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
CLSTN1	22883	broad.mit.edu	37	1	9795231	9795231	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9795231A>C	uc001aqh.2	-	14	2644	c.1885T>G	c.(1885-1887)TGT>GGT	p.C629G	CLSTN1_uc001aqi.2_Missense_Mutation_p.C619G|CLSTN1_uc010oag.1_Missense_Mutation_p.C610G|CLSTN1_uc001aqf.2_5'Flank	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1	629	Extracellular (Potential).				homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		TCGTTAAAACACCTGCCAGCA	0.587													18	89	---	---	---	---	PASS
AGTRAP	57085	broad.mit.edu	37	1	11810282	11810282	+	3'UTR	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11810282G>T	uc001asv.2	+	5					AGTRAP_uc001ast.2_3'UTR|AGTRAP_uc001asu.2_3'UTR|AGTRAP_uc001asw.2_3'UTR|AGTRAP_uc001asx.2_3'UTR	NM_020350	NP_065083	Q6RW13	ATRAP_HUMAN	angiotensin II receptor-associated protein							cytoplasmic vesicle membrane|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding		AGTRAP/BRAF(2)	stomach(2)	2	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CCTGCCCCGGGCCTTCCTCGT	0.637													4	12	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16946368	16946368	+	RNA	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946368A>G	uc010ocf.1	-	3		c.530T>C			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GGCCAGGAGGAGGCCCTCGTC	0.562													2	16	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16959602	16959602	+	Intron	SNP	C	T	T	rs1807293	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16959602C>T	uc001azf.2	-						CROCCL1_uc009vov.1_5'Flank|CROCCL1_uc001aze.2_5'Flank|CROCCL1_uc001azg.1_RNA|CROCCL1_uc001azi.1_RNA|uc001azj.1_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						TCTGCAGTGACGCCTGCCTCA	0.602													8	34	---	---	---	---	PASS
ZNF683	257101	broad.mit.edu	37	1	26691329	26691329	+	Silent	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26691329C>A	uc001bmg.1	-	4	826	c.708G>T	c.(706-708)CTG>CTT	p.L236L	ZNF683_uc001bmh.1_Silent_p.L236L|ZNF683_uc009vsj.1_Silent_p.L236L	NM_173574	NP_775845	Q8IZ20	ZN683_HUMAN	zinc finger protein 683	236					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		CCATCATCAGCAGGCTAGGCA	0.632													13	119	---	---	---	---	PASS
CACHD1	57685	broad.mit.edu	37	1	65130209	65130209	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65130209C>A	uc001dbo.1	+	15	2075	c.1970C>A	c.(1969-1971)ACC>AAC	p.T657N	CACHD1_uc001dbp.1_Missense_Mutation_p.T412N|CACHD1_uc001dbq.1_Missense_Mutation_p.T412N|CACHD1_uc010opa.1_5'Flank	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1	708	Extracellular (Potential).				calcium ion transport	integral to membrane				ovary(2)	2						GTAATGGCTACCAGCCACGTC	0.463													10	91	---	---	---	---	PASS
CYR61	3491	broad.mit.edu	37	1	86048170	86048170	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86048170T>C	uc001dle.2	+	4	930	c.706T>C	c.(706-708)TGG>CGG	p.W236R	CYR61_uc001dlg.2_Missense_Mutation_p.W65R|CYR61_uc009wcp.1_5'Flank	NM_001554	NP_001545	O00622	CYR61_HUMAN	cysteine-rich, angiogenic inducer, 61 precursor	236	TSP type-1.				cell proliferation|chemotaxis|positive regulation of BMP signaling pathway|positive regulation of cell migration|positive regulation of osteoblast differentiation|positive regulation of osteoblast proliferation|positive regulation of protein kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell growth|regulation of ERK1 and ERK2 cascade|wound healing, spreading of cells	extracellular region	heparin binding|insulin-like growth factor binding			central_nervous_system(1)	1				all cancers(265;0.0216)|Epithelial(280;0.0441)		AACAACTTCATGGTCCCAGTG	0.458											OREG0013583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	110	---	---	---	---	PASS
WDR3	10885	broad.mit.edu	37	1	118502003	118502003	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118502003C>T	uc010oxe.1	+	27	2831	c.2765C>T	c.(2764-2766)ACT>ATT	p.T922I	WDR3_uc001ehi.2_Intron|SPAG17_uc001ehk.2_Intron	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	922						nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		GCTGATGCTACTAGCCACTTG	0.318													20	55	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142803734	142803734	+	Intron	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803734C>A	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		gttaaataaacaactatggat	0.000													3	29	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144863482	144863482	+	Intron	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144863482T>C	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron|PDE4DIP_uc001ema.2_3'UTR	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATGGCAGAGCTACTCAGCCAC	0.527			T	PDGFRB	MPD								8	160	---	---	---	---	PASS
HIST3H3	8290	broad.mit.edu	37	1	228612642	228612642	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228612642G>A	uc001hsx.1	-	1	385	c.385C>T	c.(385-387)CGC>TGC	p.R129C		NM_003493	NP_003484	Q16695	H31T_HUMAN	histone cluster 3, H3	129					nucleosome assembly|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0		Prostate(94;0.0724)				CGGATACGGCGTGCCAGCTGG	0.602													6	85	---	---	---	---	PASS
SDC1	6382	broad.mit.edu	37	2	20402069	20402069	+	3'UTR	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20402069T>C	uc002rdo.1	-	5					SDC1_uc002rdp.1_3'UTR|SDC1_uc010exv.2_Intron	NM_002997	NP_002988	P18827	SDC1_HUMAN	syndecan 1 precursor						lipid metabolic process|lipoprotein metabolic process|myoblast development|striated muscle cell development	cytoplasm|extracellular region|focal adhesion|integral to plasma membrane	cytoskeletal protein binding|protein C-terminus binding			ovary(4)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		TGGACTCCTGTCCCCTGCCAC	0.532													5	23	---	---	---	---	PASS
FBXO11	80204	broad.mit.edu	37	2	48045734	48045734	+	Intron	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48045734C>T	uc010fbl.2	-						FBXO11_uc002rwe.2_Intron|FBXO11_uc002rwf.2_Intron|FBXO11_uc002rwg.1_3'UTR|FBXO11_uc010fbk.2_Intron	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1						ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CCAGTGGCTTCTGTCCTCACC	0.413													7	15	---	---	---	---	PASS
ERCC3	2071	broad.mit.edu	37	2	128050049	128050049	+	Intron	SNP	T	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128050049T>G	uc002toh.1	-						ERCC3_uc002toe.1_5'Flank|ERCC3_uc002tof.1_Intron|ERCC3_uc002tog.1_Intron|ERCC3_uc010flx.1_Intron|ERCC3_uc010yzh.1_RNA|ERCC3_uc010fly.2_Intron	NM_000122	NP_000113	P19447	ERCC3_HUMAN	excision repair cross-complementing rodent						cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding			ovary(2)|lung(2)|breast(2)|kidney(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		gcggctggggtaatcagtcgt	0.095			Mis|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				8	14	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152474946	152474946	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152474946A>C	uc010fnx.2	-	70	10381	c.10190T>G	c.(10189-10191)GTT>GGT	p.V3397G		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3397	Nebulin 93.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		ATCAATCGGAACCCAGCCAAT	0.393													16	69	---	---	---	---	PASS
PDK1	5163	broad.mit.edu	37	2	173457705	173457705	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173457705C>A	uc002uhr.2	+	10	1199	c.1099C>A	c.(1099-1101)CAA>AAA	p.Q367K	PDK1_uc010zdz.1_Missense_Mutation_p.Q212K|PDK1_uc010zea.1_RNA|PDK1_uc002uhq.1_Missense_Mutation_p.Q387K|PDK1_uc002uhs.2_Missense_Mutation_p.Q367K|PDK1_uc010zeb.1_Missense_Mutation_p.Q387K	NM_002610	NP_002601	Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase 1 precursor	367	Histidine kinase.				glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(3)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.12)			TCTTTACGCACAATACTTCCA	0.378									Autosomal_Dominant_Polycystic_Kidney_Disease				4	160	---	---	---	---	PASS
ALS2	57679	broad.mit.edu	37	2	202591577	202591577	+	Silent	SNP	G	T	T	rs121908137		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202591577G>T	uc002uyo.2	-	18	3348	c.2992C>A	c.(2992-2994)CGA>AGA	p.R998R	ALS2_uc002uyp.3_Silent_p.R998R|ALS2_uc010ftl.2_RNA	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	998	PH.				cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						CTTATAGCTCGTAGCCACTTT	0.433													4	23	---	---	---	---	PASS
CHPF	79586	broad.mit.edu	37	2	220406592	220406592	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220406592G>T	uc002vmc.3	-	2	861	c.634C>A	c.(634-636)CTA>ATA	p.L212I	CHPF_uc010zlh.1_Missense_Mutation_p.L50I|CHPF_uc002vmd.3_Missense_Mutation_p.L212I|TMEM198_uc002vme.2_5'Flank|TMEM198_uc002vmf.2_5'Flank	NM_024536	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	212	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity|protein binding				0		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TGGCCAGTTAGGCGTGCCAGG	0.706											OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	30	---	---	---	---	PASS
CSPG5	10675	broad.mit.edu	37	3	47618408	47618408	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47618408A>G	uc003crp.3	-	2	1284	c.1108T>C	c.(1108-1110)TGC>CGC	p.C370R	CSPG5_uc003crn.2_Missense_Mutation_p.C232R|CSPG5_uc003cro.3_Missense_Mutation_p.C370R|CSPG5_uc011bbb.1_Missense_Mutation_p.C232R	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	370	Extracellular (Potential).				cell differentiation|intracellular transport|nervous system development|regulation of growth	endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction	growth factor activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		ACTGACCGGCAGGAGCCGTTA	0.617													9	76	---	---	---	---	PASS
MBD4	8930	broad.mit.edu	37	3	129150264	129150264	+	3'UTR	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129150264A>G	uc003emh.1	-	8					uc003emg.2_5'Flank|MBD4_uc003emi.1_3'UTR|MBD4_uc003emj.1_3'UTR|MBD4_uc003emk.1_3'UTR	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4						depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2						CTATGGCTGGAAAGGTGGTTG	0.373								BER_DNA_glycosylases					26	44	---	---	---	---	PASS
