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
LOC728989	728989	broad.mit.edu	37	1	146494510	146494510	+	Silent	SNP	T	C	C	rs11585592	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146494510T>C	uc001epd.2	-	4	563	c.489A>G	c.(487-489)GCA>GCG	p.A163A		NR_024442				SubName: Full=cDNA FLJ59595, highly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA;												0						TGCCAGGCAGTGCAGGGATGT	0.557													3	22	---	---	---	---	PASS
LOC728989	728989	broad.mit.edu	37	1	146494511	146494511	+	Missense_Mutation	SNP	G	A	A	rs11587748	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146494511G>A	uc001epd.2	-	4	562	c.488C>T	c.(487-489)GCA>GTA	p.A163V		NR_024442				SubName: Full=cDNA FLJ59595, highly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA;												0						GCCAGGCAGTGCAGGGATGTG	0.557													3	24	---	---	---	---	PASS
LAMC1	3915	broad.mit.edu	37	1	183077436	183077436	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183077436G>A	uc001gpy.3	+	3	1006	c.749G>A	c.(748-750)AGA>AAA	p.R250K		NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor	250	Laminin N-terminal.				axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ACTGACATCAGAGTAACTCTT	0.378													5	64	---	---	---	---	PASS
DSTYK	25778	broad.mit.edu	37	1	205126469	205126469	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205126469C>T	uc001hbw.2	-	10	2348	c.2284G>A	c.(2284-2286)GTG>ATG	p.V762M	DSTYK_uc001hbx.2_Missense_Mutation_p.V762M	NM_015375	NP_056190	Q6XUX3	DUSTY_HUMAN	receptor interacting protein kinase 5 isoform 1	762	Protein kinase.					cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1						ATTCCCTCCACCACATCTAGT	0.473													10	49	---	---	---	---	PASS
PLXNA2	5362	broad.mit.edu	37	1	208391254	208391254	+	Missense_Mutation	SNP	C	T	T	rs2782948	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208391254C>T	uc001hgz.2	-	2	772	c.14G>A	c.(13-15)CGG>CAG	p.R5Q	PLXNA2_uc001hha.3_Missense_Mutation_p.R59Q	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	5					axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGGCCAGGGCCGCCTCTGTTC	0.667													4	60	---	---	---	---	PASS
TAF1B	9014	broad.mit.edu	37	2	10053412	10053412	+	Intron	SNP	C	T	T	rs12467598	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10053412C>T	uc002qzz.2	+						TAF1B_uc010exc.2_Silent_p.A435A|TAF1B_uc002qzy.3_Intron|TAF1B_uc010yja.1_Intron|TAF1B_uc010exd.2_Intron	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATGCACCTGCCTTACTTCTGT	0.368													5	70	---	---	---	---	PASS
CRIM1	51232	broad.mit.edu	37	2	36691752	36691752	+	Silent	SNP	C	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36691752C>T	uc002rpd.2	+	5	984	c.945C>T	c.(943-945)GGC>GGT	p.G315G		NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor	315	Extracellular (Potential).|Cell attachment site (Potential).				nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TCTCTCGTGGCGATGGGACAC	0.502													36	142	---	---	---	---	PASS
SFRS7	6432	broad.mit.edu	37	2	38978477	38978477	+	5'UTR	SNP	A	C	C			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38978477A>C	uc002rqz.2	-	1					SFRS7_uc002rra.2_RNA|SFRS7_uc010ynp.1_5'UTR|GEMIN6_uc002rrb.2_5'Flank	NM_001031684	NP_001026854	Q16629	SRSF7_HUMAN	splicing factor, arginine/serine-rich 7						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|zinc ion binding				0		all_hematologic(82;0.248)				ACACACCTTCACCCGCCAAGA	0.617													6	14	---	---	---	---	PASS
EML4	27436	broad.mit.edu	37	2	42543187	42543187	+	Missense_Mutation	SNP	A	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42543187A>T	uc002rsi.2	+	18	2315	c.2053A>T	c.(2053-2055)ATA>TTA	p.I685L	EML4_uc010fap.2_Missense_Mutation_p.I627L|EML4_uc002rsj.2_Missense_Mutation_p.I374L|EML4_uc010faq.2_Missense_Mutation_p.I30L|EML4_uc010ynv.1_Intron	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	685	WD 7.				microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						GCGCTACTCAATAGGTAGGCA	0.423			T	ALK	NSCLC								21	55	---	---	---	---	PASS
NFU1	27247	broad.mit.edu	37	2	69659126	69659126	+	Missense_Mutation	SNP	A	T	T	rs4453725	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69659126A>T	uc002sfk.2	-	2	273	c.74T>A	c.(73-75)ATG>AAG	p.M25K	NFU1_uc002sfj.2_Missense_Mutation_p.M1K|NFU1_uc002sfl.2_5'UTR|NFU1_uc002sfm.2_5'UTR|NFU1_uc010fdi.2_RNA|NFU1_uc002sfn.1_Missense_Mutation_p.M25K	NM_001002755	NP_001002755	Q9UMS0	NFU1_HUMAN	HIRA interacting protein 5 isoform 2	25					iron-sulfur cluster assembly	cytosol|mitochondrion|nucleus	4 iron, 4 sulfur cluster binding|iron ion binding|protein binding				0						ATTCTTCAACATATGACAGAA	0.348													3	27	---	---	---	---	PASS
C2orf3	6936	broad.mit.edu	37	2	75907351	75907351	+	Missense_Mutation	SNP	T	C	C	rs6722682	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75907351T>C	uc002sno.2	-	12	1910	c.1780A>G	c.(1780-1782)ACT>GCT	p.T594A	C2orf3_uc010ffs.2_Missense_Mutation_p.T156A|C2orf3_uc002snn.2_Missense_Mutation_p.T425A|C2orf3_uc010fft.2_Missense_Mutation_p.T269A	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936	594					negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						TTTTCACAAGTGGAATGTTCT	0.328													3	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	95539132	95539132	+	Splice_Site	SNP	A	G	G	rs74376788	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95539132A>G	uc002stv.1	-	9		c.1317_splice	c.e9+1		TEKT4_uc002stw.1_Intron|TEKT4_uc010fhr.1_RNA					Homo sapiens cDNA FLJ44118 fis, clone TESTI4047069.																		AGCAGAACTTACACAGTCAGA	0.567													2	11	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141680622	141680622	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141680622T>G	uc002tvj.1	-	21	4203	c.3231A>C	c.(3229-3231)AAA>AAC	p.K1077N	LRP1B_uc010fnl.1_Missense_Mutation_p.K259N	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1077	Extracellular (Potential).|LDL-receptor class A 8.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTTCACAGTCTTTTTCTCCAT	0.418										TSP Lung(27;0.18)			37	40	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160287661	160287661	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160287661T>C	uc002uao.2	-	10	2259	c.1907A>G	c.(1906-1908)GAT>GGT	p.D636G	BAZ2B_uc002uap.2_Missense_Mutation_p.D634G|BAZ2B_uc002uaq.1_Intron|BAZ2B_uc002uar.1_Missense_Mutation_p.D209G	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	636	Asp/Glu-rich (acidic).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						TGAATTACTATCTGATTCTGG	0.343													13	23	---	---	---	---	PASS
