCGGCATGAAGA	0.602													42	165	---	---	---	---	PASS
KSR1	8844	broad.mit.edu	37	17	25936969	25936969	+	Intron	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25936969T>C	uc010crg.2	+						KSR1_uc002gzm.2_Intron|KSR1_uc002gzn.2_5'UTR	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras						Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		GTGTTCTGGGTCTGGGTGTGT	0.547											OREG0024262	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	31	---	---	---	---	PASS
MIR423	494335	broad.mit.edu	37	17	28444131	28444131	+	RNA	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28444131A>G	hsa-mir-423|MI0001445	+			c.35A>G			CCDC55_uc002heu.2_Intron|CCDC55_uc002hev.2_Intron|CCDC55_uc010wbl.1_Intron|CCDC55_uc010wbm.1_Intron|uc002hew.1_RNA|hsa-mir-3184|MI0014226_RNA																	0						AGAGAGCGAGACTTTTCTATT	0.532													6	17	---	---	---	---	PASS
ATAD5	79915	broad.mit.edu	37	17	29161396	29161396	+	Silent	SNP	G	T	T	rs114289357	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29161396G>T	uc002hfs.1	+	2	643	c.297G>T	c.(295-297)ACG>ACT	p.T99T	ATAD5_uc002hft.1_5'UTR	NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	99					response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AAGACTGTACGACACCTTTGG	0.343													56	153	---	---	---	---	PASS
KLHL10	317719	broad.mit.edu	37	17	39994097	39994097	+	5'UTR	SNP	A	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39994097A>T	uc010cxr.2	+	1					NT5C3L_uc010wfu.1_5'Flank|NT5C3L_uc002hyb.3_5'Flank|NT5C3L_uc002hyc.3_5'Flank|NT5C3L_uc002hyd.3_5'Flank|NT5C3L_uc002hxy.3_5'Flank|NT5C3L_uc002hxz.3_5'Flank|NT5C3L_uc002hya.3_5'Flank|KLHL10_uc010wfv.1_5'UTR|KLHL10_uc010wfw.1_5'UTR	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10							cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)				TGTAGTAGGGAAAAGGAGCGA	0.557													16	42	---	---	---	---	PASS
GPRC5C	55890	broad.mit.edu	37	17	72443073	72443073	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72443073A>G	uc002jks.2	+	3	1271	c.1232A>G	c.(1231-1233)GAA>GGA	p.E411G	GPRC5C_uc002jkp.2_Missense_Mutation_p.E456G|GPRC5C_uc002jkq.2_3'UTR|GPRC5C_uc002jkr.2_Missense_Mutation_p.E423G|GPRC5C_uc002jkt.2_Missense_Mutation_p.E411G|GPRC5C_uc002jku.2_Missense_Mutation_p.E166G	NM_018653	NP_061123	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor family C, group 5,	411	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to plasma membrane	G-protein coupled receptor activity|protein binding			ovary(2)|prostate(1)|central_nervous_system(1)|pancreas(1)	5						CTGCGGGCTGAAGACATGTAC	0.602													33	132	---	---	---	---	PASS
NPTX1	4884	broad.mit.edu	37	17	78444520	78444520	+	3'UTR	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78444520C>A	uc002jyp.1	-	5						NM_002522	NP_002513	Q15818	NPTX1_HUMAN	neuronal pentraxin I precursor						central nervous system development|synaptic transmission|transport	transport vesicle	metal ion binding				0	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			TCGGTTCATTCCTGGGGAAAA	0.627													8	19	---	---	---	---	PASS
KLHL14	57565	broad.mit.edu	37	18	30349970	30349970	+	Silent	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30349970C>T	uc002kxm.1	-	2	973	c.585G>A	c.(583-585)CTG>CTA	p.L195L		NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14	195						cytosol|endoplasmic reticulum membrane				ovary(1)	1						CCAGGCCGTGCAGCGCGGCGA	0.602													4	113	---	---	---	---	PASS
DOT1L	84444	broad.mit.edu	37	19	2229711	2229711	+	Intron	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2229711C>A	uc002lvb.3	+						DOT1L_uc002lvc.1_3'UTR	NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGTCCCCAGCCTGGGTGAGT	0.637													12	128	---	---	---	---	PASS
MPND	84954	broad.mit.edu	37	19	4352949	4352949	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4352949A>G	uc002mae.2	+	4	654	c.587A>G	c.(586-588)GAC>GGC	p.D196G	MPND_uc010dtx.2_RNA|MPND_uc002mag.2_Missense_Mutation_p.D196G|MPND_uc002maf.2_Missense_Mutation_p.D196G|MPND_uc002mah.2_Missense_Mutation_p.D84G|MPND_uc002mai.2_Missense_Mutation_p.D84G	NM_032868	NP_116257	Q8N594	MPND_HUMAN	MPN domain containing isoform 1	196							peptidase activity			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		gaggaggaggaCGTTCTGGCA	0.527													10	30	---	---	---	---	PASS
SMARCA4	6597	broad.mit.edu	37	19	11144110	11144110	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11144110G>A	uc002mqf.3	+	26	3975	c.3691G>A	c.(3691-3693)GCC>ACC	p.A1231T	SMARCA4_uc010dxp.2_Missense_Mutation_p.A1231T|SMARCA4_uc010dxo.2_Missense_Mutation_p.A1231T|SMARCA4_uc010dxq.2_Missense_Mutation_p.A1231T|SMARCA4_uc010dxr.2_Missense_Mutation_p.A1231T|SMARCA4_uc002mqj.3_Missense_Mutation_p.A1231T|SMARCA4_uc010dxs.2_Missense_Mutation_p.A1231T|SMARCA4_uc010dxt.1_Missense_Mutation_p.A451T|SMARCA4_uc002mqh.3_Missense_Mutation_p.A354T|SMARCA4_uc002mqi.1_Missense_Mutation_p.A434T	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1231	Helicase C-terminal.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GGTGATCCAGGCCGGCATGTT	0.632			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				37	105	---	---	---	---	PASS
ILVBL	10994	broad.mit.edu	37	19	15226438	15226438	+	Silent	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15226438C>T	uc002nam.2	-	15	1780	c.1659G>A	c.(1657-1659)CAG>CAA	p.Q553Q	ILVBL_uc010xof.1_Silent_p.Q194Q|ILVBL_uc010dzw.2_Silent_p.Q446Q	NM_006844	NP_006835	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	553						integral to membrane	magnesium ion binding|thiamine pyrophosphate binding|transferase activity			ovary(2)	2						CCCGAGAAATCTGTGTCCAGC	0.627													6	117	---	---	---	---	PASS
MAP1S	55201	broad.mit.edu	37	19	17838790	17838790	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17838790T>C	uc002nhe.1	+	5	2606	c.2597T>C	c.(2596-2598)CTG>CCG	p.L866P	MAP1S_uc010eba.1_Intron|MAP1S_uc002nhf.1_Missense_Mutation_p.L114P|MAP1S_uc010xpv.1_Missense_Mutation_p.L840P	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN	BPY2 interacting protein 1	866	Necessary for interaction with RASSF1 isoform A and isoform C.|Necessary for association with microtubules.				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding			central_nervous_system(1)	1						CGGAAGCCCCTGGCCCGCCCC	0.677													6	10	---	---	---	---	PASS
MAP1S	55201	broad.mit.edu	37	19	17838796	17838796	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17838796G>C	uc002nhe.1	+	5	2612	c.2603G>C	c.(2602-2604)CGC>CCC	p.R868P	MAP1S_uc010eba.1_Intron|MAP1S_uc002nhf.1_Missense_Mutation_p.R116P|MAP1S_uc010xpv.1_Missense_Mutation_p.R842P	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN	BPY2 interacting protein 1	868	Necessary for interaction with RASSF1 isoform A and isoform C.|Necessary for association with microtubules.				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding			central_nervous_system(1)	1						CCCCTGGCCCGCCCCAACTCA	0.677													4	8	---	---	---	---	PASS
KIAA0355	9710	broad.mit.edu	37	19	34791500	34791500	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34791500T>C	uc002nvd.3	+	2	981	c.122T>C	c.(121-123)CTG>CCG	p.L41P	KIAA0355_uc010edk.1_Missense_Mutation_p.L31P	NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710	41										ovary(1)	1	Esophageal squamous(110;0.162)					GGCCGAGCACTGAGTGCTCCC	0.637													21	68	---	---	---	---	PASS
KLK6	5653	broad.mit.edu	37	19	51466690	51466690	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51466690G>A	uc002pui.2	-	5	573	c.313C>T	c.(313-315)CAG>TAG	p.Q105*	KLK6_uc010eoj.2_Intron|KLK6_uc002puh.2_Nonsense_Mutation_p.Q114*|KLK6_uc002puj.2_5'UTR|KLK6_uc010ycn.1_5'UTR|KLK6_uc002pul.2_Nonsense_Mutation_p.Q105*|KLK6_uc002pum.2_5'UTR	NM_001012964	NP_001012982	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6 isoform A	105	Peptidase S1.				amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		ATGATGTCCTGGTCATGGCTG	0.597													12	52	---	---	---	---	PASS