HLTF	6596	broad.mit.edu	37	3	148786108	148786108	+	Silent	SNP	C	T	T	rs812249	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148786108C>T	uc003ewq.1	-	8	1127	c.909G>A	c.(907-909)ACG>ACA	p.T303T	HLTF_uc003ewr.1_Silent_p.T303T|HLTF_uc003ews.1_Silent_p.T303T|HLTF_uc010hve.1_Silent_p.T303T	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	303					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CTGCAATGGCCGTAAGAGTTT	0.353													5	346	---	---	---	---	PASS
CRIPAK	285464	broad.mit.edu	37	4	1389063	1389063	+	Missense_Mutation	SNP	G	C	C	rs148588369	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1389063G>C	uc003gdf.2	+	1	3724	c.764G>C	c.(763-765)CGA>CCA	p.R255P		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	255	7.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTCACGTGCCGATGTGGAGTG	0.682													4	141	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3317854	3317854	+	5'UTR	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3317854A>C	uc003ggw.2	+	2					RGS12_uc003ggu.2_5'UTR|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_RNA|RGS12_uc003ggv.2_5'UTR|RGS12_uc003ggx.1_5'UTR	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATATGGCTCCAAGGGAACAAT	0.488													12	103	---	---	---	---	PASS
FAM13A	10144	broad.mit.edu	37	4	89660254	89660254	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89660254A>C	uc003hse.1	-	20	2697	c.2489T>G	c.(2488-2490)GTG>GGG	p.V830G	FAM13A_uc011cdp.1_5'Flank|FAM13A_uc003hsa.1_Missense_Mutation_p.V301G|FAM13A_uc003hsb.1_Missense_Mutation_p.V504G|FAM13A_uc003hsd.1_Missense_Mutation_p.V504G|FAM13A_uc003hsc.1_Missense_Mutation_p.V490G|FAM13A_uc011cdq.1_Missense_Mutation_p.V476G|FAM13A_uc003hsf.1_Missense_Mutation_p.V416G|FAM13A_uc003hsg.1_Missense_Mutation_p.V301G	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	830					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						TGGCTTCATCACCTGCCGTTC	0.512													12	20	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14508563	14508563	+	3'UTR	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14508563A>C	uc003jff.2	+	57					TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					ATTCTCTTTCACCTGCCAATC	0.408													30	63	---	---	---	---	PASS
NDUFS4	4724	broad.mit.edu	37	5	52979037	52979037	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52979037G>T	uc003jpe.2	+	5	542	c.514G>T	c.(514-516)GTA>TTA	p.V172L		NM_002495	NP_002486	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4	172					brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)	AAGAACAAGAGTATCCACAAA	0.378													8	67	---	---	---	---	PASS
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99715528C>T	uc011cuw.1	-	4		c.382G>A				NR_027503				Homo sapiens glucuronidase, beta pseudogene (LOC100133050), non-coding RNA.												0						AGCGGACAGTCGAAGCCCTTC	0.607													3	19	---	---	---	---	PASS
PHF15	23338	broad.mit.edu	37	5	133914476	133914476	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133914476G>A	uc003kzo.1	+	11	2021	c.1842G>A	c.(1840-1842)GGG>GGA	p.G614G	PHF15_uc011cxt.1_Silent_p.G658G|PHF15_uc003kzk.2_Silent_p.G674G|PHF15_uc003kzm.2_Silent_p.G615G|PHF15_uc003kzn.2_3'UTR	NM_015288	NP_056103	Q9NQC1	JADE2_HUMAN	PHD finger protein 15	614	Pro-rich.				histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGCAGGACGGGCCTGGTTCAC	0.672													5	48	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140568817	140568817	+	Silent	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140568817G>T	uc003liw.1	+	3	1926	c.1926G>T	c.(1924-1926)GTG>GTT	p.V642V		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	642	Extracellular (Potential).|Cadherin 6.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCTGGTGGTGCTTGTCAAGG	0.697													4	63	---	---	---	---	PASS
GCM2	9247	broad.mit.edu	37	6	10881950	10881950	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10881950G>T	uc003mzn.3	-	1	149	c.77C>A	c.(76-78)CCG>CAG	p.P26Q	SYCP2L_uc011dim.1_Intron	NM_004752	NP_004743	O75603	GCM2_HUMAN	glial cells missing homolog 2	26	GCM.				cellular calcium ion homeostasis|cellular phosphate ion homeostasis|parathyroid gland development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				AGGCATCTGCGGATCGTTGAT	0.642													3	68	---	---	---	---	PASS
SLC26A8	116369	broad.mit.edu	37	6	35930384	35930384	+	Silent	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35930384A>C	uc003olm.2	-	12	1491	c.1380T>G	c.(1378-1380)GGT>GGG	p.G460G	SLC26A8_uc010jwa.2_RNA|SLC26A8_uc003olk.2_Silent_p.G42G|SLC26A8_uc003oln.2_Silent_p.G460G|SLC26A8_uc003oll.2_Silent_p.G355G	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	460	Helical; (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2						TCAGAATAATACCAGCCAGCA	0.463													12	25	---	---	---	---	PASS
CUL9	23113	broad.mit.edu	37	6	43183065	43183065	+	Splice_Site	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43183065G>T	uc003ouk.2	+	30	6011	c.5936_splice	c.e30+1	p.S1979_splice	CUL9_uc003oul.2_Splice_Site_p.S1951_splice|CUL9_uc010jyk.2_Splice_Site_p.S1131_splice|CUL9_uc003oun.2_Splice_Site	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						CCAAGCCCAGGTAGCCACTGC	0.587													7	26	---	---	---	---	PASS
TBX18	9096	broad.mit.edu	37	6	85448257	85448257	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85448257G>A	uc003pkl.1	-	7	1057	c.1057C>T	c.(1057-1059)CGG>TGG	p.R353W	TBX18_uc010kbq.1_Missense_Mutation_p.R195W	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	353					multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		GTCAGAGTCCGTAGTGATGGT	0.468													93	398	---	---	---	---	PASS
SHPRH	257218	broad.mit.edu	37	6	146240560	146240560	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146240560G>T	uc003qlf.2	-	22	4475	c.4076C>A	c.(4075-4077)ACA>AAA	p.T1359K	SHPRH_uc003qld.2_Missense_Mutation_p.T1363K|SHPRH_uc003qle.2_Missense_Mutation_p.T1363K|SHPRH_uc003qlg.1_Missense_Mutation_p.T915K|SHPRH_uc003qlh.2_Missense_Mutation_p.T284K|SHPRH_uc003qli.1_Missense_Mutation_p.T284K	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1359					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TAGTCGTTCTGTAGCCATTGC	0.428													10	185	---	---	---	---	PASS
NUDT1	4521	broad.mit.edu	37	7	2290680	2290680	+	3'UTR	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2290680A>C	uc003slp.1	+	5					NUDT1_uc003slq.1_3'UTR|NUDT1_uc003slr.1_3'UTR|NUDT1_uc003sls.1_3'UTR|NUDT1_uc003slt.1_3'UTR|NUDT1_uc003slu.1_3'UTR|NUDT1_uc003slv.1_3'UTR	NM_198949	NP_945187	P36639	8ODP_HUMAN	nudix-type motif 1 isoform p22						DNA protection|DNA repair|response to oxidative stress	cytoplasm	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity|GTPase activity|metal ion binding|protein binding				0		Ovarian(82;0.0253)|Melanoma(862;0.155)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.8e-14)|BRCA - Breast invasive adenocarcinoma(126;0.15)		TGGCTGCTGAACAGCCGCAAA	0.587								Direct_reversal_of_damage|Modulation_of_nucleotide_pools					11	35	---	---	---	---	PASS
GPR141	353345	broad.mit.edu	37	7	37780909	37780909	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37780909G>T	uc003tfm.1	+	1	914	c.914G>T	c.(913-915)CGT>CTT	p.R305L	uc003tfl.2_Intron	NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	305	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity	p.R305H(1)		ovary(3)	3						GTTTTGTGCCGTTAGCCACAA	0.363													6	78	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	39874495	39874495	+	3'UTR	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39874495A>G	uc010kxp.2	+	2										SubName: Full=Similar to sequence-specific single-stranded-DNA-binding protein;																		GTTTCATGCAATAAAAAGGCC	0.398													2	7	---	---	---	---	PASS
H2AFV	94239	broad.mit.edu	37	7	44874056	44874056	+	3'UTR	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44874056A>C	uc003tma.2	-	5					H2AFV_uc003tlz.2_Intron|H2AFV_uc011kca.1_5'Flank|H2AFV_uc003tmb.2_3'UTR|H2AFV_uc003tmc.2_3'UTR|H2AFV_uc003tmd.2_3'UTR	NM_012412	NP_036544	Q71UI9	H2AV_HUMAN	H2A histone family, member V isoform 1						nucleosome assembly	nucleosome|nucleus	DNA binding				0						TGTCCCAGTTACAGTACAATG	0.388													3	62	---	---	---	---	PASS
POM121	9883	broad.mit.edu	37	7	72413243	72413243	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72413243A>C	uc003twk.2	+	11	2711	c.2711A>C	c.(2710-2712)CAC>CCC	p.H904P	POM121_uc003twj.2_Missense_Mutation_p.H639P|POM121_uc010lam.1_Missense_Mutation_p.H639P	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	904	Thr-rich.|Pore side (Potential).			H -> P (in Ref. 3; BAB14097).	carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)				CAGTCCCTGCACACTGCCGTG	0.647													7	167	---	---	---	---	PASS
HIP1	3092	broad.mit.edu	37	7	75167431	75167431	+	3'UTR	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75167431A>G	uc003uds.1	-	31					HIP1_uc011kfz.1_3'UTR	NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8						GTGGCTGGGGAAATAACACAC	0.507			T	PDGFRB	CMML								7	95	---	---	---	---	PASS
TFEC	22797	broad.mit.edu	37	7	115581932	115581932	+	Intron	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115581932C>A	uc003vhj.1	-						TFEC_uc003vhk.1_Intron|TFEC_uc003vhl.3_Missense_Mutation_p.M197I|TFEC_uc011kmw.1_Missense_Mutation_p.M316I	NM_012252	NP_036384	O14948	TFEC_HUMAN	transcription factor EC isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)			CTCATGGCTACATTCTTATAA	0.363													13	244	---	---	---	---	PASS
DEFA1B	728358	broad.mit.edu	37	8	6873603	6873603	+	Missense_Mutation	SNP	T	G	G	rs145076681	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6873603T>G	uc003wqz.1	-	3	279	c.194A>C	c.(193-195)GAC>GCC	p.D65A		NM_005217	NP_005208	P59665	DEF1_HUMAN	defensin, alpha 3 preproprotein	65					chemotaxis|defense response to bacterium|defense response to fungus|immune response|killing of cells of other organism|response to virus	extracellular space					0						GCAATAGCAGTCCATGTTTTT	0.498													3	110	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	12428649	12428649	+	Intron	SNP	T	C	C	rs593329		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12428649T>C	uc003wvy.3	-						uc003wvz.1_RNA|uc003wwa.2_5'Flank					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		TGGTGCTGCTTGGAGTACCAA	0.239													3	20	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	12428650	12428650	+	Intron	SNP	G	A	A	rs593330		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12428650G>A	uc003wvy.3	-						uc003wvz.1_RNA|uc003wwa.2_5'Flank					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		GGTGCTGCTTGGAGTACCAAA	0.239													3	19	---	---	---	---	PASS