SCN5A	6331	broad.mit.edu	37	3	38627292	38627292	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38627292G>A	uc003cio.2	-	16	2871	c.2677C>T	c.(2677-2679)CGC>TGC	p.R893C	SCN5A_uc003cin.2_Missense_Mutation_p.R893C|SCN5A_uc003cil.3_Missense_Mutation_p.R893C|SCN5A_uc010hhi.2_Missense_Mutation_p.R893C|SCN5A_uc010hhk.2_Missense_Mutation_p.R893C|SCN5A_uc011ayr.1_Missense_Mutation_p.R893C|SCN5A_uc010hhj.1_Missense_Mutation_p.R504C	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	893					blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)	CAGAGGATGCGGAAGATGATG	0.547													7	107	---	---	---	---	PASS
PLCH1	23007	broad.mit.edu	37	3	155206588	155206588	+	Silent	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155206588G>A	uc011bok.1	-	19	2641	c.2364C>T	c.(2362-2364)AAC>AAT	p.N788N	PLCH1_uc011boj.1_Silent_p.N788N|PLCH1_uc011bol.1_Silent_p.N770N	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	788	C2.				lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CCCACACAGGGTTAAATCCTC	0.428													11	18	---	---	---	---	PASS
PLCH1	23007	broad.mit.edu	37	3	155314034	155314034	+	Silent	SNP	A	G	G	rs359569	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155314034A>G	uc011bok.1	-	2	454	c.177T>C	c.(175-177)AGT>AGC	p.S59S	PLCH1_uc011boj.1_Silent_p.S59S|PLCH1_uc011bol.1_Silent_p.S41S	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	59	PH.				lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTGCCTTCTCACTCTTCCTAG	0.483													12	206	---	---	---	---	PASS
KPNA4	3840	broad.mit.edu	37	3	160219839	160219839	+	3'UTR	SNP	T	C	C			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160219839T>C	uc003fdn.2	-	17						NM_002268	NP_002259	O00629	IMA4_HUMAN	karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			cacacacacatatatatatat	0.313													5	44	---	---	---	---	PASS
BCL6	604	broad.mit.edu	37	3	187447543	187447543	+	Missense_Mutation	SNP	C	T	T	rs142220629		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187447543C>T	uc003frp.3	-	5	1107	c.650G>A	c.(649-651)CGG>CAG	p.R217Q	BCL6_uc011bsf.1_Missense_Mutation_p.R217Q|BCL6_uc010hza.2_Missense_Mutation_p.R115Q|BCL6_uc003frq.1_Missense_Mutation_p.R217Q	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1	217					negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		CACAGGCATCCGGACATCCCG	0.612			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								21	32	---	---	---	---	PASS
HPGD	3248	broad.mit.edu	37	4	175416699	175416699	+	Silent	SNP	C	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175416699C>A	uc003itu.2	-	5	688	c.498G>T	c.(496-498)GCG>GCT	p.A166A	HPGD_uc003itt.2_Silent_p.A33A|HPGD_uc003itv.2_Silent_p.A166A|HPGD_uc011ckf.1_Silent_p.A45A|HPGD_uc010irp.2_Silent_p.A45A|HPGD_uc010irq.2_Intron|HPGD_uc011ckg.1_Silent_p.A98A|HPGD_uc011ckh.1_Silent_p.A45A|HPGD_uc003itw.2_Silent_p.A166A	NM_000860	NP_000851	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	166					female pregnancy|lipoxygenase pathway|negative regulation of cell cycle|parturition|prostaglandin metabolic process|transforming growth factor beta receptor signaling pathway	cytosol|nucleus	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|NAD+ binding|prostaglandin E receptor activity|protein homodimerization activity				0		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)	NADH(DB00157)	GTAGCCTCACCGCTGCTGAGC	0.408													22	48	---	---	---	---	PASS
ACTBL2	345651	broad.mit.edu	37	5	56778328	56778328	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56778328C>A	uc003jrm.2	-	1	309	c.207G>T	c.(205-207)AAG>AAT	p.K69N		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	69						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		CGATAGGATACTTCAGGGTCA	0.547													17	35	---	---	---	---	PASS
ZFYVE16	9765	broad.mit.edu	37	5	79752812	79752812	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79752812G>A	uc003kgr.3	+	14	4146	c.3844G>A	c.(3844-3846)GCA>ACA	p.A1282T	ZFYVE16_uc003kgq.3_Missense_Mutation_p.A1282T|ZFYVE16_uc003kgs.3_Missense_Mutation_p.A1282T|ZFYVE16_uc003kgt.3_Missense_Mutation_p.A370T|ZFYVE16_uc003kgu.3_Missense_Mutation_p.A34T	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1282					BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		TAGCATTGGAGCAAGTTTCAG	0.343													8	21	---	---	---	---	PASS
ELL2	22936	broad.mit.edu	37	5	95236415	95236415	+	Silent	SNP	G	A	A	rs17085249	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95236415G>A	uc003klr.3	-	7	1286	c.936C>T	c.(934-936)GAC>GAT	p.D312D		NM_012081	NP_036213	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	312					regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				central_nervous_system(1)	1		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		AAGATACAGCGTCTCTACTAG	0.274													4	44	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56417898	56417898	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56417898C>T	uc003pdf.2	-	55	9363	c.9335G>A	c.(9334-9336)AGC>AAC	p.S3112N	DST_uc003pcz.3_Missense_Mutation_p.S2934N|DST_uc011dxj.1_Missense_Mutation_p.S2963N|DST_uc011dxk.1_Missense_Mutation_p.S2974N|DST_uc003pcy.3_Missense_Mutation_p.S2608N	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5020					cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACTGAGCAAGCTATTGGCTGT	0.413													53	126	---	---	---	---	PASS
PLG	5340	broad.mit.edu	37	6	161139480	161139480	+	Silent	SNP	C	T	T	rs1130656	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161139480C>T	uc003qtm.3	+	8	1005	c.942C>T	c.(940-942)TTC>TTT	p.F314F		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	314	Kringle 3.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CAGAAAACTTCCCCTGCAAGT	0.493													5	84	---	---	---	---	PASS
STAG3L2	442582	broad.mit.edu	37	7	74298939	74298939	+	RNA	SNP	G	C	C	rs142156061	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74298939G>C	uc011kfj.1	-	6		c.728C>G						P0CL84	ST3L2_HUMAN	Homo sapiens cDNA FLJ76564 complete cds.							nucleus	binding				0						TTTCCCCCACGCCATGCCACC	0.537													3	22	---	---	---	---	PASS
POM121C	100101267	broad.mit.edu	37	7	75048146	75048146	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75048146G>A	uc003udk.3	-	15	3782	c.2897C>T	c.(2896-2898)GCG>GTG	p.A966V		NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like	1208	Pore side (Potential).				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0						CTTGGATCCCGCACCAATGGA	0.597													4	56	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	100607821	100607821	+	RNA	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100607821G>A	uc003uxk.1	+	4		c.2352G>A			uc003uxl.1_Silent_p.E556E|uc003uxm.1_RNA|uc003uxn.1_RNA|uc010lhn.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		GCGAGTATGAGCAGGTGAAGA	0.637													9	94	---	---	---	---	PASS