ZNF175	7728	broad.mit.edu	37	19	52084648	52084648	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52084648C>T	uc002pxb.2	+	3	455	c.77C>T	c.(76-78)TCA>TTA	p.S26L		NM_007147	NP_009078	Q9Y473	ZN175_HUMAN	zinc finger protein 175	26					response to virus	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		TTACAGGCATCAGTGTCATTT	0.522													13	46	---	---	---	---	PASS
DNTTIP1	116092	broad.mit.edu	37	20	44439917	44439917	+	3'UTR	SNP	C	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44439917C>G	uc002xpk.2	+	13					UBE2C_uc002xpl.2_5'Flank|UBE2C_uc002xpm.2_5'Flank|UBE2C_uc002xpn.2_5'Flank|UBE2C_uc002xpo.2_5'Flank|UBE2C_uc002xpp.2_5'Flank|UBE2C_uc002xpq.2_5'Flank	NM_052951	NP_443183	Q9H147	TDIF1_HUMAN	terminal deoxynucleotidyltransferase interacting							nucleus				ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.0122)				GGGACTGCTCCTAGATGGATC	0.577													17	75	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47266546	47266546	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47266546C>G	uc002xtw.1	-	24	3039	c.3016G>C	c.(3016-3018)GAC>CAC	p.D1006H	PREX1_uc002xtv.1_Missense_Mutation_p.D303H	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1006					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TGCTCCGGGTCAAGGCCGATG	0.463													28	156	---	---	---	---	PASS
MOCS3	27304	broad.mit.edu	37	20	49576416	49576416	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49576416A>T	uc002xvy.1	+	1	1054	c.1037A>T	c.(1036-1038)GAT>GTT	p.D346V	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	346					enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			skin(2)|ovary(1)	3						CGACTGCTGGATTCTGGGGCA	0.542													271	343	---	---	---	---	PASS
MICAL3	57553	broad.mit.edu	37	22	18368682	18368682	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18368682C>A	uc002zng.3	-	16	2556	c.2203G>T	c.(2203-2205)GAG>TAG	p.E735*	MICAL3_uc011agl.1_Nonsense_Mutation_p.E735*|MICAL3_uc002znh.2_Nonsense_Mutation_p.E735*|MICAL3_uc002znj.1_Nonsense_Mutation_p.E435*|MICAL3_uc002znk.1_Nonsense_Mutation_p.E735*|MICAL3_uc002znl.1_Nonsense_Mutation_p.E368*|MICAL3_uc002znm.2_Nonsense_Mutation_p.E236*|MICAL3_uc010grf.2_Nonsense_Mutation_p.E735*	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin	735						cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		GGCGCATTCTCTTCAAATTTG	0.562													89	189	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	33700423	33700423	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33700423C>T	uc003and.3	-	13	2101	c.1522G>A	c.(1522-1524)GCC>ACC	p.A508T	LARGE_uc011amd.1_Missense_Mutation_p.A307T|LARGE_uc003ane.3_Missense_Mutation_p.A508T|LARGE_uc010gwp.2_Missense_Mutation_p.A456T|LARGE_uc011ame.1_Missense_Mutation_p.A440T|LARGE_uc011amf.1_Missense_Mutation_p.A508T	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	508	Lumenal (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				TGGGCCTCGGCGTCTGACAGG	0.637													14	58	---	---	---	---	PASS
RPL3	6122	broad.mit.edu	37	22	39712965	39712965	+	Intron	SNP	A	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39712965A>C	uc003axi.2	-						RPL3_uc003axh.2_Intron|RPL3_uc003axj.2_5'UTR|RPL3_uc010gxx.2_Intron|RPL3_uc003axg.2_Intron|RPL3_uc003axk.1_5'UTR	NM_000967	NP_000958	P39023	RL3_HUMAN	ribosomal protein L3 isoform a						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			breast(1)|kidney(1)	2	Melanoma(58;0.04)					CCGGCTTCTAAGGAGCCTTTT	0.612											OREG0026575	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	37	---	---	---	---	PASS
MEI1	150365	broad.mit.edu	37	22	42172238	42172238	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42172238C>A	uc003baz.1	+	21	2702	c.2677C>A	c.(2677-2679)CTG>ATG	p.L893M	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc011apd.1_RNA|MEI1_uc003bbb.1_Missense_Mutation_p.L279M|MEI1_uc003bbc.1_Missense_Mutation_p.L261M|MEI1_uc010gym.1_Missense_Mutation_p.L261M|MEI1_uc003bbd.1_Missense_Mutation_p.L136M|MEI1_uc010gyn.1_RNA|MEI1_uc003bbe.1_RNA	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1	893							binding			central_nervous_system(1)|skin(1)	2						CCTGCAGCGTCTGCTAGTGGA	0.557													39	76	---	---	---	---	PASS
SMC1B	27127	broad.mit.edu	37	22	45745648	45745648	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45745648A>C	uc003bgc.2	-	23	3508	c.3456T>G	c.(3454-3456)GAT>GAG	p.D1152E	SMC1B_uc003bgd.2_Intron	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	1152	Ala/Asp-rich (DA-box).				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CATCCACTTCATCTAAAACAA	0.338													12	49	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	9486	9486	+	RNA	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:9486T>C	uc011mfi.1	+	1		c.824T>C			uc004cov.3_5'Flank|uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		AAGTTTTTTTCTTCGCAGGAT	0.507													30	262	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11848	11848	+	RNA	SNP	C	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11848C>T	uc004cov.3	+	1		c.1271C>T			uc004cow.1_5'Flank|uc004cox.3_5'Flank|uc004coy.2_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		CTTCTAGCAAGCCTCGCTAAC	0.453													5	287	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	12772	12772	+	RNA	SNP	G	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:12772G>A	uc004cox.3	+	1		c.436G>A			uc004coy.2_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TCGGCTGAGAGGGCGTAGGAA	0.423													7	217	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13064	13064	+	RNA	SNP	T	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13064T>C	uc004cox.3	+	1		c.728T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCCCACCCCAGTCTCAGCCCT	0.542													296	38	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1600092	1600093	+	Intron	DEL	TG	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1600092_1600093delTG	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc009vkl.1_Intron|SLC35E2B_uc001ahe.3_Intron|SLC35E2B_uc001ahf.3_Intron|SLC35E2B_uc001ahg.3_Intron|SLC35E2B_uc001ahh.3_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						CTGTTTTTTTTGTTTGTTTGTT	0.317													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4204647	4204649	+	IGR	DEL	ACT	-	-	rs61768843		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4204647_4204649delACT								LOC100133612 (370770 upstream) : LOC284661 (267462 downstream)																							caccaccaccactaccacaccac	0.034													3	3	---	---	---	---	
UBE4B	10277	broad.mit.edu	37	1	10238756	10238758	+	In_Frame_Del	DEL	GGG	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10238756_10238758delGGG	uc001aqs.3	+	26	4293_4295	c.3580_3582delGGG	c.(3580-3582)GGGdel	p.G1194del	UBE4B_uc001aqr.3_In_Frame_Del_p.G1065del|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_In_Frame_Del_p.G649del|UBE4B_uc001aqu.2_In_Frame_Del_p.G75del	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	1194					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding	p.G1065G(1)		ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GCGGAAGGCAGGGATCAAATCCA	0.453													56	25	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	53808181	53808182	+	IGR	DEL	GT	-	-	rs12067664		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53808181_53808182delGT								LRP8 (14360 upstream) : FLJ40434 (95862 downstream)																							TATGCTATGAgtgtgtgtgtgt	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	67255893	67255894	+	IGR	INS	-	GC	GC	rs57482302		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67255893_67255894insGC								TCTEX1D1 (11164 upstream) : INSL5 (7531 downstream)																							cacacacacacaaaacaacaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100088781	100088782	+	IGR	DEL	AA	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100088781_100088782delAA								LPPR4 (313645 upstream) : PALMD (22649 downstream)																							accctgttgcaaaaaaaaaaaa	0.050													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148855788	148855788	+	IGR	DEL	G	-	-	rs56347163		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148855788delG								NBPF16 (97477 upstream) : LOC645166 (72498 downstream)																							ccgcggcggcggggggggcgg	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181264329	181264330	+	IGR	DEL	GT	-	-	rs6701266		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181264329_181264330delGT								IER5 (204352 upstream) : CACNA1E (188386 downstream)																							gtgtgcgcgcgtgcacgcgtgc	0.094													4	2	---	---	---	---	