TNFRSF10C	8794	broad.mit.edu	37	8	22974405	22974405	+	Missense_Mutation	SNP	C	A	A	rs61736406	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22974405C>A	uc003xcy.2	+	5	842	c.641C>A	c.(640-642)ACC>AAC	p.T214N	TNFRSF10C_uc011kzr.1_RNA	NM_003841	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily,	214	TAPE 4.				apoptosis	anchored to membrane|integral to plasma membrane	TRAIL binding|transmembrane receptor activity				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAGACAATGACCACCAGCCCG	0.612													9	166	---	---	---	---	PASS
TNFRSF10C	8794	broad.mit.edu	37	8	22974415	22974415	+	Silent	SNP	G	A	A	rs11780526	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22974415G>A	uc003xcy.2	+	5	852	c.651G>A	c.(649-651)CCG>CCA	p.P217P	TNFRSF10C_uc011kzr.1_RNA	NM_003841	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily,	217	TAPE 4.				apoptosis	anchored to membrane|integral to plasma membrane	TRAIL binding|transmembrane receptor activity				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		CCACCAGCCCGGGGACTCCTG	0.607													9	142	---	---	---	---	PASS
DPYSL2	1808	broad.mit.edu	37	8	26484737	26484737	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26484737G>A	uc003xfb.1	+	6	897	c.547G>A	c.(547-549)GAA>AAA	p.E183K	DPYSL2_uc003xfa.2_Missense_Mutation_p.E288K|DPYSL2_uc011lag.1_Missense_Mutation_p.E183K|DPYSL2_uc010luk.1_RNA|DPYSL2_uc011lah.1_Missense_Mutation_p.E147K	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	183					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		TCAGATTTATGAAGTACTGAG	0.483													14	55	---	---	---	---	PASS
CPNE3	8895	broad.mit.edu	37	8	87563330	87563330	+	Splice_Site	SNP	T	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87563330T>G	uc003ydv.2	+	13	1230	c.1068_splice	c.e13+2	p.Q356_splice	CPNE3_uc003ydw.1_Splice_Site_p.Q72_splice	NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III						lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2						CAGTGGCAGGTAAGAGGAAAT	0.368													13	18	---	---	---	---	PASS
EPPK1	83481	broad.mit.edu	37	8	144945349	144945349	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144945349G>T	uc003zaa.1	-	1	2086	c.2073C>A	c.(2071-2073)TAC>TAA	p.Y691*		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	691	Plectin 13.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGGGGTCAGTGTAGCCAGTGA	0.637													4	44	---	---	---	---	PASS
POLR1E	64425	broad.mit.edu	37	9	37503236	37503236	+	3'UTR	SNP	A	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37503236A>C	uc003zzz.1	+	11					POLR1E_uc003zzy.1_3'UTR|POLR1E_uc011lqk.1_3'UTR|uc004aaa.2_5'Flank	NM_022490	NP_071935	Q9GZS1	RPA49_HUMAN	RNA polymerase I associated factor 53						rRNA transcription	cell junction|cytoplasm|nucleolus	DNA binding|DNA-directed RNA polymerase activity|protein binding				0				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		TGGCTGCATCACAGCCACTGG	0.408													13	22	---	---	---	---	PASS
CTNNAL1	8727	broad.mit.edu	37	9	111718091	111718091	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111718091G>T	uc004bdo.1	-	12	1650	c.1608C>A	c.(1606-1608)TAC>TAA	p.Y536*	CTNNAL1_uc010mts.1_Nonsense_Mutation_p.Y188*|CTNNAL1_uc010mtt.1_Nonsense_Mutation_p.Y536*|CTNNAL1_uc004bdp.1_Nonsense_Mutation_p.Y536*|CTNNAL1_uc004bdq.1_Nonsense_Mutation_p.Y22*	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1	536					cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		GAAGTGAAAGGTAGCCATACT	0.244													8	47	---	---	---	---	PASS
TOR2A	27433	broad.mit.edu	37	9	130494791	130494791	+	Intron	SNP	C	T	T	rs536262	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130494791C>T	uc004brs.3	-						TOR2A_uc004brt.3_Intron|TOR2A_uc004brw.3_3'UTR|TOR2A_uc011maj.1_3'UTR|TOR2A_uc004bru.3_Intron|TOR2A_uc004brv.3_Intron|TOR2A_uc004brx.1_Missense_Mutation_p.G96E	NM_001085347	NP_001078816	Q5JU69	TOR2A_HUMAN	torsin family 2, member A isoform a						chaperone mediated protein folding requiring cofactor	endoplasmic reticulum|extracellular region	ATP binding|nucleoside-triphosphatase activity				0						AGAGCCTGGCCCCTGGGTGTG	0.473													3	7	---	---	---	---	PASS
SPTAN1	6709	broad.mit.edu	37	9	131339198	131339198	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131339198A>G	uc004bvl.3	+	6	861	c.748A>G	c.(748-750)AAG>GAG	p.K250E	SPTAN1_uc011mbg.1_Missense_Mutation_p.K250E|SPTAN1_uc011mbh.1_Missense_Mutation_p.K262E|SPTAN1_uc004bvm.3_Missense_Mutation_p.K250E|SPTAN1_uc004bvn.3_Missense_Mutation_p.K250E	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	250	Spectrin 3.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						GAGGCAGGGGAAGCTCTTTGG	0.567													4	33	---	---	---	---	PASS
BRD3	8019	broad.mit.edu	37	9	136899859	136899859	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136899859C>T	uc004cew.2	-	11	2217	c.2029G>A	c.(2029-2031)GGG>AGG	p.G677R		NM_007371	NP_031397	Q15059	BRD3_HUMAN	bromodomain containing protein 3	677	Potential.|Ser-rich.					nucleus	protein binding		BRD3/C15orf55(3)	stomach(4)|midline_organs(3)|kidney(1)	8				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		CTCAGCTGCCCGCTGACATCC	0.617			T	NUT|C15orf55	lethal midline carcinoma of young people								4	181	---	---	---	---	PASS
PHYH	5264	broad.mit.edu	37	10	13330436	13330436	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13330436C>T	uc001imf.2	-	6	690	c.602G>A	c.(601-603)CGG>CAG	p.R201Q	PHYH_uc001ime.2_Missense_Mutation_p.R101Q|PHYH_uc001img.2_Missense_Mutation_p.R184Q	NM_006214	NP_006205	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase isoform a precursor	201					fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding				0		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	GCCGTTGTTCCGGCTGATGTG	0.627													3	88	---	---	---	---	PASS
YME1L1	10730	broad.mit.edu	37	10	27436415	27436415	+	Intron	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27436415C>T	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron|YME1L1_uc001itk.1_Silent_p.G117G	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						TTTGGAGAAACCCGCAGTGTA	0.333													3	69	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	Missense_Mutation	SNP	A	G	G	rs2257765		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38654432A>G	uc010qex.1	+	5	599	c.524A>G	c.(523-525)AAT>AGT	p.N175S	HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_Missense_Mutation_p.N173S					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						TCATCTCGCAATGCAAGGAAA	0.453													3	118	---	---	---	---	PASS
LOC441666	441666	broad.mit.edu	37	10	42832122	42832122	+	RNA	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42832122C>T	uc010qey.1	-	3		c.1853G>A				NR_024380				Homo sapiens noncoding mRNA sequence.												0						CAGTAAAAGGCTTTGCCACAT	0.348													3	20	---	---	---	---	PASS
LOC441666	441666	broad.mit.edu	37	10	42832147	42832147	+	RNA	SNP	G	T	T	rs144592176	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42832147G>T	uc010qey.1	-	3		c.1828C>A				NR_024380				Homo sapiens noncoding mRNA sequence.												0						CACAATTGTAGGGTTTCTCTC	0.353													3	18	---	---	---	---	PASS
INA	9118	broad.mit.edu	37	10	105048298	105048298	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105048298G>T	uc001kws.2	+	3	1421	c.1372G>T	c.(1372-1374)GTA>TTA	p.V458L		NM_032727	NP_116116	Q16352	AINX_HUMAN	internexin neuronal intermediate filament	458	Tail.				cell differentiation|nervous system development	neurofilament	structural constituent of cytoskeleton			ovary(1)|breast(1)	2				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		GGCATCTAAGGTAGCCTCTAA	0.423													10	136	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115422474	115422474	+	Silent	SNP	A	G	G	rs3127122	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115422474A>G	uc001laj.2	-	3	383	c.219T>C	c.(217-219)AAT>AAC	p.N73N	NRAP_uc001lak.2_Silent_p.N73N|NRAP_uc001lal.3_Silent_p.N73N	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	73	Nebulin 1.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TCACATTTAGATTTAATGGAG	0.259													5	175	---	---	---	---	PASS
CNGA4	1262	broad.mit.edu	37	11	6261464	6261464	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6261464C>T	uc001mco.2	+	4	547	c.440C>T	c.(439-441)GCG>GTG	p.A147V	CNGA4_uc010raa.1_Intron|CNGA4_uc001mcn.2_Missense_Mutation_p.A107V	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	147	Extracellular (Potential).				response to stimulus|sensory perception of smell		cAMP binding			skin(1)	1		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTTCTCCGCGCGCCCCGCCTC	0.587													5	205	---	---	---	---	PASS
MRVI1	10335	broad.mit.edu	37	11	10622488	10622488	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10622488G>T	uc010rcc.1	-	15	2380	c.1994C>A	c.(1993-1995)TCA>TAA	p.S665*	MRVI1_uc001miw.2_Nonsense_Mutation_p.S656*|MRVI1_uc010rcb.1_Nonsense_Mutation_p.S657*|MRVI1_uc009ygb.1_Nonsense_Mutation_p.S350*|MRVI1_uc001mix.2_Nonsense_Mutation_p.S350*|MRVI1_uc001miz.2_Nonsense_Mutation_p.S574*|MRVI1_uc009ygc.1_Nonsense_Mutation_p.S574*|MRVI1_uc010rcd.1_Nonsense_Mutation_p.S459*|MRVI1_uc009ygd.1_Nonsense_Mutation_p.S350*|MRVI1_uc010rce.1_RNA	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN	JAW1-related protein isoform c	638					platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		GCTGCGGCTTGAATTCTGATT	0.507													6	93	---	---	---	---	PASS
RAB3IL1	5866	broad.mit.edu	37	11	61665702	61665702	+	3'UTR	SNP	T	G	G	rs36099026		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61665702T>G	uc001nso.2	-	10					RAB3IL1_uc001nsp.2_3'UTR	NM_013401	NP_037533	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1								protein binding			skin(2)|central_nervous_system(1)	3						TGTTCTGGGGTGGGTGTTTGC	0.642											OREG0021017	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	108	---	---	---	---	PASS