ZC3HAV1	56829	broad.mit.edu	37	7	138740037	138740037	+	Missense_Mutation	SNP	G	C	C	rs2297236	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138740037G>C	uc003vun.2	-	10	2489	c.2101C>G	c.(2101-2103)CAG>GAG	p.Q701E		NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1	701					response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						TTTGCTGGCTGATGGCTACAA	0.443													5	67	---	---	---	---	PASS
IKBKB	3551	broad.mit.edu	37	8	42178169	42178169	+	Intron	SNP	T	G	G			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42178169T>G	uc003xow.1	+						IKBKB_uc010lxh.1_3'UTR|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547	O14920	IKKB_HUMAN	inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)	ATGTGGCGGGTCCCCTGGTCT	0.378													7	14	---	---	---	---	PASS
HOOK3	84376	broad.mit.edu	37	8	42852766	42852766	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42852766T>C	uc003xpr.2	+	16	1848	c.1606T>C	c.(1606-1608)TCA>CCA	p.S536P	HOOK3_uc010lxq.1_Missense_Mutation_p.S536P	NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein	536	Potential.				cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			GGATCAAGGCTCAAAAGCAGA	0.308			T	RET	papillary thyroid								5	22	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139662012	139662012	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139662012T>C	uc003yvd.2	-	46	3790	c.3343A>G	c.(3343-3345)AAT>GAT	p.N1115D	COL22A1_uc011ljo.1_Missense_Mutation_p.N395D	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1115	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GGGCAGTCATTGCACACATCC	0.532										HNSCC(7;0.00092)			54	61	---	---	---	---	PASS
APBA1	320	broad.mit.edu	37	9	72131722	72131722	+	Silent	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72131722G>A	uc004ahh.2	-	2	681	c.405C>T	c.(403-405)GCC>GCT	p.A135A		NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,	135					axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						CGGCGTGCTCGGCCTCTGCCT	0.692													18	55	---	---	---	---	PASS
C9orf171	389799	broad.mit.edu	37	9	135374898	135374898	+	Silent	SNP	T	C	C	rs562350	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135374898T>C	uc004cbn.2	+	4	591	c.543T>C	c.(541-543)AAT>AAC	p.N181N	C9orf171_uc004cbo.2_Silent_p.N145N	NM_207417	NP_997300	Q6ZQR2	CI171_HUMAN	hypothetical protein LOC389799	181										ovary(4)|large_intestine(1)	5						GTCAGCTCAATGACATCCGCA	0.602													7	159	---	---	---	---	PASS
UNC93B1	81622	broad.mit.edu	37	11	67759287	67759287	+	Silent	SNP	C	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67759287C>A	uc001omw.1	-	12	1604	c.1524G>T	c.(1522-1524)GCG>GCT	p.A508A		NM_030930	NP_112192	Q9H1C4	UN93B_HUMAN	unc-93 homolog B1	508	Helical; (Potential).				innate immune response|intracellular protein transport|response to virus|toll-like receptor 3 signaling pathway|toll-like receptor 7 signaling pathway|toll-like receptor 9 signaling pathway	early phagosome|endoplasmic reticulum membrane|endosome|integral to membrane|lysosome					0						GGTAGGAGACCGCGGCCGCCA	0.741													3	8	---	---	---	---	PASS
GUCY1A2	2977	broad.mit.edu	37	11	106558447	106558447	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106558447G>A	uc001pjg.1	-	8	2417	c.2027C>T	c.(2026-2028)CCG>CTG	p.P676L	GUCY1A2_uc010rvo.1_Missense_Mutation_p.P697L|GUCY1A2_uc009yxn.1_Missense_Mutation_p.P707L	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	676					intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)		ACGAGACCGCGGAATGAATGT	0.418													40	82	---	---	---	---	PASS
KCNA1	3736	broad.mit.edu	37	12	5022041	5022041	+	3'UTR	SNP	G	A	A	rs4766310	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5022041G>A	uc001qnh.2	+	2						NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A						synaptic transmission	juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity			ovary(1)|skin(1)	2					Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AAAAAACAAAGGCAAGCAAAC	0.383													6	73	---	---	---	---	PASS
KIAA1467	57613	broad.mit.edu	37	12	13208628	13208628	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13208628G>A	uc001rbi.2	+	2	204	c.181G>A	c.(181-183)GAC>AAC	p.D61N	KIAA1467_uc009zhx.1_RNA	NM_020853	NP_065904	A2RU67	K1467_HUMAN	hypothetical protein LOC57613	61						integral to membrane				central_nervous_system(2)|skin(1)	3		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)		GCCAGAACCCGACTCAGATGC	0.557													28	47	---	---	---	---	PASS
MYF5	4617	broad.mit.edu	37	12	81110765	81110765	+	5'UTR	SNP	A	G	G	rs1163261	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81110765A>G	uc001szg.2	+	1						NM_005593	NP_005584	P13349	MYF5_HUMAN	myogenic factor 5						muscle cell fate commitment|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1						GGATTTGCCCATCGGCGGAGG	0.632													3	27	---	---	---	---	PASS
IKBIP	121457	broad.mit.edu	37	12	99007356	99007356	+	3'UTR	SNP	T	C	C	rs1048908	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99007356T>C	uc001tfv.2	-	3					IKBIP_uc001tfw.2_3'UTR	NM_201612	NP_963906	Q70UQ0	IKIP_HUMAN	IKK interacting protein isoform 2						induction of apoptosis|response to X-ray	endoplasmic reticulum membrane|integral to membrane	protein binding				0						ATCTCAATAATGTCAAACTAA	0.264													4	49	---	---	---	---	PASS
OAS1	4938	broad.mit.edu	37	12	113344830	113344830	+	5'UTR	SNP	C	G	G			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113344830C>G	uc001tud.2	+	1					OAS1_uc010syn.1_5'UTR|OAS1_uc010syo.1_5'UTR|OAS1_uc001tub.2_5'UTR|OAS1_uc001tuc.2_5'UTR|OAS1_uc009zwf.2_5'UTR	NM_016816	NP_058132	P00973	OAS1_HUMAN	2',5'-oligoadenylate synthetase 1 isoform 1						interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(2)	2						TCTGTTGCCACTCTCTCTCCT	0.488													12	60	---	---	---	---	PASS
MED13L	23389	broad.mit.edu	37	12	116446812	116446812	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116446812G>A	uc001tvw.2	-	10	1461	c.1406C>T	c.(1405-1407)ACA>ATA	p.T469I		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	469					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TCTTTCTGCTGTTTTGTGCTT	0.478													40	69	---	---	---	---	PASS