IPO9	55705	broad.mit.edu	37	1	201841735	201841737	+	Intron	DEL	AAC	-	-	rs35521088		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201841735_201841737delAAC	uc001gwz.2	+							NM_018085	NP_060555	Q96P70	IPO9_HUMAN	importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2						ctatctcaaaaacaacaacaaca	0.138													4	2	---	---	---	---	
KDM5B	10765	broad.mit.edu	37	1	202701185	202701186	+	Intron	DEL	AC	-	-	rs71817590	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202701185_202701186delAC	uc001gyf.2	-						KDM5B_uc009xag.2_Intron|KDM5B_uc001gyg.1_Intron	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B						negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						AAAAAAAAAAACAACTTGATTT	0.371													2	4	---	---	---	---	
LAX1	54900	broad.mit.edu	37	1	203742885	203742891	+	Intron	DEL	TTTTTTT	-	-	rs10714327		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203742885_203742891delTTTTTTT	uc001haa.2	+						LAX1_uc010pql.1_Intron|LAX1_uc001hab.2_Intron	NM_017773	NP_060243	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1 isoform a						B cell activation|immune response|inactivation of MAPK activity|intracellular signal transduction|negative regulation of T cell activation	Golgi apparatus|integral to membrane|plasma membrane	protein kinase binding|SH2 domain binding			central_nervous_system(2)	2	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GTTGCTCttcttttttttttttttttt	0.367													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203873270	203873270	+	IGR	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203873270delA								SNRPE (32992 upstream) : C1orf157 (128305 downstream)																							tctttttgttaaaaaaaaaaa	0.075													4	2	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205036040	205036041	+	Intron	INS	-	G	G	rs151113569	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205036040_205036041insG	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron|CNTN2_uc001hbs.2_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CACACAGCATTGCAGAGGCACC	0.317													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	205437150	205437151	+	RNA	INS	-	GTGT	GTGT	rs147610079	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205437150_205437151insGTGT	uc001hco.1	+	3		c.1754_1755insGTGT								Homo sapiens cDNA FLJ38314 fis, clone FCBBF3022765.																		GGGAAAGAGGAgtgtgtgtgtg	0.287													3	4	---	---	---	---	
C1orf31	388753	broad.mit.edu	37	1	234519320	234519321	+	Intron	DEL	AC	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234519320_234519321delAC	uc001hwc.2	+						C1orf31_uc001hwb.2_Intron	NM_001012985	NP_001013003	Q5JTJ3	CA031_HUMAN	hypothetical protein LOC388753							mitochondrion	cytochrome-c oxidase activity				0	Ovarian(103;0.0339)	all_cancers(173;0.241)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			GTTACAGCTGacacacacacac	0.124													4	2	---	---	---	---	
GKN2	200504	broad.mit.edu	37	2	69179711	69179711	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69179711delT	uc002sfa.2	-						GKN2_uc002sfb.3_Intron	NM_182536	NP_872342	Q86XP6	GKN2_HUMAN	trefoil factor interactions(z) 1 precursor							extracellular region					0						TAAAGGATTATTATTAAACAT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73583886	73583893	+	IGR	DEL	AAGGAAGG	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73583886_73583893delAAGGAAGG								EGR4 (63057 upstream) : ALMS1 (28993 downstream)																							aaaagaaagaaaggaaggaaggaaggaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73956941	73956941	+	IGR	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73956941delT								NAT8B (28474 upstream) : TPRKB (16 downstream)																							gtgcctggccTTTTTTTTTTT	0.109													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88565001	88565002	+	IGR	DEL	GT	-	-	rs66578201		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88565001_88565002delGT								THNSL2 (78856 upstream) : FOXI3 (182724 downstream)																							ACCAAGCTCCgtgtgtgtgtgt	0.198													3	3	---	---	---	---	
LOC541471	541471	broad.mit.edu	37	2	112009045	112009064	+	Intron	DEL	TGCGATCATCGTCACCTCAT	-	-	rs56084934		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112009045_112009064delTGCGATCATCGTCACCTCAT	uc002the.2	-											Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0						ccaccaccactgcgatcatcgtcacctcatcaccaccatc	0.127													4	3	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197090717	197090717	+	Intron	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197090717delA	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						ATTGCCTACTAGGTAGTGAGA	0.323													4	3	---	---	---	---	
FAM117B	150864	broad.mit.edu	37	2	203526872	203526873	+	Intron	DEL	TG	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203526872_203526873delTG	uc010zhx.1	+						FAM117B_uc010zhw.1_Intron	NM_173511	NP_775782	Q6P1L5	F117B_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)											ovary(1)	1						tatgtgtgtatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
CYP20A1	57404	broad.mit.edu	37	2	204137273	204137274	+	Intron	INS	-	A	A	rs72103565		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204137273_204137274insA	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	NM_177538	NP_803882	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0						aaccctgactcaaaaaaaaaaa	0.104													4	2	---	---	---	---	
USP37	57695	broad.mit.edu	37	2	219324314	219324317	+	Intron	DEL	TTTG	-	-	rs11890042		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219324314_219324317delTTTG	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron	NM_020935	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37						ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TCCTGTTTTTTTTGTTTGTTTGTT	0.294													2	4	---	---	---	---	
ZFAND2B	130617	broad.mit.edu	37	2	220071889	220071889	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220071889delT	uc002vka.2	+						ZFAND2B_uc010zkt.1_Intron|ZFAND2B_uc010fwd.1_Intron|ZFAND2B_uc002vjy.1_Intron|ZFAND2B_uc002vjz.1_Intron|ZFAND2B_uc002vkb.1_5'Flank	NM_138802	NP_620157	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B							endoplasmic reticulum	protein binding|zinc ion binding				0		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGGGGGGGGGTGGTCAGCGGC	0.627													4	3	---	---	---	---	
AGFG1	3267	broad.mit.edu	37	2	228418211	228418212	+	Intron	INS	-	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228418211_228418212insA	uc002vpc.2	+						AGFG1_uc002vpd.2_Intron|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495	P52594	AGFG1_HUMAN	HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4						gatcatgtctcaaaaaaaaaaa	0.134													4	4	---	---	---	---	
GRM7	2917	broad.mit.edu	37	3	7456573	7456574	+	Intron	INS	-	T	T	rs79755836		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7456573_7456574insT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)	CCTTCTGTTAATTTTTTTTTTT	0.203													4	2	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10116600	10116601	+	Intron	INS	-	TAC	TAC	rs144258025	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10116600_10116601insTAC	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TACATTTAGGTtactactacta	0.213			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				3	4	---	---	---	---	