ESRRA	2101	broad.mit.edu	37	11	64083442	64083442	+	3'UTR	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64083442A>G	uc001nzq.1	+	7					ESRRA_uc001nzr.1_3'UTR|ESRRA_uc001nzs.1_3'UTR|PRDX5_uc001nzu.2_5'Flank|PRDX5_uc001nzv.2_5'Flank|PRDX5_uc001nzw.2_5'Flank|PRDX5_uc001nzx.2_5'Flank	NM_004451	NP_004442	P11474	ERR1_HUMAN	estrogen-related receptor alpha						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein domain specific binding|sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0						GGACTGAGGCAAGGGGTGGGA	0.637													4	77	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88781056	88781056	+	5'UTR	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88781056C>A	uc001pcq.2	-	1					GRM5_uc009yvm.2_5'UTR|GRM5_uc009yvn.1_5'UTR	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	GAAAGGAGTTCAAGCCAATAA	0.463													4	23	---	---	---	---	PASS
SLC2A14	144195	broad.mit.edu	37	12	7982567	7982567	+	Missense_Mutation	SNP	G	A	A	rs145793375	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7982567G>A	uc001qtk.2	-	10	1170	c.377C>T	c.(376-378)GCC>GTC	p.A126V	SLC2A14_uc001qtl.2_Missense_Mutation_p.A103V|SLC2A14_uc001qtm.2_Missense_Mutation_p.A103V|SLC2A14_uc010sgg.1_Missense_Mutation_p.A17V|SLC2A14_uc001qtn.2_Missense_Mutation_p.A126V|SLC2A14_uc001qto.2_Intron|SLC2A14_uc010sgh.1_Missense_Mutation_p.A141V	NM_153449	NP_703150	Q8TDB8	GTR14_HUMAN	glucose transporter 14	126	Helical; Name=3; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)		GCCACCAGTGGCAGCCAACAG	0.478													3	69	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	9723393	9723393	+	RNA	SNP	G	A	A	rs141653604	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9723393G>A	uc001qwb.1	+	8		c.6073G>A								Homo sapiens mRNA; cDNA DKFZp686A1124 (from clone DKFZp686A1124).																		CCAGGTTAACGGTCATAACCG	0.473													13	52	---	---	---	---	PASS
SLCO1B1	10599	broad.mit.edu	37	12	21350054	21350054	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21350054C>A	uc001req.3	+	8	1006	c.902C>A	c.(901-903)ACA>AAA	p.T301K		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	301	Cytoplasmic (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)	GTGCTGGAAACAAATGATGAA	0.328													30	122	---	---	---	---	PASS
RECQL	5965	broad.mit.edu	37	12	21623127	21623127	+	3'UTR	SNP	A	G	G	rs143505576	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21623127A>G	uc001rex.2	-	16					RECQL_uc001rey.2_3'UTR|PYROXD1_uc001rew.2_3'UTR|PYROXD1_uc009ziq.2_3'UTR|PYROXD1_uc009zir.2_3'UTR	NM_032941	NP_116559	P46063	RECQ1_HUMAN	RecQ protein-like						DNA recombination|DNA repair|DNA replication	nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|DNA strand annealing activity|protein binding			ovary(1)|lung(1)	2						TAACATTCATATCAGGCATCA	0.299								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					3	172	---	---	---	---	PASS
GALNT4	8693	broad.mit.edu	37	12	89917323	89917323	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89917323C>G	uc001tbd.2	-	1	1213	c.1004G>C	c.(1003-1005)GGA>GCA	p.G335A	POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc001tbc.2_Intron|POC1B_uc010sun.1_Intron|GALNT4_uc001tbe.2_Missense_Mutation_p.G332A|GALNT4_uc010suo.1_Missense_Mutation_p.G27A	NM_003774	NP_003765	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	335	Catalytic subdomain B.|Lumenal (Potential).				carbohydrate metabolic process	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0						GTTTTCACCTCCCCACACTTC	0.522													42	257	---	---	---	---	PASS
SFRS9	8683	broad.mit.edu	37	12	120899912	120899912	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120899912G>T	uc001tyi.2	-	4	722	c.576C>A	c.(574-576)TAC>TAA	p.Y192*		NM_003769	NP_003760	Q13242	SRSF9_HUMAN	splicing factor, arginine/serine-rich 9	192	Interacts with SAFB1.|Arg/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAGACCGTGAGTAGCCATAGC	0.483													6	26	---	---	---	---	PASS
CLMN	79789	broad.mit.edu	37	14	95670748	95670748	+	Missense_Mutation	SNP	C	T	T	rs145924471		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95670748C>T	uc001yef.2	-	9	1054	c.938G>A	c.(937-939)CGC>CAC	p.R313H		NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin	313						integral to membrane	actin binding				0				Epithelial(152;0.193)		TTCTTTGATGCGAACAAAAGT	0.338													4	174	---	---	---	---	PASS
MIR409	574413	broad.mit.edu	37	14	101531657	101531657	+	RNA	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101531657C>A	hsa-mir-409|MI0001735	+			c.21C>A			MIR412_hsa-mir-412|MI0002464_5'Flank|uc010txp.1_5'Flank|MIR369_hsa-mir-369|MI0000777_5'Flank|MIR410_hsa-mir-410|MI0002465_5'Flank|MIR656_hsa-mir-656|MI0003678_5'Flank																	0						GGAGAGGTTACCCGAGCAACT	0.587													6	44	---	---	---	---	PASS
SECISBP2L	9728	broad.mit.edu	37	15	49305008	49305008	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49305008G>T	uc001zxe.1	-	12	1702	c.1568C>A	c.(1567-1569)ACT>AAT	p.T523N	SECISBP2L_uc001zxd.1_Missense_Mutation_p.T478N|SECISBP2L_uc010bep.1_Missense_Mutation_p.T285N	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	523										breast(1)|skin(1)	2						AGAAGCTGCAGTAACCACTAA	0.363													5	57	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	63125610	63125610	+	Intron	SNP	T	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63125610T>G	uc002alb.3	+						TLN2_uc002alc.3_Intron|TLN2_uc010uic.1_Intron|uc002ale.1_RNA	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						AATAGGCAGGTGAAGAGCCAG	0.438													13	74	---	---	---	---	PASS
NOX5	79400	broad.mit.edu	37	15	69348910	69348910	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69348910C>A	uc002ars.1	+	16	2192	c.2172C>A	c.(2170-2172)TTC>TTA	p.F724L	NOX5_uc002arp.1_Missense_Mutation_p.F706L|NOX5_uc002arq.1_Missense_Mutation_p.F678L|NOX5_uc010bid.1_Missense_Mutation_p.F689L|NOX5_uc002arr.1_Missense_Mutation_p.F696L|NOX5_uc010bie.1_Missense_Mutation_p.F524L|NOX5_uc010bif.1_RNA	NM_024505	NP_078781	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	724	Extracellular (Potential).				angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2						TCCAGGTGTTCCAGAAAGTGG	0.557													26	145	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	76075521	76075521	+	3'UTR	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76075521G>A	uc010umm.1	+	10					uc002bba.1_5'Flank					SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6;																		gagaggctgcgaaagcaggaa	0.194													5	218	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102292811	102292811	+	Silent	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102292811C>A	uc010usj.1	+	4	458	c.399C>A	c.(397-399)CGC>CGA	p.R133R	uc002bxo.2_RNA|uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		CCTGCACTCGCGTGGGAACGA	0.607													4	19	---	---	---	---	PASS
C16orf62	57020	broad.mit.edu	37	16	19661780	19661780	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19661780G>A	uc002dgn.1	+	25	2117	c.2105G>A	c.(2104-2106)CGG>CAG	p.R702Q	C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Missense_Mutation_p.R451Q	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	702						integral to membrane				ovary(1)	1						GCATTTGTCCGGGTATGTTCT	0.378													4	186	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30731617	30731617	+	Silent	SNP	A	C	C	rs145842115	byFrequency	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30731617A>C	uc002dze.1	+	19	3337	c.2952A>C	c.(2950-2952)CCA>CCC	p.P984P	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Silent_p.P841P|SRCAP_uc010bzz.1_Silent_p.P554P	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	984	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			CTGACCCCCCACCCCGGCCCA	0.572													36	77	---	---	---	---	PASS
MYLK3	91807	broad.mit.edu	37	16	46761073	46761073	+	Intron	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46761073G>A	uc002eei.3	-						MYLK3_uc010vge.1_Intron|MYLK3_uc002eej.1_3'UTR	NM_182493	NP_872299	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3						cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis	cytosol	ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	7		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				tctgTGGATAGAGCTCTCAAT	0.323													7	16	---	---	---	---	PASS
CMTM4	146223	broad.mit.edu	37	16	66651149	66651149	+	3'UTR	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66651149C>A	uc002epz.2	-	5					CMTM4_uc002eqa.2_3'UTR	NM_178818	NP_848933	Q8IZR5	CKLF4_HUMAN	chemokine-like factor superfamily 4 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		GAAATAGATACACAGTTCAAG	0.403													3	86	---	---	---	---	PASS
LRRC36	55282	broad.mit.edu	37	16	67375899	67375899	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67375899G>A	uc002esv.2	+	2	129	c.110G>A	c.(109-111)GGC>GAC	p.G37D	LRRC36_uc002esw.2_RNA	NM_018296	NP_060766	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36 isoform 1	37											0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		TCTTATGCTGGCAAAATCCAT	0.378													4	159	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161097	90161097	+	Intron	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90161097A>G	uc002fqp.2	+						uc002fqq.2_Silent_p.S109S					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		AGGGCAGCTCAAAATCCAGGA	0.632													5	39	---	---	---	---	PASS
KRT27	342574	broad.mit.edu	37	17	38938611	38938611	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38938611G>A	uc002hvg.2	-	1	176	c.135C>T	c.(133-135)TTC>TTT	p.F45F		NM_181537	NP_853515	Q7Z3Y8	K1C27_HUMAN	keratin 27	45	Head.|Gly-rich.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.000812)				AAGCACAAGAGAAGCCACTTC	0.617													3	11	---	---	---	---	PASS