CHFR	55743	broad.mit.edu	37	12	133434118	133434118	+	Silent	SNP	G	A	A	rs138280939		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133434118G>A	uc001ulf.2	-	9	1059	c.975C>T	c.(973-975)TGC>TGT	p.C325C	CHFR_uc001ulc.1_RNA|CHFR_uc001ule.2_Silent_p.C313C|CHFR_uc010tbs.1_Silent_p.C325C|CHFR_uc001uld.2_Silent_p.C284C|CHFR_uc010tbt.1_Silent_p.C233C	NM_001161344	NP_001154816	Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains	325	RING-type.				cell division|mitosis|mitotic cell cycle checkpoint|modification-dependent protein catabolic process|protein polyubiquitination	PML body	nucleotide binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		AGCAAGCCGCGCAGAACGTGT	0.597													3	28	---	---	---	---	PASS
CSNK1A1L	122011	broad.mit.edu	37	13	37679268	37679268	+	Missense_Mutation	SNP	G	T	T	rs9576175	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37679268G>T	uc001uwm.1	-	1	534	c.126C>A	c.(124-126)GAC>GAA	p.D42E		NM_145203	NP_660204	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	42	Protein kinase.				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)	1		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		TCACTGCTACGTCCTCGCCGT	0.542													7	119	---	---	---	---	PASS
TMTC4	84899	broad.mit.edu	37	13	101316518	101316518	+	Missense_Mutation	SNP	T	G	G	rs74554757		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101316518T>G	uc001vou.2	-	3	395	c.235A>C	c.(235-237)ACC>CCC	p.T79P	TMTC4_uc001vot.2_Missense_Mutation_p.T98P|TMTC4_uc010tja.1_Intron	NM_001079669	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat	79						integral to membrane	binding			ovary(2)|breast(1)	3	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TTGTGGCTGGTGTTGCTGCTC	0.577													5	15	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22695084	22695084	+	Intron	SNP	C	T	T	rs4982579	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22695084C>T	uc001wbw.2	+						uc010aiv.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Missense_Mutation_p.S92F					SubName: Full=Alpha-chain C region; Flags: Fragment;																		AAAGAACTTTCCAGCATCCTG	0.463													3	26	---	---	---	---	PASS
OR4N4	283694	broad.mit.edu	37	15	22383189	22383189	+	Silent	SNP	G	A	A	rs1820851	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22383189G>A	uc001yuc.1	+	7	1698	c.717G>A	c.(715-717)ACG>ACA	p.T239T	LOC727924_uc001yub.1_Intron|OR4N4_uc010tzv.1_Missense_Mutation_p.M239I	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	239	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CCATGTCCACGTGCACCACTC	0.493													5	54	---	---	---	---	PASS
HAPLN3	145864	broad.mit.edu	37	15	89421405	89421405	+	Silent	SNP	G	A	A	rs7182726	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89421405G>A	uc002bnc.2	-	5	1007	c.879C>T	c.(877-879)ATC>ATT	p.I293I	HAPLN3_uc002bne.2_RNA|HAPLN3_uc002bnd.2_Silent_p.I355I	NM_178232	NP_839946	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	293	Link 2.				cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding				0	Lung NSC(78;0.0392)|all_lung(78;0.077)					CCACCTTGGCGATCGTGGCAT	0.642													8	158	---	---	---	---	PASS
VASN	114990	broad.mit.edu	37	16	4432596	4432596	+	Missense_Mutation	SNP	A	C	C	rs76495149		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4432596A>C	uc002cwj.1	+	2	1873	c.1718A>C	c.(1717-1719)AAC>ACC	p.N573T	CORO7_uc002cwe.2_Intron|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc002cwh.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron|CORO7_uc002cwi.1_Intron|CORO7_uc010uxj.1_Intron|CORO7_uc010btp.1_Intron	NM_138440	NP_612449	Q6EMK4	VASN_HUMAN	slit-like 2 precursor	573	Extracellular (Potential).					extracellular region|integral to membrane					0						CGCGAGGGCAACCTGCCGCTC	0.771													4	12	---	---	---	---	PASS
ITGAM	3684	broad.mit.edu	37	16	31336719	31336719	+	Silent	SNP	G	A	A	rs1143682	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31336719G>A	uc002ebq.2	+	20	2597	c.2499G>A	c.(2497-2499)ACG>ACA	p.T833T	ITGAM_uc002ebr.2_Silent_p.T834T|ITGAM_uc010can.2_Silent_p.T239T|ITGAM_uc002ebs.1_Silent_p.T239T|ITGAM_uc010vfj.1_RNA	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor	833	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						AGGTGTCCACGCTCCAGGTAG	0.562													5	94	---	---	---	---	PASS
SLC13A5	284111	broad.mit.edu	37	17	6607201	6607201	+	Silent	SNP	C	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6607201C>A	uc002gdj.2	-	4	631	c.543G>T	c.(541-543)CTG>CTT	p.L181L	SLC13A5_uc010vtf.1_Silent_p.L181L|SLC13A5_uc010clq.2_Silent_p.L138L|SLC13A5_uc002gdk.2_Silent_p.L164L|SLC13A5_uc002gdl.1_Silent_p.L163L	NM_177550	NP_808218	Q86YT5	S13A5_HUMAN	solute carrier family 13, member 5 isoform a	181						integral to membrane	citrate transmembrane transporter activity				0						GCTCACCTGGCAGCTCCTTGG	0.642													6	28	---	---	---	---	PASS
PIK3R6	146850	broad.mit.edu	37	17	8753200	8753200	+	5'UTR	SNP	G	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8753200G>T	uc002glq.1	-	2					PIK3R6_uc002glr.1_RNA|PIK3R6_uc002gls.1_RNA	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						platelet activation	cytosol					0						CACAGAGGTGGTTCTGCAAAA	0.502													5	2	---	---	---	---	PASS
PIK3R5	23533	broad.mit.edu	37	17	8792171	8792171	+	Silent	SNP	T	C	C	rs11650737	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8792171T>C	uc002glt.2	-	10	1000	c.933A>G	c.(931-933)CTA>CTG	p.L311L	PIK3R5_uc010vuz.1_Silent_p.L311L|PIK3R5_uc002glu.3_5'UTR|PIK3R5_uc010coa.1_Missense_Mutation_p.Y260C|PIK3R5_uc010cob.1_5'UTR	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	311				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121).	platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						CTGGCTGGAGTAGCTCCTGTT	0.468													3	30	---	---	---	---	PASS
KRT10	3858	broad.mit.edu	37	17	38978462	38978462	+	Missense_Mutation	SNP	C	T	T	rs77919366	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38978462C>T	uc002hvi.2	-	1	402	c.376G>A	c.(376-378)GGC>AGC	p.G126S	KRT10_uc010cxd.2_5'Flank|TMEM99_uc002hvj.1_Intron	NM_000421	NP_000412	P13645	K1C10_HUMAN	keratin 10	126	Head.|Gly-rich.		G -> S.		epidermis development		protein binding|structural constituent of epidermis				0		Breast(137;0.000301)				cctccaaagccgcctccaCCA	0.428													3	30	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45247328	45247328	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45247328C>T	uc002ild.3	-	4	459	c.332G>A	c.(331-333)GGT>GAT	p.G111D	CDC27_uc002ile.3_Missense_Mutation_p.G111D|CDC27_uc002ilf.3_Missense_Mutation_p.G111D|CDC27_uc010wkp.1_Missense_Mutation_p.G50D|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	111	TPR 1.				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						AGCTGAATCACCAAACTCAGT	0.328													7	88	---	---	---	---	PASS