ABHD14B	84836	broad.mit.edu	37	3	52003893	52003894	+	Intron	DEL	GA	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52003893_52003894delGA	uc003dcm.2	-						PCBP4_uc003dch.1_5'Flank|PCBP4_uc003dci.1_5'Flank|PCBP4_uc003dcj.1_5'Flank|PCBP4_uc003dck.1_5'Flank|ABHD14B_uc010hly.2_Intron|ABHD14B_uc011bdy.1_Intron|ABHD14B_uc003dcn.2_Intron|ABHD14B_uc011bdz.1_Frame_Shift_Del_p.F173fs	NM_032750	NP_116139	Q96IU4	ABHEB_HUMAN	abhydrolase domain containing 14B							cytoplasm|nucleus	hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000548)|KIRC - Kidney renal clear cell carcinoma(197;0.00072)		CCCAGATGAGGAAAGCCCAGGG	0.554													47	30	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	142895155	142895155	+	IGR	DEL	C	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142895155delC								CHST2 (53345 upstream) : SLC9A9 (88910 downstream)																							GGCCTCAGGGCCCCCCCCCAG	0.746													4	3	---	---	---	---	
NMD3	51068	broad.mit.edu	37	3	160953121	160953121	+	Intron	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160953121delA	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			ttctgttaggaaaaaaaaaaa	0.075													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	172434336	172434337	+	IGR	INS	-	TGTG	TGTG	rs151086518	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172434336_172434337insTGTG								NCEH1 (5328 upstream) : ECT2 (34195 downstream)																							gagacagaagctgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6005550	6005552	+	IGR	DEL	TGA	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6005550_6005552delTGA								C4orf50 (15384 upstream) : JAKMIP1 (22374 downstream)																							gtgatgatggtgatggtgatgat	0.000													4	2	---	---	---	---	
SPINK2	6691	broad.mit.edu	37	4	57678103	57678103	+	Intron	DEL	C	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57678103delC	uc003hcg.1	-							NM_021114	NP_066937	P20155	ISK2_HUMAN	serine protease inhibitor, Kazal type 2							extracellular region	serine-type endopeptidase inhibitor activity				0	Glioma(25;0.08)|all_neural(26;0.181)					AAAAttttttctttttttttt	0.129													3	3	---	---	---	---	
SCARB2	950	broad.mit.edu	37	4	77102448	77102449	+	Intron	DEL	AG	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77102448_77102449delAG	uc003hju.1	-						SCARB2_uc011cbu.1_Intron	NM_005506	NP_005497	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2						cell adhesion|protein targeting to lysosome	integral to plasma membrane|lysosomal lumen|lysosomal membrane|membrane fraction	enzyme binding|receptor activity				0			Lung(101;0.196)			GGCCTAGGATAGAGTCTTCTCA	0.416													5	3	---	---	---	---	
MAP9	79884	broad.mit.edu	37	4	156274607	156274609	+	Intron	DEL	ATT	-	-	rs33994283		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156274607_156274609delATT	uc003ios.2	-						MAP9_uc011cin.1_Intron|MAP9_uc010iqa.1_Intron|MAP9_uc003iot.1_Intron	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein						cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TCTGATATTCATTATACTTAGAA	0.167													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163961448	163961448	+	IGR	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163961448delA								FSTL5 (876262 upstream) : NAF1 (86412 downstream)																							aagggaagggaaaggaaggag	0.000													4	2	---	---	---	---	
KIAA1712	80817	broad.mit.edu	37	4	175238739	175238739	+	3'UTR	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175238739delT	uc003itr.2	+	12					KIAA1712_uc010iro.2_Intron|KIAA1712_uc003its.2_RNA	NM_001040157	NP_001035247	Q9C0F1	CEP44_HUMAN	HBV PreS1-transactivated protein 3 isoform a							centrosome|midbody|spindle pole					0		Prostate(90;0.00276)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;4.06e-18)|Epithelial(43;1.18e-15)|OV - Ovarian serous cystadenocarcinoma(60;4.65e-09)|GBM - Glioblastoma multiforme(59;0.00098)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0949)		CTTGTGTCACTTTTTTTTTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188317989	188317990	+	IGR	DEL	AC	-	-	rs34146311		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188317989_188317990delAC								FAT1 (670139 upstream) : ZFP42 (598935 downstream)																							ATATGTGTATacacacacacac	0.272													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190301050	190301067	+	IGR	DEL	ACACACACACCTGCAAGC	-	-	rs146941846		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190301050_190301067delACACACACACCTGCAAGC								None (None upstream) : FRG1 (560907 downstream)																							gcaccagcaaacacacacacctgcaagcacacacacac	0.050													3	3	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5305440	5305441	+	Intron	INS	-	C	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5305440_5305441insC	uc003jdl.2	+							NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						cacacacacatccacaccacac	0.000													4	2	---	---	---	---	
RAB3C	115827	broad.mit.edu	37	5	57911813	57911814	+	Intron	DEL	AC	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57911813_57911814delAC	uc003jrp.2	+							NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		acacacacagacacacacacac	0.322													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166832775	166832776	+	Intron	DEL	AC	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166832775_166832776delAC	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		acacacacaaacacacacacac	0.302													4	4	---	---	---	---	
ZNF354B	117608	broad.mit.edu	37	5	178293700	178293702	+	Intron	DEL	CTT	-	-	rs139238783		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178293700_178293702delCTT	uc003mjl.2	+						ZNF354B_uc003mjm.2_Intron	NM_058230	NP_478137	Q96LW1	Z354B_HUMAN	zinc finger protein 354B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTACCTCATCCTTCTTCATCGAC	0.419													2	4	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34078892	34078897	+	Intron	DEL	ACACAC	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34078892_34078897delACACAC	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc010jvk.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	caggccacatacacacacacacacac	0.432													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57531985	57531986	+	IGR	INS	-	ACA	ACA	rs142123826	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57531985_57531986insACA								PRIM2 (18610 upstream) : GUSBL2 (714173 downstream)																							caccaggaggcacaacaattcc	0.000													4	2	---	---	---	---	
ORC3L	23595	broad.mit.edu	37	6	88321663	88321663	+	Intron	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88321663delA	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)		AAAGACTTAGAAAATTTTAGT	0.199													5	4	---	---	---	---	
PREP	5550	broad.mit.edu	37	6	105729419	105729419	+	Intron	DEL	C	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105729419delC	uc003prc.2	-							NM_002726	NP_002717	P48147	PPCE_HUMAN	prolyl endopeptidase						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	ttctgccctaccacaTTTTTT	0.169													4	2	---	---	---	---	
NCOA7	135112	broad.mit.edu	37	6	126215915	126215915	+	Intron	DEL	T	-	-	rs111496290		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126215915delT	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		caagctgtacttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	143291237	143291238	+	Intron	INS	-	CA	CA	rs139185363	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143291237_143291238insCA	uc003qje.1	-											Homo sapiens cDNA FLJ32928 fis, clone TESTI2007405.																		acacacacacgcacacacagaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157054433	157054434	+	IGR	DEL	TG	-	-	rs111854004		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157054433_157054434delTG								MIR1202 (786420 upstream) : ARID1B (44652 downstream)																							CTTTCTTCTTtgtgtgtgtgtg	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21144860	21144863	+	IGR	DEL	TGTT	-	-	rs72213360	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21144860_21144863delTGTT								RPL23P8 (277421 upstream) : SP4 (322826 downstream)																							tgtgtgtgtgtgtttgtgtgtgtg	0.309													4	2	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28388028	28388029	+	Intron	DEL	CA	-	-	rs66561710	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28388028_28388029delCA	uc003szo.2	+							NM_182899	NP_878902	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						ctctctctctcacacacacaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95729963	95729964	+	IGR	DEL	TG	-	-	rs13229900		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95729963_95729964delTG								DYNC1I1 (2228 upstream) : SLC25A13 (19569 downstream)																							ttgagggttttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108645600	108645601	+	IGR	INS	-	GT	GT	rs141029318	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108645600_108645601insGT								C7orf66 (120963 upstream) : EIF3IP1 (953683 downstream)																							ATAGCAAAGGAgtgtgtgtgtg	0.287													4	2	---	---	---	---	