MPP2	4355	broad.mit.edu	37	17	41955101	41955101	+	3'UTR	SNP	T	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41955101T>G	uc010wip.1	-	13					MPP2_uc002ien.1_3'UTR|MPP2_uc010wim.1_3'UTR|MPP2_uc002ieo.1_3'UTR|MPP2_uc010win.1_3'UTR|MPP2_uc010wio.1_3'UTR	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2						signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		TGGCAGGGGGTCACAGGTCAG	0.582													9	25	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587708	43587708	+	Intron	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587708A>G	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						AACAACCACCATCTCCAAATC	0.348													5	84	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587730	43587730	+	Intron	SNP	A	C	C	rs142536398	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587730A>C	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						GTATTGATTCATTTTATTCAT	0.328													3	72	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45219282	45219282	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45219282G>A	uc002ild.3	-	12	1615	c.1488C>T	c.(1486-1488)TAC>TAT	p.Y496Y	CDC27_uc002ile.3_Silent_p.Y502Y|CDC27_uc002ilf.3_Silent_p.Y495Y|CDC27_uc010wkp.1_Silent_p.Y435Y|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	496					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						AACCAGTATTGTAGTGGTGAG	0.378													18	477	---	---	---	---	PASS
SMURF2	64750	broad.mit.edu	37	17	62541851	62541851	+	3'UTR	SNP	A	G	G	rs59188589		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62541851A>G	uc002jep.1	-	19					SMURF2_uc002jeq.1_3'UTR|SMURF2_uc002jer.1_3'UTR	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			AAAAAAAAAAAGGGGGGGGGG	0.393													5	2	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3075746	3075746	+	Silent	SNP	G	A	A	rs16944353	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3075746G>A	uc002klp.2	-	35	4996	c.4662C>T	c.(4660-4662)GCC>GCT	p.A1554A	MYOM1_uc002klq.2_Silent_p.A1458A	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	1554						striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						ATTCAGCATAGGCCTCATCGT	0.443													10	16	---	---	---	---	PASS
PRKCSH	5589	broad.mit.edu	37	19	11558391	11558391	+	Silent	SNP	G	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11558391G>A	uc002mrt.2	+	11	1323	c.987G>A	c.(985-987)GAG>GAA	p.E329E	PRKCSH_uc002mru.2_Silent_p.E329E|PRKCSH_uc010xlz.1_Silent_p.E329E|PRKCSH_uc010dya.2_Silent_p.E111E|PRKCSH_uc002mrv.1_Silent_p.E329E|PRKCSH_uc010dyb.2_Silent_p.E329E	NM_002743	NP_002734	P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H isoform 1	329	Glu-rich (acidic).				innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding				0						ctgaagaagaggaggaggagg	0.438													3	11	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22363643	22363643	+	Silent	SNP	C	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22363643C>T	uc002nqs.1	-	3	1194	c.876G>A	c.(874-876)TCG>TCA	p.S292S		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	292	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GCTTTGAGGACGAGTTGGAAG	0.438													6	277	---	---	---	---	PASS
ZNF492	57615	broad.mit.edu	37	19	22836805	22836805	+	Missense_Mutation	SNP	G	A	A	rs139107317	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22836805G>A	uc002nqw.3	+	3	362	c.118G>A	c.(118-120)GCT>ACT	p.A40T		NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492	40	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				TGAGATGGTAGCTGAACCCCC	0.408													4	189	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22940373	22940373	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22940373T>C	uc010xrh.1	-	5	2065	c.2065A>G	c.(2065-2067)AAG>GAG	p.K689E		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TGAATTATCTTATGTTTTCTA	0.343													4	172	---	---	---	---	PASS
LSR	51599	broad.mit.edu	37	19	35758823	35758823	+	3'UTR	SNP	G	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35758823G>C	uc002nyl.2	+	10					LSR_uc002nym.2_3'UTR|LSR_uc002nyn.2_3'UTR|LSR_uc002nyo.2_3'UTR|LSR_uc010xsr.1_3'UTR|LSR_uc002nyp.2_3'UTR|USF2_uc010xss.1_5'Flank|USF2_uc002nyq.1_5'Flank|USF2_uc002nyr.1_5'Flank|USF2_uc002nys.1_5'Flank|USF2_uc002nyt.1_5'Flank|USF2_uc002nyu.1_5'Flank|USF2_uc002nyv.1_5'Flank	NM_205834	NP_991403	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor						embryo development|liver development	chylomicron|integral to membrane|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle	receptor activity				0	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CACTGATGAAGCCCTGCCATA	0.498													16	22	---	---	---	---	PASS
HRC	3270	broad.mit.edu	37	19	49656664	49656664	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49656664C>A	uc002pmv.2	-	1	2018	c.1831G>T	c.(1831-1833)GGT>TGT	p.G611C		NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	611					muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		GGCCACTTACCTGTGTCCTCA	0.597													3	72	---	---	---	---	PASS
SIRPB1	10326	broad.mit.edu	37	20	1585397	1585397	+	Intron	SNP	T	C	C	rs148754551	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1585397T>C	uc010gai.2	-						SIRPB1_uc002wfk.3_Intron|SIRPB1_uc002wfl.3_Missense_Mutation_p.T248A	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1						cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1						CCTCGGATGGTCTCAGACAAG	0.627													5	51	---	---	---	---	PASS
NCAM2	4685	broad.mit.edu	37	21	22849736	22849736	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22849736A>G	uc002yld.1	+	15	2270	c.2021A>G	c.(2020-2022)TAT>TGT	p.Y674C	NCAM2_uc011acb.1_Missense_Mutation_p.Y532C	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	674	Fibronectin type-III 2.|Extracellular (Potential).				neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGATTGGGATATTCTGAACCG	0.368													21	129	---	---	---	---	PASS
FTCD	10841	broad.mit.edu	37	21	47558836	47558836	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47558836T>C	uc002zif.2	-	11	1306	c.1262A>G	c.(1261-1263)GAA>GGA	p.E421G	FTCD_uc002zie.2_Intron|FTCD_uc002zig.2_Missense_Mutation_p.E421G|FTCD_uc002zih.2_Missense_Mutation_p.E421G|FTCD_uc010gqf.2_Intron|FTCD_uc010gqg.1_Missense_Mutation_p.E290G	NM_006657	NP_006648	O95954	FTCD_HUMAN	formiminotransferase cyclodeaminase	421	Cyclodeaminase/cyclohydrolase (By similarity).				folic acid-containing compound metabolic process|histidine catabolic process	centriole|cytosol|Golgi apparatus	folic acid binding|formimidoyltetrahydrofolate cyclodeaminase activity|glutamate formimidoyltransferase activity			pancreas(1)|skin(1)	2	Breast(49;0.214)			Colorectal(79;0.235)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	CCTCATTGCTTCCTGCCATAA	0.627													4	26	---	---	---	---	PASS
GGT5	2687	broad.mit.edu	37	22	24622217	24622217	+	Silent	SNP	C	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24622217C>A	uc002zzo.3	-	8	1473	c.1056G>T	c.(1054-1056)CTG>CTT	p.L352L	GGT5_uc002zzp.3_Silent_p.L352L|GGT5_uc002zzr.3_Silent_p.L320L|GGT5_uc002zzq.3_Silent_p.L320L|GGT5_uc011ajm.1_Silent_p.L275L|GGT5_uc011ajn.1_RNA	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b	352	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3						TCTCCCCCAGCAGGTCCCGGG	0.682													3	52	---	---	---	---	PASS
SUN2	25777	broad.mit.edu	37	22	39132222	39132222	+	3'UTR	SNP	T	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39132222T>G	uc003awh.1	-	19					SUN2_uc011anz.1_3'UTR|SUN2_uc011aoa.1_3'UTR|SUN2_uc003awi.1_3'UTR|SUN2_uc010gxq.1_3'UTR|SUN2_uc010gxr.1_3'UTR|SUN2_uc010gxs.1_Intron	NM_015374	NP_056189	Q9UH99	SUN2_HUMAN	unc-84 homolog B						centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex	lamin binding|microtubule binding			large_intestine(1)|skin(1)	2						AGCGGCGGGGTGCTGTTCACC	0.627													8	14	---	---	---	---	PASS
COX7B	1349	broad.mit.edu	37	X	77160816	77160816	+	3'UTR	SNP	A	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77160816A>G	uc004ecu.1	+	3						NM_001866	NP_001857	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb precursor						respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TTGATGCCAAATTAAAGCACT	0.343													4	48	---	---	---	---	PASS
PRAMEF11	440560	broad.mit.edu	37	1	12888267	12888268	+	Intron	INS	-	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12888267_12888268insG	uc001auk.2	-							NM_001146344	NP_001139816	O60813	PRA11_HUMAN	PRAME family member 11												0						CCACCACCATCCCCCTTGGGCC	0.609													4	2	---	---	---	---	
RAP1GAP	5909	broad.mit.edu	37	1	21934994	21934995	+	Intron	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21934994_21934995insA	uc001bex.2	-						RAP1GAP_uc001bev.2_Intron|RAP1GAP_uc001bew.2_Intron|RAP1GAP_uc001bey.2_Intron	NM_002885	NP_002876	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein isoform c						regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CGCCTTCCCCCAGGCCACTCCA	0.639													4	4	---	---	---	---	
ZBTB8OS	339487	broad.mit.edu	37	1	33100582	33100582	+	Intron	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33100582delT	uc001bvp.2	-						ZBTB8OS_uc001bvo.1_Intron|ZBTB8OS_uc001bvq.2_Intron	NM_178547	NP_848642	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite												0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TGTTGGAATCTTTTTTTTTTT	0.219													4	2	---	---	---	---	
COL9A2	1298	broad.mit.edu	37	1	40769637	40769637	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40769637delG	uc001cfh.1	-	26	1401	c.1331delC	c.(1330-1332)CCAfs	p.P444fs	COL9A2_uc001cfi.1_Frame_Shift_Del_p.P263fs	NM_001852	NP_001843	Q14055	CO9A2_HUMAN	alpha 2 type IX collagen precursor	444	Triple-helical region 3 (COL3).				axon guidance|skeletal system development	collagen type IX				ovary(2)	2	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			GGCCACCCCTGGGTCACCCTG	0.736													4	2	---	---	---	---	
KANK4	163782	broad.mit.edu	37	1	62712977	62712977	+	Intron	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62712977delT	uc001dah.3	-						KANK4_uc001dai.3_Intron|KANK4_uc001daf.3_Intron|KANK4_uc001dag.3_Intron	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38											ovary(3)|skin(2)|lung(1)	6						AAACAGCTACTtttttttttt	0.244													6	3	---	---	---	---	
SFRS11	9295	broad.mit.edu	37	1	70687370	70687371	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70687370_70687371insG	uc001des.2	+	2	175_176	c.51_52insG	c.(49-54)GGCGGGfs	p.G17fs	SFRS11_uc009wbi.2_Frame_Shift_Ins_p.G17fs|SFRS11_uc009wbj.1_Frame_Shift_Ins_p.G17fs|SFRS11_uc010oqo.1_Frame_Shift_Ins_p.G17fs|SFRS11_uc001det.2_Frame_Shift_Ins_p.G17fs|SFRS11_uc001deu.2_Frame_Shift_Ins_p.G17fs	NM_004768	NP_004759	Q05519	SRS11_HUMAN	splicing factor, arginine/serine-rich 11	17_18	Poly-Gly.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0						GCCCCAGCGGCGGGCCcggtgg	0.495													253	7	---	---	---	---	