C17orf77	146723	broad.mit.edu	37	17	72588326	72588326	+	Missense_Mutation	SNP	A	C	C	rs493430	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72588326A>C	uc002jla.1	+	3	503	c.141A>C	c.(139-141)AGA>AGC	p.R47S	CD300LD_uc002jkz.2_Missense_Mutation_p.S6A	NM_152460	NP_689673	Q96MU5	CQ077_HUMAN	hypothetical protein LOC146723	47						extracellular region					0						AGCAGCAGAGATGGGGACAGC	0.562													4	57	---	---	---	---	PASS
MOCOS	55034	broad.mit.edu	37	18	33795858	33795858	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33795858C>A	uc002kzq.3	+	8	1738	c.1715C>A	c.(1714-1716)GCA>GAA	p.A572E		NM_017947	NP_060417	Q96EN8	MOCOS_HUMAN	molybdenum cofactor sulfurase	572					Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	lyase activity|Mo-molybdopterin cofactor sulfurase activity|molybdenum ion binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	GAGAAAGCTGCAGGAGTCCTG	0.522													3	29	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14730143	14730143	+	3'UTR	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14730143G>A	uc002mzi.3	-	16					EMR3_uc010dzp.2_3'UTR|EMR3_uc010xnv.1_3'UTR	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						TCCTCTCCAAGGATGATATGT	0.363													10	6	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40367908	40367908	+	Missense_Mutation	SNP	G	A	A	rs73558346	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40367908G>A	uc002omp.3	-	29	13060	c.13052C>T	c.(13051-13053)ACC>ATC	p.T4351I		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4351						extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TTCTGGGCAGGTGATCTCTGT	0.612													4	45	---	---	---	---	PASS
CYP2A6	1548	broad.mit.edu	37	19	41350672	41350672	+	Silent	SNP	G	A	A	rs59389036	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41350672G>A	uc002opl.3	-	8	1188	c.1167C>T	c.(1165-1167)ACC>ACT	p.T389T		NM_000762	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A,	389					coumarin catabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|enzyme binding|heme binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Chlorzoxazone(DB00356)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Formoterol(DB00983)|Halothane(DB01159)|Letrozole(DB01006)|Methoxsalen(DB00553)|Metyrapone(DB01011)|Nicotine(DB00184)|Pilocarpine(DB01085)|Tolbutamide(DB01124)|Tranylcypromine(DB00752)	GGAACACTTCGGTGCCCTGGT	0.572													4	30	---	---	---	---	PASS
TPRX1	284355	broad.mit.edu	37	19	48305603	48305603	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48305603G>A	uc002php.1	-	2	736	c.665C>T	c.(664-666)CCG>CTG	p.P222L		NM_198479	NP_940881	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox	222	Gly-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		gcctgggatcgggcctgggtt	0.000													2	2	---	---	---	---	PASS
GPR32	2854	broad.mit.edu	37	19	51273918	51273918	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51273918C>T	uc010ycf.1	+	1	61	c.61C>T	c.(61-63)CGT>TGT	p.R21C		NM_001506	NP_001497	O75388	GPR32_HUMAN	G protein-coupled receptor 32	21	Extracellular (Potential).					integral to plasma membrane	N-formyl peptide receptor activity			upper_aerodigestive_tract(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GGTCCTGACACGTGATCGCTC	0.522													20	22	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11047499	11047499	+	3'UTR	SNP	G	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11047499G>T	uc002yit.1	-	5						NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCCAGCCGTTGGTTGGTACAG	0.343													17	263	---	---	---	---	PASS
KRTAP12-4	386684	broad.mit.edu	37	21	46074565	46074565	+	5'UTR	SNP	C	G	G	rs12482041	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46074565C>G	uc002zfs.1	-	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198698	NP_941971	P60329	KR124_HUMAN	keratin associated protein 12-4							keratin filament				ovary(1)	1						GCGCAGAGGACAGGGCTGGTC	0.632													2	8	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22662940	22662940	+	Intron	SNP	T	C	C	rs11702949	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22662940T>C	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						CAGATGGTCTTTCTTGTTTTT	0.303													5	9	---	---	---	---	PASS
GSTT1	2952	broad.mit.edu	37	22	24384213	24384213	+	Silent	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24384213G>A	uc002zze.3	-	1	72	c.19C>T	c.(19-21)CTG>TTG	p.L7L	GSTT1_uc002zzf.3_RNA|GSTT1_uc010gug.2_RNA|GSTT1_uc011ajl.1_5'UTR|GSTT1_uc010guh.2_RNA|GSTT1_uc010gui.1_RNA	NM_000853	NP_000844	P30711	GSTT1_HUMAN	glutathione S-transferase theta 1	7	GST N-terminal.				glutathione metabolic process	cytosol|soluble fraction	glutathione peroxidase activity|glutathione transferase activity			ovary(1)	1					Glutathione(DB00143)	AGCAGGTCCAGGTACAGCTCC	0.587									Myelodysplasia_and_Acute_Myeloid_Leukemia_(AML)_Familial				31	66	---	---	---	---	PASS
UPB1	51733	broad.mit.edu	37	22	24891292	24891292	+	5'UTR	SNP	C	G	G	rs2070474	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24891292C>G	uc003aaf.2	+	1					UPB1_uc003aae.2_5'UTR|UPB1_uc011ajt.1_5'UTR|C22orf45_uc003aad.1_5'Flank	NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)					GGGCGCCTGACCGGGCCTGGG	0.662													4	42	---	---	---	---	PASS
KLHDC7B	113730	broad.mit.edu	37	22	50987891	50987891	+	Silent	SNP	G	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50987891G>A	uc003bmi.2	+	1	1430	c.1296G>A	c.(1294-1296)GCG>GCA	p.A432A		NM_138433	NP_612442	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	432	Kelch 3.									central_nervous_system(1)	1		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCCCACGCGCGCCACTCCCCG	0.672													54	128	---	---	---	---	PASS
CXorf38	159013	broad.mit.edu	37	X	40506697	40506697	+	Silent	SNP	A	G	G	rs6610447	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40506697A>G	uc004dew.2	-	1	81	c.76T>C	c.(76-78)TTA>CTA	p.L26L	CXorf38_uc011mko.1_Silent_p.L26L|CXorf38_uc004dev.1_5'UTR|CXorf38_uc010nhd.2_RNA	NM_144970	NP_659407	Q8TB03	CX038_HUMAN	hypothetical protein LOC159013	26										ovary(1)	1						CGCAGCAGTAACAGGCAGTGG	0.687													4	36	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	48163105	48163105	+	Missense_Mutation	SNP	A	G	G	rs4598385	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48163105A>G	uc010nib.1	-	4	301	c.214T>C	c.(214-216)TGT>CGT	p.C72R		NM_174962	NP_777622			synovial sarcoma, X breakpoint 9																		CCTGTATTACACATGAAAGGT	0.418													6	116	---	---	---	---	PASS