FOXP2	93986	broad.mit.edu	37	7	114330185	114330185	+	3'UTR	DEL	T	-	-	rs143759073		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114330185delT	uc003vhb.2	+	17					FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_3'UTR|FOXP2_uc003vha.2_3'UTR|FOXP2_uc011kmu.1_3'UTR|FOXP2_uc011kmv.1_3'UTR|FOXP2_uc010ljz.1_3'UTR	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						cttcttcttcttttttttttt	0.289													4	2	---	---	---	---	
RBM28	55131	broad.mit.edu	37	7	127976817	127976817	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127976817delT	uc003vmp.2	-						RBM28_uc003vmo.2_5'Flank|RBM28_uc011koj.1_Intron|RBM28_uc011kok.1_Intron	NM_018077	NP_060547	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28						mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2						TCTCTTACACtttttttttga	0.209													4	2	---	---	---	---	
RBM33	155435	broad.mit.edu	37	7	155537474	155537475	+	Intron	INS	-	TT	TT	rs141889195	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155537474_155537475insTT	uc010lqk.1	+						RBM33_uc011kvv.1_Intron|RBM33_uc003wmg.2_5'Flank	NM_053043	NP_444271	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		TAGCTGTGTGGTTTTTTTCCCC	0.312													2	4	---	---	---	---	
UBXN2B	137886	broad.mit.edu	37	8	59329546	59329547	+	Intron	INS	-	TA	TA			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59329546_59329547insTA	uc003xtl.2	+							NM_001077619	NP_001071087	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B							cytosol|endoplasmic reticulum|Golgi apparatus|nucleus				ovary(2)	2						TAAAAAGAAATTATAATCCTTT	0.312													26	20	---	---	---	---	
LRRCC1	85444	broad.mit.edu	37	8	86042301	86042301	+	Intron	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86042301delA	uc003ycw.2	+						LRRCC1_uc010lzz.1_Intron|LRRCC1_uc010maa.1_Intron|LRRCC1_uc003ycx.2_Intron|LRRCC1_uc003ycy.2_Intron	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a						cell division|mitosis	centriole|nucleus					0						CAGGTAAATGAAAAATGTATC	0.299													101	67	---	---	---	---	
ATP6V0D2	245972	broad.mit.edu	37	8	87151457	87151457	+	Intron	DEL	A	-	-	rs35331724		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87151457delA	uc003ydp.1	+							NM_152565	NP_689778	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0						acttggtctcaaaaaaaaaaa	0.129													3	3	---	---	---	---	
SPAG1	6674	broad.mit.edu	37	8	101252794	101252795	+	Frame_Shift_Del	DEL	CT	-	-	rs4734455		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101252794_101252795delCT	uc003yjh.1	+	18	2530_2531	c.2444_2445delCT	c.(2443-2445)GCTfs	p.A815fs	SPAG1_uc003yji.1_Frame_Shift_Del_p.A815fs	NM_172218	NP_757367	Q07617	SPAG1_HUMAN	sperm associated antigen 1	815					single fertilization	cytoplasm	GTP binding|hydrolase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		ATTATAAATGCTCTCAGTACCA	0.426													89	56	---	---	---	---	
UBR5	51366	broad.mit.edu	37	8	103289611	103289611	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103289611delT	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			AGATAACTACttttttttttt	0.224													6	3	---	---	---	---	
BAALC	79870	broad.mit.edu	37	8	104162580	104162581	+	Intron	DEL	TC	-	-	rs34233321		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104162580_104162581delTC	uc003yld.2	+						BAALC_uc003yle.2_Intron	NM_024812	NP_079088	Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic isoform 1							centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			tgtgtgtgtgtctgtgtgtctg	0.000													3	3	---	---	---	---	
MTBP	27085	broad.mit.edu	37	8	121530792	121530792	+	Intron	DEL	T	-	-	rs34427476		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121530792delT	uc003ypc.1	+							NM_022045	NP_071328	Q96DY7	MTBP_HUMAN	Mdm2, transformed 3T3 cell double minute 2, p53						cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			ATGTTAGATCTTTTTTTTCTC	0.323													5	9	---	---	---	---	
EFR3A	23167	broad.mit.edu	37	8	132998636	132998644	+	Intron	DEL	TCATTTAAT	-	-	rs72073007		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132998636_132998644delTCATTTAAT	uc003yte.2	+							NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A							plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTTGTGTCTGTCATTTAATTCATTTAATT	0.297													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135375783	135375790	+	IGR	DEL	GTGTGTGT	-	-	rs36156813		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135375783_135375790delGTGTGTGT								ST3GAL1 (791600 upstream) : ZFAT (114243 downstream)																							TTTGCTCtgcgtgtgtgtgtgtgtgtgt	0.317													3	3	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143337221	143337221	+	Intron	DEL	C	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143337221delC	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					accaccatcaccatcaccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66460838	66460838	+	5'Flank	DEL	T	-	-	rs113014075		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66460838delT	uc004aeb.2	-						uc004aec.2_Intron					Homo sapiens cDNA clone IMAGE:3941306, partial cds.																		ccaccttgagttgatttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68403480	68403481	+	IGR	DEL	CA	-	-	rs4284135	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68403480_68403481delCA								FAM27B (609291 upstream) : MIR1299 (598758 downstream)																							agtgtgtgtgcatgtgtgtgcc	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68420364	68420366	+	IGR	DEL	ATA	-	-	rs67838644		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68420364_68420366delATA								FAM27B (626175 upstream) : MIR1299 (581873 downstream)																							TTCTATGCATATAATTCATATAA	0.281													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430364	68430365	+	IGR	INS	-	A	A	rs140332329		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430364_68430365insA								FAM27B (636175 upstream) : MIR1299 (571874 downstream)																							TTATGCAGAAGAAAAAATTAAC	0.322													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69511231	69511232	+	IGR	INS	-	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69511231_69511232insT								ANKRD20A4 (86123 upstream) : LOC100133920 (140129 downstream)																							GTGTTTTCATCTTTTTTTTTTT	0.535													6	3	---	---	---	---	