COL24A1	255631	broad.mit.edu	37	1	86453266	86453268	+	Intron	DEL	TCT	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86453266_86453268delTCT	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		TTAGTCTCTCTCTTCTTCTTCTT	0.360													184	7	---	---	---	---	
PSMA5	5686	broad.mit.edu	37	1	109952507	109952507	+	Intron	DEL	A	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109952507delA	uc001dxn.2	-						PSMA5_uc010ovj.1_Intron	NM_002790	NP_002781	P28066	PSA5_HUMAN	proteasome alpha 5 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	protein binding|threonine-type endopeptidase activity				0		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.045)|Colorectal(144;0.116)|Epithelial(280;0.187)|all cancers(265;0.196)|LUSC - Lung squamous cell carcinoma(189;0.235)		ctcatctcttaaaaaaaaaac	0.149													129	7	---	---	---	---	
CHI3L2	1117	broad.mit.edu	37	1	111772303	111772304	+	Intron	INS	-	AAAAAAA	AAAAAAA	rs61237890		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111772303_111772304insAAAAAAA	uc001eam.2	+						CHI3L2_uc001ean.2_Intron|CHI3L2_uc001eao.2_5'Flank|CHI3L2_uc009wga.2_5'Flank	NM_004000	NP_003991	Q15782	CH3L2_HUMAN	chitinase 3-like 2 isoform a						chitin catabolic process	extracellular space	cation binding|chitinase activity			central_nervous_system(1)	1		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		gactccgtctcaaaaaaaaaaa	0.193													6	5	---	---	---	---	
NUP210L	91181	broad.mit.edu	37	1	153982269	153982269	+	Intron	DEL	A	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153982269delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			acccagtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
CFHR4	10877	broad.mit.edu	37	1	196879301	196879302	+	Intron	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196879301_196879302insA	uc001gto.2	+						CFHR4_uc009wyy.2_Intron|CFHR4_uc001gtp.2_Intron	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor							extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						aaaaagtaaagaaaaaaaaaaA	0.109													4	2	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236228307	236228308	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236228307_236228308insC	uc001hxo.2	-	1	174_175	c.72_73insG	c.(70-75)GGGCCTfs	p.G24fs	NID1_uc009xgd.2_Frame_Shift_Ins_p.G24fs|uc001hxp.1_Frame_Shift_Ins_p.A150fs	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	24_25					cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	CAGCCCACAGGCCCCGCCAGCA	0.708													4	2	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32340026	32340027	+	Intron	INS	-	T	T	rs67016851		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32340026_32340027insT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ATAAAGTTAAAttttttttttt	0.114													9	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58479808	58479808	+	IGR	DEL	A	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58479808delA								FANCL (11293 upstream) : None (None downstream)																							TTTGtaaattaaaaaaaaaaa	0.234													5	4	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77057642	77057645	+	Intron	DEL	GTGT	-	-	rs72344502		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77057642_77057645delGTGT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		CAgtgtgtgcgtgtgtgtgtgtgt	0.304													4	2	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89082220	89082223	+	Intron	DEL	TGAT	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89082220_89082223delTGAT	uc010fhf.2	+						FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TGTGTACATATGATTGATTATGTA	0.328													56	9	---	---	---	---	
UGGT1	56886	broad.mit.edu	37	2	128910509	128910509	+	Intron	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128910509delT	uc002tps.2	+						UGGT1_uc010fme.1_Intron|UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						AACCTTATGCTTTTTTTGACT	0.353													348	7	---	---	---	---	
NEB	4703	broad.mit.edu	37	2	152417311	152417312	+	Intron	INS	-	C	C	rs150437657	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152417311_152417312insC	uc010fnx.2	-						NEB_uc002txr.2_Intron	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCTCACACACTCCCTACTAACT	0.411													10	5	---	---	---	---	
GALNT5	11227	broad.mit.edu	37	2	158165415	158165416	+	Intron	INS	-	T	T	rs140945706	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158165415_158165416insT	uc002tzg.2	+						GALNT5_uc010zci.1_Intron	NM_014568	NP_055383	Q7Z7M9	GALT5_HUMAN	N-acetylgalactosaminyltransferase 5						glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)|skin(1)	4						TTGACAAGTCCtttttttttta	0.307													4	4	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159992541	159992562	+	Intron	DEL	GTGTGTGTGTGTGTGTGTGTGC	-	-	rs55994009	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159992541_159992562delGTGTGTGTGTGTGTGTGTGTGC	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uah.1_5'Flank	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgCGCGCGCGCGC	0.396													5	4	---	---	---	---	
SLC4A10	57282	broad.mit.edu	37	2	162729068	162729068	+	Intron	DEL	A	-	-	rs5835886		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162729068delA	uc002ubx.3	+						SLC4A10_uc010fpa.1_Intron|SLC4A10_uc010zcr.1_Intron|SLC4A10_uc002uby.3_Intron|SLC4A10_uc010zcs.1_Intron	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5						TTGCCTATTCAAAAAAAAAAA	0.303													3	3	---	---	---	---	
ARL8B	55207	broad.mit.edu	37	3	5213916	5213917	+	Intron	INS	-	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5213916_5213917insT	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654	Q9NVJ2	ARL8B_HUMAN	ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)		TGTGTAAGTGGTTTTTTTTTGT	0.371													393	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	83790732	83790733	+	IGR	INS	-	GGAG	GGAG	rs13089076		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83790732_83790733insGGAG								None (None upstream) : None (None downstream)																							aaggaaggaaaggagggaggga	0.089													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103257382	103257382	+	IGR	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103257382delT								None (None upstream) : None (None downstream)																							TTTACACAGCTTTTTTTTTTT	0.348													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	122242444	122242444	+	IGR	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122242444delT								KPNA1 (8658 upstream) : PARP9 (4318 downstream)																							cttttctttcttttttttttt	0.000													4	2	---	---	---	---	
TFRC	7037	broad.mit.edu	37	3	195792272	195792273	+	Intron	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195792272_195792273insA	uc003fvz.3	-						TFRC_uc003fwa.3_Intron|TFRC_uc010hzy.2_Intron|TFRC_uc011btr.1_Intron	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor						cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		GAAAAGAAAACAAAAAAAAAgc	0.322			T	BCL6	NHL								7	5	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39280429	39280429	+	Intron	DEL	T	-	-	rs5857667		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39280429delT	uc003gtv.2	+						WDR19_uc011byi.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						TTTTGATGTATTTTTTTTAAT	0.388													6	5	---	---	---	---	
MANBA	4126	broad.mit.edu	37	4	103592591	103592592	+	Intron	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103592591_103592592insA	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		TCATAATTTGGAAAAAAAAAAC	0.327													48	7	---	---	---	---	
YTHDC2	64848	broad.mit.edu	37	5	112862509	112862509	+	Intron	DEL	A	-	-	rs141139411		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112862509delA	uc003kqn.2	+						YTHDC2_uc010jce.1_Intron|YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TTGTTTATAGAAAAAAAAAAA	0.209													37	8	---	---	---	---	
CLINT1	9685	broad.mit.edu	37	5	157236506	157236506	+	Intron	DEL	A	-	-	rs72318416		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157236506delA	uc003lxj.1	-						CLINT1_uc003lxi.1_Intron|CLINT1_uc011ddv.1_Intron	NM_014666	NP_055481	Q14677	EPN4_HUMAN	epsin 4						endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			gaagtctattaaAAAAAAAAA	0.154													14	7	---	---	---	---	
BTNL9	153579	broad.mit.edu	37	5	180486891	180486892	+	3'UTR	INS	-	G	G	rs151240170	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180486891_180486892insG	uc003mmt.2	+	11						NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor							integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGACTGGCCCCGGGGGGCCCCC	0.683													4	2	---	---	---	---	
ZNF76	7629	broad.mit.edu	37	6	35253702	35253703	+	Intron	INS	-	C	C	rs142304763	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35253702_35253703insC	uc003oki.1	+						ZNF76_uc011dsy.1_Intron|ZNF76_uc011dsz.1_Intron|ZNF76_uc003okj.1_Intron|ZNF76_uc011dsx.1_Intron	NM_003427	NP_003418	P36508	ZNF76_HUMAN	zinc finger protein 76 (expressed in testis)						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGTGATGGGTTCGGCAAGGCAA	0.505													5	3	---	---	---	---	
REV3L	5980	broad.mit.edu	37	6	111685194	111685195	+	Intron	DEL	AC	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111685194_111685195delAC	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron|REV3L_uc003pva.1_Intron	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		ATAAAAAAAAACACACACACAC	0.307								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					173	7	---	---	---	---	
PEX1	5189	broad.mit.edu	37	7	92135419	92135420	+	Intron	INS	-	AAGACTTAAAATTTCT	AAGACTTAAAATTTCT	rs145764168	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92135419_92135420insAAGACTTAAAATTTCT	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_Intron	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTAGAAAGCCAAAGAAATTTTA	0.272													16	7	---	---	---	---	