GPR112	139378	broad.mit.edu	37	X	135431236	135431236	+	Missense_Mutation	SNP	T	C	C	rs5930932	byFrequency	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135431236T>C	uc004ezu.1	+	6	5662	c.5371T>C	c.(5371-5373)TTT>CTT	p.F1791L	GPR112_uc010nsb.1_Missense_Mutation_p.F1586L|GPR112_uc010nsc.1_Missense_Mutation_p.F1558L	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	1791	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)					CACCAATTGCTTTTCTTCTAA	0.383													5	77	---	---	---	---	PASS
MDS2	259283	broad.mit.edu	37	1	23908221	23908221	+	Intron	DEL	C	-	-	rs10634856		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23908221delC	uc001bhi.3	+											Homo sapiens MDS2 gene.											ovary(2)	2						AGGCTCAAttctttttttttt	0.119			T	ETV6	MDS								13	6	---	---	---	---	
GBP5	115362	broad.mit.edu	37	1	89732536	89732537	+	Intron	DEL	AT	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89732536_89732537delAT	uc001dnc.2	-						GBP5_uc001dnd.2_Intron|GBP5_uc001dne.1_Intron	NM_052942	NP_443174	Q96PP8	GBP5_HUMAN	guanylate-binding protein 5							plasma membrane	GTP binding|GTPase activity			ovary(1)	1				all cancers(265;0.00784)|Epithelial(280;0.0286)		AGCTGGGTGAATATATATATAT	0.218													9	4	---	---	---	---	
HIST2H3C	126961	broad.mit.edu	37	1	149821913	149821916	+	5'Flank	DEL	GGAG	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149821913_149821916delGGAG	uc001esy.2	+						HIST2H2AA3_uc001esx.2_5'Flank	NM_021059	NP_066403	Q71DI3	H32_HUMAN	histone cluster 2, H3c						blood coagulation|nucleosome assembly	nucleoplasm|nucleosome	DNA binding|protein binding				0	Breast(34;0.0124)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.221)			GGCGACCCGCggagggagggaggg	0.490													2	4	---	---	---	---	
CFHR4	10877	broad.mit.edu	37	1	196883940	196883941	+	Intron	INS	-	A	A	rs35868341		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196883940_196883941insA	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						TCTTGAGACTTAAAAAAAAAAA	0.208													7	4	---	---	---	---	
ITSN2	50618	broad.mit.edu	37	2	24521335	24521335	+	Intron	DEL	T	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24521335delT	uc002rfe.2	-						ITSN2_uc002rff.2_Intron|ITSN2_uc002rfg.2_Intron|ITSN2_uc010eyd.2_Intron	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					agctggctaattttttttttt	0.000													4	2	---	---	---	---	
RGPD1	400966	broad.mit.edu	37	2	87204958	87204958	+	Intron	DEL	T	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87204958delT	uc010fgv.2	+						RMND5A_uc002srs.3_Intron|RGPD1_uc002ssb.2_Intron|RGPD1_uc002ssc.2_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0						Gttatttttattttttttttt	0.318													9	4	---	---	---	---	
RGPD1	400966	broad.mit.edu	37	2	88091357	88091357	+	Intron	DEL	A	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88091357delA	uc010fhc.1	-						RGPD1_uc002ssm.1_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1						intracellular transport		binding				0						accctgtcttaaaaaaaaaaa	0.194													8	5	---	---	---	---	
NCAPH	23397	broad.mit.edu	37	2	97017424	97017424	+	Intron	DEL	C	-	-	rs772153		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97017424delC	uc002svz.1	+						NCAPH_uc010fhu.1_Intron|NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)				aaaaaaaaaacaaaaacaaaC	0.189													4	2	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159992543	159992562	+	Intron	DEL	GTGTGTGTGTGTGTGTGTGC	-	-	rs70994268	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159992543_159992562delGTGTGTGTGTGTGTGTGTGC	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						gtgtgtgtgtgtgtgtgtgtgtgtgtgtgCGCGCGCGCGC	0.400													4	2	---	---	---	---	
MARCH7	64844	broad.mit.edu	37	2	160605489	160605489	+	Intron	DEL	C	-	-	rs72017785		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160605489delC	uc002uax.2	+						MARCH7_uc010foq.2_Intron|MARCH7_uc010zcn.1_Intron|MARCH7_uc010for.2_Intron|MARCH7_uc002uay.2_Intron	NM_022826	NP_073737	Q9H992	MARH7_HUMAN	axotrophin								ligase activity|zinc ion binding				0						tttttcttttctttttttttt	0.129													4	8	---	---	---	---	
ZAK	51776	broad.mit.edu	37	2	174123373	174123373	+	Intron	DEL	A	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174123373delA	uc002uhz.2	+						uc002uib.2_Intron	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)			TATTGAGACTAAAAAAAAAAT	0.264													6	3	---	---	---	---	
CCDC39	339829	broad.mit.edu	37	3	180372434	180372434	+	Intron	DEL	A	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180372434delA	uc010hxe.2	-						CCDC39_uc003fkn.2_Intron	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			aagaaaaaggaaaaaaaaaaa	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154051107	154051108	+	IGR	INS	-	TCA	TCA	rs143546943	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154051107_154051108insTCA								FHDC1 (150259 upstream) : TRIM2 (23162 downstream)																							catcaccacccccaccaccacc	0.000													4	2	---	---	---	---	
DPY19L1	23333	broad.mit.edu	37	7	35057722	35057722	+	Intron	DEL	T	-	-	rs151162813		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35057722delT	uc003tem.3	-							NM_015283	NP_056098	Q2PZI1	D19L1_HUMAN	dpy-19-like 1							integral to membrane					0						AGTATCTATATTTTTTTCACT	0.209													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64324829	64324829	+	IGR	DEL	A	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64324829delA								LOC168474 (10651 upstream) : ZNF273 (18042 downstream)																							TGAGACCGGCaaaaaaaaaaa	0.239													4	2	---	---	---	---	
SPDYE2	441273	broad.mit.edu	37	7	102197800	102197800	+	Intron	DEL	G	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102197800delG	uc011kkx.1	+						UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_Intron|POLR2J3_uc011kkw.1_Intron|SPDYE2_uc003vaa.1_Intron	NM_001031618	NP_001026789	Q495Y8	SPDE2_HUMAN	speedy homolog E2												0						ttttttttttgtgtgtgtgtg	0.254													6	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151904428	151904429	+	Frame_Shift_Ins	INS	-	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151904428_151904429insA	uc003wla.2	-	24	4016_4017	c.3797_3798insT	c.(3796-3798)GGAfs	p.G1266fs	MLL3_uc003wkz.2_Frame_Shift_Ins_p.G327fs	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	1266					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		CACCATCTGTTCCTTCCACTCC	0.381			N		medulloblastoma								51	28	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110509658	110509659	+	Intron	DEL	TC	-	-	rs139411634	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110509658_110509659delTC	uc003yne.2	+							NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AAAAAACCGttctttttttttt	0.223										HNSCC(38;0.096)			5	3	---	---	---	---	