TBC1D2	55357	broad.mit.edu	37	9	100975615	100975615	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100975615delT	uc011lvb.1	-						TBC1D2_uc004ayp.2_5'UTR|TBC1D2_uc004ayq.2_Intron|TBC1D2_uc004ayr.2_Intron|TBC1D2_uc004ayo.3_Intron	NM_018421	NP_060891	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2							cell junction|cytoplasmic membrane-bounded vesicle|nucleus	Rab GTPase activator activity			ovary(3)	3		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		TTTCCAATAATGGCAACAGAA	0.383													9	5	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111784100	111784100	+	Intron	DEL	A	-	-	rs72758402	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111784100delA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		CCACCCCCCCAAAAAAAGCAa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6043198	6043199	+	IGR	INS	-	TG	TG	rs56093144		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6043198_6043199insTG								IL15RA (23056 upstream) : IL2RA (10307 downstream)																							GAAGGAGACCAtgtgtgtgtgt	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42672240	42672241	+	IGR	INS	-	TAAG	TAAG	rs71529068		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42672240_42672241insTAAG								None (None upstream) : LOC441666 (155074 downstream)																							TGGCACATATTTTTGTTACCTC	0.366													5	7	---	---	---	---	
IPMK	253430	broad.mit.edu	37	10	59959205	59959206	+	Intron	INS	-	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59959205_59959206insA	uc001jkb.2	-							NM_152230	NP_689416	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase							nucleus	ATP binding|inositol trisphosphate 6-kinase activity			ovary(1)	1						gatttgagaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61444172	61444172	+	Intron	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61444172delA	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						TCCTAAAGTGAAAAAAAAAAA	0.323													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86535365	86535366	+	IGR	INS	-	T	T	rs72828679		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86535365_86535366insT								FAM190B (257089 upstream) : GRID1 (823946 downstream)																							ttttctttttcttttttttttt	0.000													7	4	---	---	---	---	
FAM53B	9679	broad.mit.edu	37	10	126445736	126445737	+	Intron	DEL	CA	-	-	rs140005609		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126445736_126445737delCA	uc001lhu.1	-							NM_014661	NP_055476	Q14153	FA53B_HUMAN	hypothetical protein LOC9679											ovary(1)|pancreas(1)	2		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		CACTCCCTCCcacacacacaca	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	11268701	11268702	+	IGR	DEL	TC	-	-	rs61874576	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11268701_11268702delTC								ZBED5 (389081 upstream) : GALNTL4 (23719 downstream)																							tctccgtgtgtctctctctctc	0.144													4	2	---	---	---	---	
E2F8	79733	broad.mit.edu	37	11	19255692	19255693	+	Intron	INS	-	A	A	rs76020624		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19255692_19255693insA	uc001mpm.2	-						E2F8_uc009yhv.2_Intron|E2F8_uc001mpn.3_Intron	NM_024680	NP_078956	A0AVK6	E2F8_HUMAN	E2F family member 8						cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1						agactccgtctaaaaaaaaaaa	0.119													7	4	---	---	---	---	
HTR3A	3359	broad.mit.edu	37	11	113856419	113856420	+	Intron	DEL	GT	-	-	rs72026178		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113856419_113856420delGT	uc010rxb.1	+						HTR3A_uc010rxa.1_Intron|HTR3A_uc009yyx.2_Intron|HTR3A_uc010rxc.1_Intron	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A						digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)	TTTGGAAGGGgtgtgtgtgtgt	0.228													4	2	---	---	---	---	
NINJ2	4815	broad.mit.edu	37	12	690344	690345	+	Intron	DEL	TG	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:690344_690345delTG	uc001qil.2	-						NINJ2_uc010sdr.1_Intron|NINJ2_uc010sds.1_Intron	NM_016533	NP_057617	Q9NZG7	NINJ2_HUMAN	ninjurin 2						nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane				ovary(2)	2	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)			tgtgtgtgtctgtgtgtgtgtc	0.178													4	2	---	---	---	---	
BICD1	636	broad.mit.edu	37	12	32520417	32520417	+	Intron	DEL	A	-	-	rs63514564		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32520417delA	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			TGTATTTAAGAAAAAAAAAAA	0.303													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48661155	48661166	+	IGR	DEL	CTTCCTTCCTTT	-	-	rs12810981	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48661155_48661166delCTTCCTTCCTTT								OR10AD1 (64080 upstream) : H1FNT (61597 downstream)																							tccttccttccttccttcctttcttccttcct	0.094													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54620593	54620594	+	IGR	INS	-	AA	AA	rs1486339	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54620593_54620594insAA								SMUG1 (37836 upstream) : CBX5 (4138 downstream)																							cacacacacacaATAAGAATTG	0.322													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68079608	68079611	+	IGR	DEL	TGTG	-	-	rs3046037		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68079608_68079611delTGTG								DYRK2 (23165 upstream) : IFNG (468939 downstream)																							cctggctaattgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
CPM	1368	broad.mit.edu	37	12	69252514	69252514	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69252514delT	uc001sup.2	-						CPM_uc001sur.2_Intron|CPM_uc001suq.2_Intron	NM_198320	NP_938079	P14384	CBPM_HUMAN	carboxypeptidase M precursor						anatomical structure morphogenesis|proteolysis	anchored to membrane|cytoplasm|nucleus|plasma membrane	metallocarboxypeptidase activity|zinc ion binding				0	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			ATTTTTGTGGTTTTTTTTTTT	0.323													7	5	---	---	---	---	
PAH	5053	broad.mit.edu	37	12	103248748	103248749	+	Intron	INS	-	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103248748_103248749insA	uc001tjq.1	-						PAH_uc010swc.1_3'UTR	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase						catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GGAGGGAAGGCAGAGCACAGTG	0.450													8	5	---	---	---	---	
C12orf42	374470	broad.mit.edu	37	12	103644653	103644654	+	Intron	DEL	TG	-	-	rs34339282		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103644653_103644654delTG	uc001tjs.2	-									Q96LP6	CL042_HUMAN	Homo sapiens cDNA FLJ25323 fis, clone TST00323.											ovary(1)|central_nervous_system(1)	2						CTTTTATCACtgtgtgtgtgtg	0.322													4	3	---	---	---	---	
GLT8D2	83468	broad.mit.edu	37	12	104409171	104409172	+	Intron	INS	-	ACAC	ACAC	rs141368200		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104409171_104409172insACAC	uc001tkh.1	-						GLT8D2_uc001tki.1_Intron	NM_031302	NP_112592	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2							integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)|skin(1)	2						aacaacaacaaacacacacaca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110072327	110072328	+	IGR	INS	-	ACC	ACC	rs147833484	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110072327_110072328insACC								MVK (37257 upstream) : C12orf34 (79862 downstream)																							ccaccaccactaccaccaccac	0.020													9	4	---	---	---	---	
CCDC63	160762	broad.mit.edu	37	12	111318577	111318578	+	Intron	INS	-	CTG	CTG			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111318577_111318578insCTG	uc001trv.1	+						CCDC63_uc009zvt.1_Intron|CCDC63_uc010sye.1_Intron|CCDC63_uc001trw.1_Intron	NM_152591	NP_689804	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63											skin(6)|ovary(1)|pancreas(1)	8						agtggtgataatgatgatggtg	0.000													4	2	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111775846	111775846	+	Intron	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111775846delA	uc001tsa.1	+							NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						tcaaaaaaagaaaaaaaaaaa	0.249													6	3	---	---	---	---	
SLC24A6	80024	broad.mit.edu	37	12	113747852	113747852	+	Intron	DEL	A	-	-	rs11297438		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113747852delA	uc001tvc.2	-						SLC24A6_uc001tuz.2_Intron|SLC24A6_uc001tva.2_Intron|SLC24A6_uc001tvb.2_Intron	NM_024959	NP_079235	Q6J4K2	NCKX6_HUMAN	solute carrier family 24 member 6 precursor						response to stimulus|sodium ion transport	integral to membrane|plasma membrane	calcium:cation antiporter activity			central_nervous_system(1)	1						agctattaccaaaaaAAAAAA	0.174													4	2	---	---	---	---	