REEP4	80346	broad.mit.edu	37	8	21996234	21996235	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21996234_21996235insG	uc003xau.1	-	7	1078_1079	c.625_626insC	c.(625-627)CGGfs	p.R209fs	REEP4_uc010ltt.1_Frame_Shift_Ins_p.P163fs	NM_025232	NP_079508	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	209						integral to membrane				skin(1)	1				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		GGCTGGCGCCCGGGGGACTGCC	0.663													253	11	---	---	---	---	
OTUD6B	51633	broad.mit.edu	37	8	92083177	92083177	+	Intron	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92083177delT	uc003yeu.3	+						uc003yet.2_5'Flank|OTUD6B_uc011lgh.1_Intron	NM_016023	NP_057107	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B											ovary(2)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(11;0.0187)			GTTAATGAAGTTTTTTTTTTT	0.358													5	4	---	---	---	---	
TG	7038	broad.mit.edu	37	8	133984820	133984821	+	Intron	DEL	TG	-	-	rs1554541		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133984820_133984821delTG	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TGTGGTTTTTTGTTTTTTTTTT	0.351													138	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	43840027	43840028	+	Intron	INS	-	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43840027_43840028insT	uc004acz.1	+											Homo sapiens cDNA FLJ30083 fis, clone BGGI12001097, weakly similar to Homo sapiens contactin associated protein (Caspr) mRNA.																		ATGGGGGCATCTTTTTTTTTTT	0.436													6	5	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112900482	112900483	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112900482_112900483insC	uc004bei.2	+	9	3546_3547	c.3354_3355insC	c.(3352-3357)GGGCCCfs	p.G1118fs	PALM2-AKAP2_uc004bek.3_Frame_Shift_Ins_p.G886fs|PALM2-AKAP2_uc004bej.3_Frame_Shift_Ins_p.G886fs|PALM2-AKAP2_uc004bel.1_Frame_Shift_Ins_p.G696fs|AKAP2_uc011lwi.1_Frame_Shift_Ins_p.G744fs|AKAP2_uc004bem.2_Frame_Shift_Ins_p.G744fs|PALM2-AKAP2_uc010mtw.1_Frame_Shift_Ins_p.G704fs|AKAP2_uc011lwj.1_Frame_Shift_Ins_p.G655fs|PALM2-AKAP2_uc004ben.2_Frame_Shift_Ins_p.G655fs	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	655_656							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						GGGAAAGGGGGCCCCCCCAGCC	0.564													36	11	---	---	---	---	
ZNF79	7633	broad.mit.edu	37	9	130207628	130207629	+	3'UTR	INS	-	C	C	rs147295876	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130207628_130207629insC	uc004bqw.3	+	5					ZNF79_uc011maf.1_3'UTR|ZNF79_uc011mag.1_3'UTR	NM_007135	NP_009066	Q15937	ZNF79_HUMAN	zinc finger protein 79						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1						CCTTCAATAAACAGCCACTATT	0.460													4	5	---	---	---	---	
LAMC3	10319	broad.mit.edu	37	9	133967312	133967313	+	3'UTR	INS	-	CC	CC	rs145123981		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133967312_133967313insCC	uc004caa.1	+	28					LAMC3_uc010mze.1_3'UTR	NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor						cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GTGGATAGTCACTCCCTGCCGA	0.594													3	3	---	---	---	---	
FBXO18	84893	broad.mit.edu	37	10	5945295	5945295	+	Intron	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5945295delT	uc001iis.2	+						FBXO18_uc001iir.2_Intron|FBXO18_uc009xig.2_Intron|FBXO18_uc001iit.2_Intron	NM_178150	NP_835363	Q8NFZ0	FBX18_HUMAN	F-box only protein, helicase, 18 isoform 2						DNA repair	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(2)|skin(1)	3						TTCCATGAAGttttttttttt	0.164													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	71193238	71193239	+	IGR	INS	-	AC	AC	rs139709581	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71193238_71193239insAC								TACR2 (16564 upstream) : TSPAN15 (17987 downstream)																							TATCTATATCTACACACACACA	0.262													5	4	---	---	---	---	
KIAA1274	27143	broad.mit.edu	37	10	72245965	72245966	+	Intron	INS	-	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72245965_72245966insT	uc001jrd.3	+							NM_014431	NP_055246	Q9ULE6	PALD_HUMAN	KIAA1274											ovary(2)|central_nervous_system(1)	3						AAGTCAATATCTTTTTTTTTTT	0.426													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	99823423	99823430	+	IGR	DEL	TCTTTCTT	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99823423_99823430delTCTTTCTT								CRTAC1 (32838 upstream) : C10orf28 (70951 downstream)																							cctccctccctctttctttctttctttc	0.000													4	3	---	---	---	---	
EPS8L2	64787	broad.mit.edu	37	11	725877	725878	+	Intron	INS	-	C	C	rs144060424	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:725877_725878insC	uc001lqt.2	+						EPS8L2_uc001lqu.2_Intron|EPS8L2_uc010qwk.1_Intron|EPS8L2_uc001lqv.2_Intron|EPS8L2_uc001lqw.2_Intron|EPS8L2_uc001lqx.2_Intron|EPS8L2_uc001lqy.2_Intron	NM_022772	NP_073609	Q9H6S3	ES8L2_HUMAN	epidermal growth factor receptor pathway							cytoplasm				pancreas(1)	1		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGGGTCGCAGCCCCCAGCTTC	0.752													6	7	---	---	---	---	
MRVI1	10335	broad.mit.edu	37	11	10701940	10701941	+	Intron	INS	-	A	A	rs148524669	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10701940_10701941insA	uc010rcc.1	-						MRVI1_uc009ygb.1_Intron|MRVI1_uc001mix.2_Intron|MRVI1_uc001miz.2_Intron|MRVI1_uc009ygc.1_Intron|MRVI1_uc010rcd.1_Intron|MRVI1_uc009ygd.1_Intron	NM_001100167	NP_001093637	Q9Y6F6	MRVI1_HUMAN	JAW1-related protein isoform c						platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		aggaaggaaggaaggaaggaag	0.025													4	5	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19177150	19177150	+	Intron	DEL	G	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19177150delG	uc001mpi.2	+						ZDHHC13_uc001mpj.2_Intron	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform						positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						aaaaaaaaaaGATTGTTTCCA	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49327166	49327167	+	IGR	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49327166_49327167insA								FOLH1 (96944 upstream) : LOC440040 (252913 downstream)																							GTAAAGTTAGcaaaaaaaaaaa	0.208													12	10	---	---	---	---	
SF3B2	10992	broad.mit.edu	37	11	65825443	65825444	+	Intron	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65825443_65825444insA	uc001ogy.1	+							NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2						interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3						aactccgtctcaaaaaaaaaaa	0.183													6	4	---	---	---	---	
MED17	9440	broad.mit.edu	37	11	93535275	93535276	+	Intron	INS	-	T	T	rs142446531		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93535275_93535276insT	uc001pem.3	+							NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCTGTAGAGTGttttttttttt	0.139													5	3	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108788635	108788637	+	In_Frame_Del	DEL	TGA	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108788635_108788637delTGA	uc001pkm.2	+	17	2405_2407	c.2340_2342delTGA	c.(2338-2343)AGTGAT>AGT	p.D788del	DDX10_uc001pkl.1_In_Frame_Del_p.D788del	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	788							ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		TGGATTGGAGtgatgatgatgat	0.310			T	NUP98	AML*								207	9	---	---	---	---	
NEDD1	121441	broad.mit.edu	37	12	97339670	97339670	+	Intron	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97339670delT	uc001teu.3	+						NEDD1_uc001tev.3_Intron|NEDD1_uc010svc.1_Intron|NEDD1_uc001tew.2_Intron|NEDD1_uc001tex.2_Intron	NM_152905	NP_690869	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally						cell division|G2/M transition of mitotic cell cycle|mitosis	cytosol					0						ACCTTACTTGTTTTTTTTTTA	0.318													101	7	---	---	---	---	
MYL2	4633	broad.mit.edu	37	12	111349074	111349074	+	Intron	DEL	T	-	-	rs147632472	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111349074delT	uc001try.3	-						MYL2_uc001trx.3_Intron	NM_000432	NP_000423	P10916	MLRV_HUMAN	slow cardiac myosin regulatory light chain 2						cardiac myofibril assembly|heart contraction|muscle filament sliding|negative regulation of cell growth|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	cytosol|myosin complex|sarcomere	actin monomer binding|calcium ion binding|myosin heavy chain binding|structural constituent of muscle			ovary(1)	1						GACGGATAGCTGGGGGGTGGG	0.493													4	2	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	130919595	130919596	+	Intron	INS	-	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130919595_130919596insT	uc001uil.2	-						RIMBP2_uc001uim.2_Intron|RIMBP2_uc001uin.1_Intron	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CCACCAGAAtcttttttttttt	0.327													6	3	---	---	---	---	
ULK1	8408	broad.mit.edu	37	12	132403267	132403275	+	Intron	DEL	GGGTGTGTG	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132403267_132403275delGGGTGTGTG	uc001uje.2	+							NM_003565	NP_003556	O75385	ULK1_HUMAN	Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		TCTGGCTGGAGGGTgtgtggggtgtgtgg	0.316													8	4	---	---	---	---	
UFM1	51569	broad.mit.edu	37	13	38932175	38932176	+	Intron	DEL	TG	-	-	rs72454711		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38932175_38932176delTG	uc001uwu.2	+						UFM1_uc010abz.2_Intron|UFM1_uc010aca.2_Intron	NM_016617	NP_057701	P61960	UFM1_HUMAN	ubiquitin-fold modifier 1 precursor						protein ufmylation	cytoplasm|nucleus	protein binding				0		Lung NSC(96;3.18e-06)|Prostate(109;0.00314)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;1.05e-08)|Epithelial(112;1.44e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000855)|BRCA - Breast invasive adenocarcinoma(63;0.00342)|GBM - Glioblastoma multiforme(144;0.0132)		CTTATAGTTTtgtgtgtgtgtg	0.228													7	7	---	---	---	---	
SIP1	8487	broad.mit.edu	37	14	39601187	39601188	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39601187_39601188insT	uc001wuq.2	+	8	681_682	c.659_660insT	c.(658-660)GCTfs	p.A220fs	SIP1_uc001wur.2_Frame_Shift_Ins_p.A220fs|SIP1_uc001wus.2_Frame_Shift_Ins_p.A205fs|SIP1_uc010amx.2_RNA	NM_003616	NP_003607	O14893	GEMI2_HUMAN	SMN-interacting protein 1 isoform alpha	220					ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)		GCTTTATTGGCTTGTCTTGAAA	0.347													381	11	---	---	---	---	