AQP7	364	broad.mit.edu	37	9	33386780	33386781	+	Intron	INS	-	A	A	rs144468472	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33386780_33386781insA	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_Intron|AQP7_uc010mjt.2_Intron|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_Intron|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		aatggtaggtcggggggcccag	0.257													6	3	---	---	---	---	
TTLL11	158135	broad.mit.edu	37	9	124855330	124855331	+	In_Frame_Ins	INS	-	TGGCCT	TGGCCT			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124855330_124855331insTGGCCT	uc004blt.1	-	1	555_556	c.367_368insAGGCCA	c.(367-369)ACA>AAGGCCACA	p.122_123insKA	TTLL11_uc011lyl.1_In_Frame_Ins_p.122_123insKA|TTLL11_uc004blr.2_RNA|TTLL11_uc004blu.1_In_Frame_Ins_p.122_123insKA	NM_194252	NP_919228	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	122_123					protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0						cgtctccgctgtggcctcggcc	0.351													6	5	---	---	---	---	
CRB2	286204	broad.mit.edu	37	9	126129223	126129224	+	Intron	INS	-	A	A	rs34525565		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126129223_126129224insA	uc004bnx.1	+						CRB2_uc004bnw.1_Intron	NM_173689	NP_775960	Q5IJ48	CRUM2_HUMAN	crumbs homolog 2 precursor							extracellular region|integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						gattctatctcaaaaaaaaaaa	0.208													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42400455	42400455	+	IGR	DEL	T	-	-	rs71264011		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42400455delT								None (None upstream) : LOC441666 (426860 downstream)																							cttctttgtgttgtgtgtatt	0.000													74	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81304161	81304163	+	IGR	DEL	GAG	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81304161_81304163delGAG								EIF5AL1 (27971 upstream) : SFTPA2 (11446 downstream)																							aaaagaaaaagagagagagaaag	0.177													4	2	---	---	---	---	
BTRC	8945	broad.mit.edu	37	10	103292541	103292542	+	Intron	INS	-	TA	TA	rs28634652	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103292541_103292542insTA	uc001kta.2	+						BTRC_uc001ktb.2_Intron|BTRC_uc001ktc.2_Intron	NM_033637	NP_378663	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing protein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex				ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		gtgtgtgtgtgtgtgtgcgcgt	0.302													3	3	---	---	---	---	
INSC	387755	broad.mit.edu	37	11	15134193	15134194	+	Intron	INS	-	G	G	rs148001480	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15134193_15134194insG	uc001mly.2	+						INSC_uc001mlz.2_5'Flank	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a						cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5						tATTGGGAAGTGGGGGGGGGGC	0.401													4	2	---	---	---	---	
NXF1	10482	broad.mit.edu	37	11	62561637	62561638	+	Intron	INS	-	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62561637_62561638insA	uc001nvf.1	-						TMEM223_uc001nve.2_5'Flank|NXF1_uc001nvg.1_Intron	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1						gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3						aacttgtctccaaaaaaaaaac	0.218													4	2	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	102996095	102996096	+	Intron	DEL	CT	-	-	rs11347094		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102996095_102996096delCT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		ATGCTAAAGGCTTTTTTTTTTT	0.287													3	3	---	---	---	---	
GLB1L3	112937	broad.mit.edu	37	11	134178316	134178316	+	Intron	DEL	T	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134178316delT	uc009zdf.2	+						GLB1L3_uc010scu.1_Intron|GLB1L3_uc001qho.3_Intron	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		accaccatcatcaccatcacc	0.000													4	2	---	---	---	---	
C12orf4	57102	broad.mit.edu	37	12	4634594	4634595	+	Intron	INS	-	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4634594_4634595insA	uc001qms.2	-						C12orf4_uc001qmt.2_Intron	NM_020374	NP_065107	Q9NQ89	CL004_HUMAN	hypothetical protein LOC57102												0			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		AACAAACAAACAAAAAAACAAA	0.317													32	20	---	---	---	---	
MFAP5	8076	broad.mit.edu	37	12	8808654	8808655	+	Intron	DEL	TC	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8808654_8808655delTC	uc001qut.1	-						MFAP5_uc001qus.2_Intron|MFAP5_uc009zge.1_Intron	NM_003480	NP_003471	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5 precursor							microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)					CATTCATAAttctttttttttt	0.144													6	3	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66911514	66911515	+	Intron	INS	-	T	T	rs112804687		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66911514_66911515insT	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stl.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		agaggcaaaccttttttttttc	0.050													4	2	---	---	---	---	
ANKRD13A	88455	broad.mit.edu	37	12	110463769	110463769	+	Intron	DEL	C	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110463769delC	uc001tpx.2	+						ANKRD13A_uc009zvl.1_Intron|ANKRD13A_uc010sxw.1_Intron|ANKRD13A_uc001tpy.2_Intron|ANKRD13A_uc001tpz.2_5'Flank	NM_033121	NP_149112	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13												0						CTCTCTCTCTCtttttttttt	0.204													4	2	---	---	---	---	
RAN	5901	broad.mit.edu	37	12	131359282	131359283	+	Intron	INS	-	GTAA	GTAA			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131359282_131359283insGTAA	uc001uir.2	+						RAN_uc010tbk.1_Intron|RAN_uc010tbl.1_Intron|RAN_uc001uis.2_Intron	NM_006325	NP_006316	P62826	RAN_HUMAN	ras-related nuclear protein						androgen receptor signaling pathway|cell division|DNA metabolic process|mitosis|mitotic spindle organization|positive regulation of transcription, DNA-dependent|protein export from nucleus|RNA export from nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|melanosome|nuclear pore|nucleoplasm	androgen receptor binding|chromatin binding|GTP binding|GTPase activity|transcription coactivator activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		TCTTCAGGTGTGTAAAATTAAA	0.342													25	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57508748	57508749	+	IGR	DEL	GA	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57508748_57508749delGA								OTX2 (231564 upstream) : EXOC5 (160447 downstream)																							TGAAGTTAAGGAGAGAAAAAAG	0.376													15	9	---	---	---	---	