FBXO21	23014	broad.mit.edu	37	12	117588762	117588765	+	Intron	DEL	TGTG	-	-	rs72424045		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117588762_117588765delTGTG	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_Intron	NM_033624	NP_296373	O94952	FBX21_HUMAN	F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		CAAATAAGTTtgtgtgtgtgtgtg	0.299											OREG0022165	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117646197	117646198	+	IGR	DEL	GT	-	-	rs66886445		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117646197_117646198delGT								FBXO21 (17897 upstream) : NOS1 (4781 downstream)																							TTCTGACAGCgtgtgtgtgtgt	0.520													5	3	---	---	---	---	
CAMKK2	10645	broad.mit.edu	37	12	121690305	121690306	+	Intron	INS	-	CTGGTGATCCGC	CTGGTGATCCGC	rs146470009	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121690305_121690306insCTGGTGATCCGC	uc001tzu.2	-						CAMKK2_uc001tzt.2_Intron|CAMKK2_uc001tzv.2_Intron|CAMKK2_uc001tzw.2_Intron|CAMKK2_uc001tzx.2_Intron|CAMKK2_uc001tzy.2_Intron|CAMKK2_uc001tzz.1_Intron|CAMKK2_uc001uaa.1_Intron|CAMKK2_uc001uab.2_Intron|CAMKK2_uc001uac.2_Intron	NM_006549	NP_006540	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase						calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity	cytoplasm	ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity			lung(1)|large_intestine(1)|stomach(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					actcctaacctctgcctcagcc	0.084													7	5	---	---	---	---	
CLIP1	6249	broad.mit.edu	37	12	122821509	122821510	+	Intron	INS	-	T	T	rs35632864		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122821509_122821510insT	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_Intron	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CTATTTTTGTGttttttttttt	0.144													3	4	---	---	---	---	
SLC15A4	121260	broad.mit.edu	37	12	129285429	129285430	+	Frame_Shift_Ins	INS	-	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129285429_129285430insA	uc001uhu.2	-	6	1436_1437	c.1383_1384insT	c.(1381-1386)ATTGGGfs	p.I461fs	SLC15A4_uc001uhv.2_RNA	NM_145648	NP_663623	Q8N697	S15A4_HUMAN	solute carrier family 15, member 4	461_462	Helical; (Potential).				oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		TCGCTGATCCCAATCAGCAAGT	0.540													95	51	---	---	---	---	
OR7E37P	26636	broad.mit.edu	37	13	42005884	42005885	+	RNA	INS	-	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42005884_42005885insA	uc001uyg.1	-	1		c.256_257insT				NR_002163				Homo sapiens olfactory receptor, family 7, subfamily E, member 37 pseudogene (OR7E37P), non-coding RNA.												0						ACTGAGGACAGAAAAAAAAAAG	0.436													4	2	---	---	---	---	
KIAA0317	9870	broad.mit.edu	37	14	75137987	75137987	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75137987delT	uc001xqb.2	-						KIAA0317_uc010tut.1_Intron|KIAA0317_uc001xqc.2_Intron	NM_001039479	NP_001034568	O15033	K0317_HUMAN	hypothetical protein LOC9870						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)		AAAACCTAGGTTTTTTTTTTT	0.388													4	2	---	---	---	---	
APBA2	321	broad.mit.edu	37	15	29142328	29142329	+	Intron	INS	-	AC	AC			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29142328_29142329insAC	uc010uat.1	+						APBA2_uc010azj.2_Intron|APBA2_uc010uas.1_Intron	NM_001130414	NP_001123886	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		caaaagacacgacacacacaca	0.069													2	4	---	---	---	---	
EIF2AK4	440275	broad.mit.edu	37	15	40235776	40235777	+	Intron	INS	-	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40235776_40235777insT	uc001zkm.1	+						EIF2AK4_uc001zkl.2_Intron	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha						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)		TTTGTGTTTTATTGGTTCTACA	0.312													30	16	---	---	---	---	
WDR72	256764	broad.mit.edu	37	15	54004802	54004803	+	Intron	INS	-	A	A	rs112182674		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54004802_54004803insA	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		ACCCCACCGCCAAAAAAAAAAA	0.188													4	3	---	---	---	---	
AAGAB	79719	broad.mit.edu	37	15	67496224	67496224	+	Intron	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67496224delT	uc002aqk.3	-						AAGAB_uc002aql.2_Intron|AAGAB_uc010uju.1_Intron	NM_024666	NP_078942	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0						CCCCAGGGAATTTTTTTTTTT	0.363													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	80907910	80907911	+	IGR	DEL	TA	-	-	rs145244983		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80907910_80907911delTA								ARNT2 (17638 upstream) : FAM108C1 (79741 downstream)																							ggggagtgtgtatggtgtgtgt	0.074													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11911165	11911166	+	IGR	DEL	GA	-	-	rs56913169		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11911165_11911166delGA								ZC3H7A (20077 upstream) : BCAR4 (2528 downstream)																							acaaaaAAACGacacacacaca	0.059													3	4	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12662161	12662162	+	Intron	INS	-	A	A	rs71388727	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12662161_12662162insA	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GGAGTGCTGTTAAAAAAAAAAA	0.450													6	4	---	---	---	---	
XPO6	23214	broad.mit.edu	37	16	28167920	28167921	+	Intron	INS	-	AA	AA	rs150507094	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28167920_28167921insAA	uc002dpa.1	-						XPO6_uc002dpb.1_Intron|XPO6_uc010vcp.1_Intron	NM_015171	NP_055986	Q96QU8	XPO6_HUMAN	exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2						AATTCTCCTTCAAAAAAatata	0.252													6	6	---	---	---	---	
TGFB1I1	7041	broad.mit.edu	37	16	31488980	31488981	+	3'UTR	INS	-	A	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31488980_31488981insA	uc002ecd.1	+	11					TGFB1I1_uc002ece.1_3'UTR|TGFB1I1_uc010caq.1_3'UTR	NM_001042454	NP_001035919	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced						androgen receptor signaling pathway|cell adhesion|negative regulation of cell proliferation|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|positive regulation of transforming growth factor beta receptor signaling pathway|transcription from RNA polymerase II promoter|ubiquitin-dependent SMAD protein catabolic process|Wnt receptor signaling pathway	cytoplasm|cytoskeleton|focal adhesion|nuclear matrix	androgen receptor binding|I-SMAD binding|Roundabout binding|transcription coactivator activity|zinc ion binding				0						GCCTTGCTCTCAGAGCGGGAGG	0.673													8	7	---	---	---	---	
GPT2	84706	broad.mit.edu	37	16	46933199	46933199	+	Intron	DEL	C	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46933199delC	uc002eel.2	+						GPT2_uc002eem.2_Intron	NM_133443	NP_597700	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase 2 isoform 1						2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	tttcctgcctcaacctccTGA	0.244													4	2	---	---	---	---	
PLD2	5338	broad.mit.edu	37	17	4725787	4725788	+	Intron	INS	-	A	A	rs138872940		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4725787_4725788insA	uc002fzc.2	+						PLD2_uc002fzd.2_Intron	NM_002663	NP_002654	O14939	PLD2_HUMAN	phospholipase D2						cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5					Choline(DB00122)	aactccgtctcaaaaaaaaaaa	0.218													3	3	---	---	---	---	
SREBF1	6720	broad.mit.edu	37	17	17740165	17740165	+	5'UTR	DEL	C	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17740165delC	uc002gru.1	-	1					SREBF1_uc002grt.1_5'UTR|SREBF1_uc010cpq.1_5'UTR	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription						cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1						GCCCGCCGGGCCCGCCGCCTC	0.766													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	40189397	40189404	+	IGR	DEL	ACACACAC	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40189397_40189404delACACACAC								NKIRAS2 (11743 upstream) : DHX58 (64018 downstream)																							GGCACAGGTTacacacacacacacacac	0.351													3	3	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42284469	42284469	+	3'UTR	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42284469delT	uc002igb.2	-	20					UBTF_uc002igc.2_3'UTR|UBTF_uc010czs.2_3'UTR|UBTF_uc002igd.2_3'UTR|UBTF_uc010czt.2_3'UTR	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CCCCACCGTATTTTTTTTTTT	0.562													6	4	---	---	---	---	