ATP5S	27109	broad.mit.edu	37	14	50789101	50789102	+	Intron	INS	-	ATAC	ATAC	rs148370941	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50789101_50789102insATAC	uc001wxw.1	+						ATP5S_uc001wxv.2_Intron|ATP5S_uc001wxx.1_Intron|ATP5S_uc010ant.1_Intron	NM_001003803	NP_001003803	Q99766	ATP5S_HUMAN	ATP synthase, H+ transporting, mitochondrial F0						ATP biosynthetic process	mitochondrial inner membrane|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity			ovary(1)|skin(1)	2	all_epithelial(31;0.000636)|Breast(41;0.0102)			OV - Ovarian serous cystadenocarcinoma(311;0.0685)		GGATCTCACTAATTTATCTTCC	0.297													9	5	---	---	---	---	
DNAL1	83544	broad.mit.edu	37	14	74125865	74125867	+	Intron	DEL	TTT	-	-	rs36115036		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74125865_74125867delTTT	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615	Q4LDG9	DNAL1_HUMAN	axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)		TATAGTACAAttttttttttttt	0.138													17	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5995601	5995601	+	IGR	DEL	T	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5995601delT								FAM86A (847812 upstream) : A2BP1 (73531 downstream)																							ctcagagagattaataactcc	0.000													4	2	---	---	---	---	
CP110	9738	broad.mit.edu	37	16	19553060	19553063	+	Intron	DEL	GAAG	-	-	rs149433681		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19553060_19553063delGAAG	uc002dgl.3	+						CP110_uc002dgk.3_Intron			O43303	CP110_HUMAN	RecName: Full=Centrosomal protein of 110 kDa;          Short=Cep110;						centriole replication|G2/M transition of mitotic cell cycle|regulation of cytokinesis	centriole|cytosol	protein binding				0						AGGGAAGGGAGAAGGAAGGAAGGA	0.196													5	6	---	---	---	---	
MT1X	4501	broad.mit.edu	37	16	56718015	56718015	+	3'UTR	DEL	A	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56718015delA	uc002ejy.2	+	3					MT1X_uc002ejz.2_RNA	NM_005952	NP_005943	P80297	MT1X_HUMAN	metallothionein 1X						response to metal ion		metal ion binding				0						ATAAACCTGGAtttttttttt	0.398													176	7	---	---	---	---	
FOXF1	2294	broad.mit.edu	37	16	86545125	86545126	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86545125_86545126insC	uc002fjl.2	+	1	993_994	c.950_951insC	c.(949-951)AACfs	p.N317fs	uc002fjk.1_5'Flank	NM_001451	NP_001442	Q12946	FOXF1_HUMAN	forkhead box F1	317					branching involved in open tracheal system development|cardiac left ventricle morphogenesis|embryonic ectodermal digestive tract morphogenesis|endocardial cushion development|in utero embryonic development|lung vasculature development|midgut development|pancreas development|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|ureter development|venous blood vessel development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|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 factor binding				0						CTGCACCAGAACAGCCACAACG	0.683													5	5	---	---	---	---	
VPS53	55275	broad.mit.edu	37	17	602753	602754	+	Intron	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:602753_602754insA	uc002frn.2	-						VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		AGTTTTGCTTTAAAAAAAAAAA	0.208													26	7	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2888574	2888574	+	Intron	DEL	T	-	-	rs71377564		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2888574delT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						AACAGTGATGTTTTTTTTTTT	0.398													8	4	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39920786	39920787	+	Intron	INS	-	GAAA	GAAA	rs60346985		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39920786_39920787insGAAA	uc002hxq.2	-						JUP_uc010wfs.1_Intron|JUP_uc002hxr.2_Intron|JUP_uc002hxs.2_Intron	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		gactccgtcagaaaaaaaaaaa	0.188													4	2	---	---	---	---	
ITGB3	3690	broad.mit.edu	37	17	45367839	45367841	+	Intron	DEL	AGA	-	-	rs78819126		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45367839_45367841delAGA	uc002ilj.2	+						ITGB3_uc002ili.1_Intron|ITGB3_uc010wkr.1_Intron	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)	aggaaggaagagagaaagaagga	0.453													7	5	---	---	---	---	
RNF43	54894	broad.mit.edu	37	17	56435501	56435502	+	Frame_Shift_Ins	INS	-	G	G	rs144487242	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56435501_56435502insG	uc002iwf.2	-	8	3591_3592	c.1635_1636insC	c.(1633-1638)TCCAGCfs	p.S545fs	RNF43_uc010wnv.1_Frame_Shift_Ins_p.S504fs|RNF43_uc002iwh.3_Frame_Shift_Ins_p.S545fs|RNF43_uc002iwg.3_Frame_Shift_Ins_p.S545fs|RNF43_uc010dcw.2_Frame_Shift_Ins_p.S418fs	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	545_546	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGGACATGGCTGGAAACCTGGG	0.624													195	7	---	---	---	---	
ZADH2	284273	broad.mit.edu	37	18	72913186	72913186	+	3'UTR	DEL	T	-	-	rs67264905		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72913186delT	uc002llx.2	-	2					ZADH2_uc010dqv.2_3'UTR	NM_175907	NP_787103	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain							peroxisome	oxidoreductase activity|zinc ion binding				0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		TATTAGCACATTTTTTTTTTT	0.303													5	3	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	8969553	8969554	+	Intron	INS	-	TT	TT	rs36058947		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8969553_8969554insTT	uc002mkp.2	-						MUC16_uc010dwi.2_Intron|MUC16_uc010dwj.2_Intron|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						tttttcttttcttttttttttt	0.178													5	4	---	---	---	---	
ZNF699	374879	broad.mit.edu	37	19	9408812	9408812	+	Intron	DEL	T	-	-	rs144670815		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9408812delT	uc002mlc.1	-							NM_198535	NP_940937	Q32M78	ZN699_HUMAN	zinc finger protein 699						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						aatttatttattttttttttt	0.184													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14997642	14997642	+	IGR	DEL	A	-	-	rs34351275		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14997642delA								OR7A17 (5475 upstream) : OR7C2 (54659 downstream)																							ccatctcactaaaaaaaaaaa	0.184													4	4	---	---	---	---	
NLRP2	55655	broad.mit.edu	37	19	55511961	55511961	+	Intron	DEL	A	-	-	rs34129339		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55511961delA	uc002qij.2	+						NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		actgtcttttaaaaaaaaaaa	0.194													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58889651	58889662	+	Intron	DEL	CATTCTCCCATT	-	-	rs114216255	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58889651_58889662delCATTCTCCCATT	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		tccatccatccattctcccattcatccatcct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11114454	11114455	+	IGR	DEL	AA	-	-	rs71860936		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11114454_11114455delAA								BAGE (15517 upstream) : None (None downstream)																							ATTTTTTTTTAAAAAGCAAGTT	0.307													14	7	---	---	---	---	
TMPRSS15	5651	broad.mit.edu	37	21	19725531	19725532	+	Intron	INS	-	T	T			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19725531_19725532insT	uc002ykw.2	-							NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor						proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						CATTCTATTTATTTTTTTTAAA	0.257													4	6	---	---	---	---	
IL10RB	3588	broad.mit.edu	37	21	34660710	34660711	+	Intron	DEL	AG	-	-	rs66834406		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660710_34660711delAG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						acacacacacagacacGCCTCT	0.401													6	4	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22657416	22657419	+	Intron	DEL	ACTA	-	-	rs138873705		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22657416_22657419delACTA	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_Intron|LOC96610_uc010gto.2_Intron					Parts of antibodies, mostly variable regions.												0						ATGATGAAATACTAACTGTTTTAC	0.402													5	3	---	---	---	---	
SLC2A11	66035	broad.mit.edu	37	22	24199261	24199261	+	Intron	DEL	G	-	-	rs71184919		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24199261delG	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_5'UTR|SLC2A11_uc011ajd.1_5'Flank|SLC2A11_uc002zyp.3_5'Flank	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						GTGTGTGTGTGGGGGGGGGGG	0.612													9	4	---	---	---	---	
NHS	4810	broad.mit.edu	37	X	17743354	17743355	+	Intron	INS	-	A	A	rs10712155		TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17743354_17743355insA	uc004cxx.2	+						NHS_uc011mix.1_Intron|NHS_uc004cxy.2_Intron|NHS_uc004cxz.2_Intron|NHS_uc004cya.2_Intron	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1							nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)					TTCTGTTAAAGAAAAAAAAAAA	0.351													36	8	---	---	---	---	
PDHA1	5160	broad.mit.edu	37	X	19363864	19363864	+	Intron	DEL	C	-	-			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19363864delC	uc004czg.3	+						PDHA1_uc004czh.3_Intron|PDHA1_uc011mjc.1_Intron|PDHA1_uc011mjd.1_Intron|PDHA1_uc010nfk.2_Intron	NM_000284	NP_000275	P08559	ODPA_HUMAN	pyruvate dehydrogenase E1 alpha 1 precursor						glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)	TTTGCAGGGTCCCCCCCCCCC	0.468													6	3	---	---	---	---	
HUWE1	10075	broad.mit.edu	37	X	53565685	53565686	+	Intron	INS	-	CT	CT	rs3008197	by1000genomes	TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53565685_53565686insCT	uc004dsp.2	-						HUWE1_uc004dsn.2_Intron|HUWE1_uc004dsq.1_Intron	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1						base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						acacacacacactctctctctc	0.302													4	5	---	---	---	---	
ATRX	546	broad.mit.edu	37	X	76763679	76763680	+	3'UTR	INS	-	A	A			TCGA-CH-5746-01A-11D-1576-08	TCGA-CH-5746-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76763679_76763680insA	uc004ecp.3	-	35					ATRX_uc004ecq.3_3'UTR|ATRX_uc004eco.3_3'UTR	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ATGCCCTATTTAAAAAAAAAAA	0.312			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						4	2	---	---	---	---	