SYNE2	23224	broad.mit.edu	37	14	64449256	64449256	+	Intron	DEL	G	-	-	rs58023000		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64449256delG	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		aaaaaaaaaagaaaagaaaaa	0.174													2	9	---	---	---	---	
TMEM63C	57156	broad.mit.edu	37	14	77709477	77709477	+	Intron	DEL	A	-	-	rs409306	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77709477delA	uc001xtf.2	+						TMEM63C_uc010asq.1_Intron	NM_020431	NP_065164	Q9P1W3	TM63C_HUMAN	transmembrane protein 63C							integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		GGATGGGGGGAGCCCCCTGGG	0.622													7	6	---	---	---	---	
CCPG1	9236	broad.mit.edu	37	15	55657618	55657619	+	Intron	DEL	TT	-	-	rs111247245		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55657618_55657619delTT	uc002acv.1	-						CCPG1_uc002acy.2_Intron|CCPG1_uc002acu.1_Intron|CCPG1_uc002acw.1_Intron|CCPG1_uc002acx.2_Intron|CCPG1_uc010bfk.1_Intron|CCPG1_uc002acz.1_Intron	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)		Cttttttttgtttttttttttt	0.050													5	3	---	---	---	---	
MCTP2	55784	broad.mit.edu	37	15	94816934	94816934	+	Intron	DEL	T	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94816934delT	uc010boj.2	+						MCTP2_uc010urg.1_Intron|MCTP2_uc002bti.2_Intron|MCTP2_uc002btg.3_Intron|MCTP2_uc002bth.3_Intron	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TGGCAAGTAGTCAAGTTGTAC	0.448													4	2	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	21071848	21071848	+	Intron	DEL	T	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21071848delT	uc010vbe.1	-							NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		tttttttttcttttttttttt	0.209													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21393227	21393228	+	IGR	INS	-	TT	TT			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21393227_21393228insTT								NCRNA00169 (63315 upstream) : NPIPL3 (20223 downstream)																							ATGGGAGGttgttttttttttt	0.257													3	6	---	---	---	---	
DNAH17	8632	broad.mit.edu	37	17	76425003	76425003	+	Intron	DEL	T	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76425003delT	uc010dhp.1	-						DNAH17_uc002jvq.2_Intron|DNAH17_uc002jvs.2_Intron					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CATTTCTTTCTTTaaaaaaaa	0.443													4	2	---	---	---	---	
MKNK2	2872	broad.mit.edu	37	19	2037846	2037847	+	3'UTR	INS	-	C	C	rs1064543	by1000genomes	TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2037846_2037847insC	uc002lus.2	-	14					MKNK2_uc002luq.1_Intron|MKNK2_uc010xgu.1_3'UTR|MKNK2_uc010xgv.1_3'UTR|MKNK2_uc002lur.2_Intron|MKNK2_uc002lut.1_3'UTR	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAAAAAAAAAAAAACAAACAAA	0.525													48	7	---	---	---	---	
ITGB1BP3	27231	broad.mit.edu	37	19	3938842	3938842	+	Intron	DEL	G	-	-	rs7508648		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3938842delG	uc002lyz.3	+						ITGB1BP3_uc010xia.1_Intron	NM_170678	NP_733778	Q9NPI5	NRK2_HUMAN	integrin beta 1 binding protein 3						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		ttttttttttgttttgttttt	0.224													8	10	---	---	---	---	
EVI5L	115704	broad.mit.edu	37	19	7926938	7926938	+	Intron	DEL	C	-	-	rs3217320		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7926938delC	uc002min.2	+						EVI5L_uc010xjz.1_Intron	NM_145245	NP_660288	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like isoform							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						GGGCAGAGCGCCCCCTAGGGC	0.736													5	5	---	---	---	---	
psiTPTE22	387590	broad.mit.edu	37	22	17131536	17131537	+	Intron	INS	-	CTG	CTG	rs34452519		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17131536_17131537insCTG	uc002zls.1	+						psiTPTE22_uc002zlt.2_Intron					Homo sapiens cDNA FLJ10437 fis, clone NT2RP1000581.												0						TGCCCACTCTTCTGGTCTCATG	0.470													4	2	---	---	---	---	
ZDHHC8	29801	broad.mit.edu	37	22	20130158	20130159	+	Intron	INS	-	A	A			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20130158_20130159insA	uc002zrq.2	+						ZDHHC8_uc002zrr.1_Intron|ZDHHC8_uc010gsa.2_Intron	NM_013373	NP_037505	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC domain containing 8							cytoplasmic vesicle membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Colorectal(54;0.0993)					ATGTGGCTCTTATGGCTCCTTG	0.663													5	4	---	---	---	---	
XBP1	7494	broad.mit.edu	37	22	29192858	29192859	+	Intron	INS	-	T	T			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29192858_29192859insT	uc011akl.1	-						XBP1_uc003aec.2_5'UTR|XBP1_uc003aed.2_Intron|XBP1_uc003aef.2_Intron	NM_001079539	NP_001073007	P17861	XBP1_HUMAN	X-box binding protein 1 isoform XBP1(S)						immune response	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1						TCATTATTAGATCTTAGTACTG	0.356													1	5	---	---	---	---	
PDHA1	5160	broad.mit.edu	37	X	19363864	19363864	+	Intron	DEL	C	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									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													9	4	---	---	---	---	
MTMR1	8776	broad.mit.edu	37	X	149887055	149887055	+	Intron	DEL	C	-	-	rs58857458		TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149887055delC	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feg.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_5'Flank	NM_003828	NP_003819	Q13613	MTMR1_HUMAN	myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					CGTTTGGTGTCCttttttttt	0.393													2	9	---	---	---	---	
DKC1	1736	broad.mit.edu	37	X	153994771	153994771	+	Intron	DEL	A	-	-			TCGA-G9-6373-01	TCGA-G9-6373-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153994771delA	uc004fmm.2	+						DKC1_uc010nvf.2_Intron|SNORA36A_uc004fmn.2_5'Flank	NM_001363	NP_001354	O60832	DKC1_HUMAN	dyskerin isoform 1						cell proliferation|pseudouridine synthesis|rRNA processing|telomere maintenance via telomerase	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTTCATTAAGAAAAAAAAAAA	0.418									Congenital_Dyskeratosis				4	2	---	---	---	---	