GPATCH8	23131	broad.mit.edu	37	17	42514114	42514115	+	Intron	INS	-	C	C	rs146935319	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42514114_42514115insC	uc002igw.1	-						GPATCH8_uc002igv.1_Intron|GPATCH8_uc010wiz.1_Intron	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8							intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		ACCTTGGCTGACGTCCAGTTGG	0.371													3	3	---	---	---	---	
ITGA3	3675	broad.mit.edu	37	17	48148009	48148010	+	Intron	DEL	AA	-	-	rs72396175		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48148009_48148010delAA	uc010dbl.2	+						ITGA3_uc010dbm.2_Intron	NM_002204	NP_002195	P26006	ITA3_HUMAN	integrin alpha 3 isoform a precursor						blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3						agactgtctcaaaaaaaaaaaa	0.010													3	3	---	---	---	---	
NME1-NME2	654364	broad.mit.edu	37	17	49231520	49231521	+	Intron	INS	-	T	T	rs60023424	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49231520_49231521insT	uc002itk.2	+						NME1_uc010dbx.1_Intron|NME1_uc002ith.1_Intron|NME1_uc002iti.1_Intron|NME1-NME2_uc002itj.2_Intron	NM_002512	NP_002503	P22392	NDKB_HUMAN	nucleoside diphosphate kinase B						cell adhesion|CTP biosynthetic process|GTP biosynthetic process|negative regulation of apoptosis|nucleobase, nucleoside and nucleotide interconversion|positive regulation of epithelial cell proliferation|positive regulation of keratinocyte differentiation|UTP biosynthetic process	cytosol|lamellipodium|nucleus|ruffle	ATP binding|DNA binding|metal ion binding|nucleoside diphosphate kinase activity|protein binding|protein histidine kinase activity|sequence-specific DNA binding transcription factor activity				0			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			GTCTCTCTCTCTTTTTTTTTTT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	2878502	2878502	+	IGR	DEL	A	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2878502delA								ZNF556 (1 upstream) : ZNF57 (22394 downstream)																							cgtctctactaaaaaaaaaaa	0.000													4	2	---	---	---	---	
STAP2	55620	broad.mit.edu	37	19	4325134	4325134	+	Intron	DEL	A	-	-	rs71833543		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4325134delA	uc002mab.2	-						STAP2_uc002mac.2_Intron|STAP2_uc002mad.2_Intron	NM_001013841	NP_001013863	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2							cytoplasm|nucleus	protein binding			central_nervous_system(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		agactgtctcaaaaaaaaaaa	0.279													5	3	---	---	---	---	
SERINC3	10955	broad.mit.edu	37	20	43135278	43135279	+	Intron	INS	-	T	T	rs142737926	by1000genomes	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43135278_43135279insT	uc002xme.2	-						SERINC3_uc002xmf.1_Intron|SERINC3_uc010ggs.1_Intron|SERINC3_uc010zwp.1_Intron	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1							integral to membrane|plasma membrane	protein binding			skin(3)	3		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)			AGTTACCTGGGTTTTTTTTTAA	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48574697	48574698	+	IGR	INS	-	C	C	rs143909127		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48574697_48574698insC								RNF114 (4277 upstream) : SNAI1 (24829 downstream)																							ttttttttttttcgagatggag	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10755006	10755007	+	IGR	INS	-	CC	CC	rs145672671		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10755006_10755007insCC								None (None upstream) : TPTE (151736 downstream)																							agttttgaaaatctctttgtag	0.000													4	2	---	---	---	---	
RWDD2B	10069	broad.mit.edu	37	21	30391672	30391672	+	5'UTR	DEL	A	-	-	rs66619103		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30391672delA	uc002yms.2	-	1					RWDD2B_uc002ymt.2_5'UTR|RWDD2B_uc002ymu.2_RNA|RWDD2B_uc002ymv.2_5'UTR	NM_016940	NP_058636	P57060	RWD2B_HUMAN	RWD domain containing 2B												0						GACCTACCGGAAAAAAAAAAA	0.567													4	2	---	---	---	---	
TTC3	7267	broad.mit.edu	37	21	38460511	38460517	+	Frame_Shift_Del	DEL	GTATATG	-	-	rs113425690		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38460511_38460517delGTATATG	uc002yvz.2	+	4	308_314	c.203_209delGTATATG	c.(202-210)AGTATATGGfs	p.S68fs	TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Frame_Shift_Del_p.S68fs|TTC3_uc002ywb.2_Frame_Shift_Del_p.S68fs|TTC3_uc010gnf.2_5'UTR|TTC3_uc011aed.1_Intron|TTC3_uc010gne.1_Frame_Shift_Del_p.S68fs	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	68_70					protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)				GACATCTGCAGTATATGGTGTAGTAAA	0.290													48	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44755941	44755943	+	IGR	DEL	CAA	-	-	rs67038982		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44755941_44755943delCAA								CRYAA (163028 upstream) : SIK1 (78455 downstream)																							ccaccaccaccaacaccaccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16920274	16920275	+	IGR	DEL	AT	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16920274_16920275delAT								OR11H1 (470470 upstream) : CCT8L2 (151373 downstream)																							TTATAGTGACATGTATGAAAAC	0.267													6	7	---	---	---	---	
MAOB	4129	broad.mit.edu	37	X	43634303	43634306	+	Intron	DEL	TTTT	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43634303_43634306delTTTT	uc004dfz.3	-						MAOB_uc011mkx.1_Intron|MAOB_uc011mky.1_Intron	NM_000898	NP_000889	P27338	AOFB_HUMAN	monoamine oxidase B						xenobiotic metabolic process	integral to membrane|mitochondrial outer membrane	electron carrier activity|primary amine oxidase activity			ovary(1)|central_nervous_system(1)	2					Amantadine(DB00915)|Bupropion(DB01156)|Carbidopa(DB00190)|Citalopram(DB00215)|Dopamine(DB00988)|Entacapone(DB00494)|Furazolidone(DB00614)|Ginkgo biloba(DB01381)|Ibuprofen(DB01050)|Imipramine(DB00458)|Iproniazid(DB04818)|Isocarboxazid(DB01247)|Levodopa(DB01235)|Maprotiline(DB00934)|Meclizine(DB00737)|Moclobemide(DB01171)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Rasagiline(DB01367)|Selegiline(DB01037)|Tranylcypromine(DB00752)	AATTGGGTTGtttttttttttttt	0.324													4	2	---	---	---	---	
KDM5C	8242	broad.mit.edu	37	X	53227036	53227042	+	Frame_Shift_Del	DEL	GTAGACC	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53227036_53227042delGTAGACC	uc004drz.2	-	18	3066_3072	c.2533_2539delGGTCTAC	c.(2533-2541)GGTCTACAGfs	p.G845fs	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Frame_Shift_Del_p.G778fs|KDM5C_uc004dsa.2_Frame_Shift_Del_p.G844fs	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	845_847					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18						AGGGTCATCTGTAGACCAGCCACCCTG	0.536			N|F|S		clear cell renal carcinoma								5	7	---	---	---	---	
KLHL4	56062	broad.mit.edu	37	X	86890606	86890606	+	Frame_Shift_Del	DEL	T	-	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86890606delT	uc004efb.2	+	9	1938	c.1756delT	c.(1756-1758)TCAfs	p.S586fs	KLHL4_uc004efa.2_Frame_Shift_Del_p.S586fs	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1	586	Kelch 4.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						CTGCCTCAAATCAATGGAATA	0.398													20	50	---	---	---	---	
RBMX2	51634	broad.mit.edu	37	X	129537509	129537510	+	Intron	INS	-	T	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129537509_129537510insT	uc004evt.2	+							NM_016024	NP_057108	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2								nucleotide binding|RNA binding			breast(3)|ovary(1)	4						cacctggctgatttttttttgt	0.000													4	2	---	---	---	---	
