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
CROCCL1	84809	broad.mit.edu	37	1	16946407	16946407	+	RNA	SNP	T	G	G	rs10796418	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946407T>G	uc010ocf.1	-	3		c.491A>C			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						AGCAATCTCCTCACTCAGCTG	0.672													5	27	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16946438	16946438	+	RNA	SNP	G	C	C	rs28392876	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946438G>C	uc010ocf.1	-	3		c.460C>G			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GCCTTCCGCCGGGCCAGCAGC	0.672													4	24	---	---	---	---	PASS
EPHA10	284656	broad.mit.edu	37	1	38187334	38187334	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38187334C>A	uc009vvi.2	-	11	2230	c.2144G>T	c.(2143-2145)CGA>CTA	p.R715L	EPHA10_uc001cbt.2_5'Flank|EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	715	Cytoplasmic (Potential).|Protein kinase.					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGCCCTACCTCGGGTAACAAC	0.657													3	38	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120539834	120539834	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120539834A>T	uc001eik.2	-	4	793	c.537T>A	c.(535-537)TGT>TGA	p.C179*	NOTCH2_uc001eil.2_Nonsense_Mutation_p.C179*|NOTCH2_uc001eim.3_Nonsense_Mutation_p.C96*	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	179	Extracellular (Potential).|EGF-like 4.				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CATCAGTCTCACATTTCTGCC	0.552			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				9	81	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145209116	145209116	+	5'UTR	SNP	T	C	C	rs114878133	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145209116T>C	uc001emp.3	+	1					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_5'UTR|NOTCH2NL_uc001emm.3_5'UTR|NOTCH2NL_uc001emo.2_5'UTR|NOTCH2NL_uc010oyh.1_RNA	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACGAGGCTGCTTCGCTGCACA	0.736													4	7	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32824954	32824954	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32824954A>C	uc010ezu.2	+	70	14113	c.13979A>C	c.(13978-13980)TAT>TCT	p.Y4660S		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	4660	Ubiquitin-conjugating.				anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					CCAAACCTTTATAATGATGGC	0.333													3	39	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	167992447	167992447	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167992447C>T	uc002udx.2	+	2	455	c.437C>T	c.(436-438)TCG>TTG	p.S146L	XIRP2_uc010fpn.2_Missense_Mutation_p.S146L|XIRP2_uc010fpo.2_Missense_Mutation_p.S146L|XIRP2_uc010fpp.2_Missense_Mutation_p.S146L|XIRP2_uc002udy.2_5'UTR	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	Error:Variant_position_missing_in_A4UGR9_after_alignment					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						AGTTTGTGCTCGCCAGCTTTT	0.423													28	45	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179404631	179404631	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179404631C>T	uc010zfg.1	-	301	90681	c.90457G>A	c.(90457-90459)GTC>ATC	p.V30153I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V23848I|TTN_uc010zfi.1_Missense_Mutation_p.V23781I|TTN_uc010zfj.1_Missense_Mutation_p.V23656I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	31080							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTCTGATGACGCCACCTTGC	0.398													24	55	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179585679	179585679	+	Silent	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179585679G>A	uc010zfg.1	-	76	19559	c.19335C>T	c.(19333-19335)GAC>GAT	p.D6445D	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.D3106D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7372							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCAGCTGGCGTCACCAACAC	0.433													20	44	---	---	---	---	PASS
ZNF621	285268	broad.mit.edu	37	3	40573524	40573524	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40573524G>A	uc003ckm.2	+	5	479	c.263G>A	c.(262-264)GGT>GAT	p.G88D	ZNF621_uc003ckn.2_Missense_Mutation_p.G88D|ZNF621_uc003cko.2_Missense_Mutation_p.G53D|ZNF621_uc011aze.1_Missense_Mutation_p.G80D	NM_001098414	NP_001091884	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	88					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		TGGTCAGGTGGTGAGTCCTGG	0.403													13	81	---	---	---	---	PASS
ZXDC	79364	broad.mit.edu	37	3	126160695	126160695	+	Silent	SNP	G	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126160695G>T	uc003eiv.2	-	8	2361	c.2307C>A	c.(2305-2307)CTC>CTA	p.L769L	ZXDC_uc010hsh.2_RNA	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	769					positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)		TGGGCACCACGAGGCTCCCAC	0.592													3	49	---	---	---	---	PASS
SEC61A1	29927	broad.mit.edu	37	3	127779441	127779441	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127779441A>G	uc003ekb.2	+	7	737	c.553A>G	c.(553-555)ACT>GCT	p.T185A	SEC61A1_uc003ekc.2_Missense_Mutation_p.T132A|SEC61A1_uc003ekd.2_Missense_Mutation_p.T65A	NM_013336	NP_037468	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit	185	Helical; (Potential).				protein targeting to ER	integral to endoplasmic reticulum membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|protein binding|ribosome binding			ovary(1)	1						CTTCATTGCAACTAACATCTG	0.478													29	45	---	---	---	---	PASS
PIK3R4	30849	broad.mit.edu	37	3	130435328	130435328	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130435328C>T	uc003enj.2	-	9	2824	c.2243G>A	c.(2242-2244)CGT>CAT	p.R748H		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	748					fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12						TTTCTTCTGACGCATGTGAAG	0.443													5	101	---	---	---	---	PASS
DRD5	1816	broad.mit.edu	37	4	9783992	9783992	+	Silent	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9783992C>T	uc003gmb.3	+	1	735	c.339C>T	c.(337-339)TGC>TGT	p.C113C		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	113	Extracellular (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)	GAGCGTTCTGCGACGTCTGGG	0.627													25	28	---	---	---	---	PASS
CHD1	1105	broad.mit.edu	37	5	98218811	98218811	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98218811C>T	uc003knf.2	-	18	2847	c.2699G>A	c.(2698-2700)CGA>CAA	p.R900Q		NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	900	Helicase C-terminal.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TTGCCCAATTCGATGGGCTCT	0.338													10	22	---	---	---	---	PASS
YTHDC2	64848	broad.mit.edu	37	5	112876726	112876726	+	Silent	SNP	T	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112876726T>C	uc003kqn.2	+	9	1455	c.1272T>C	c.(1270-1272)CCT>CCC	p.P424P	YTHDC2_uc010jce.1_Silent_p.P424P|YTHDC2_uc010jcf.1_Silent_p.P124P	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	424							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)		GTTTCAAGCCTGAATCTCAGA	0.383													3	68	---	---	---	---	PASS
PCDHGA6	56109	broad.mit.edu	37	5	140754115	140754115	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140754115G>A	uc003ljy.1	+	1	465	c.465G>A	c.(463-465)ATG>ATA	p.M155I	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Missense_Mutation_p.M155I	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	155	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCACTAATGGAGGTCTATG	0.448													3	49	---	---	---	---	PASS
MYLIP	29116	broad.mit.edu	37	6	16145318	16145318	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16145318T>C	uc003nbq.2	+	6	1255	c.1018T>C	c.(1018-1020)TCA>CCA	p.S340P	MYLIP_uc003nbr.2_Missense_Mutation_p.S159P	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	340					cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			GGACCTCGTTTCAAGAAACAA	0.517													10	123	---	---	---	---	PASS
HLA-A	3105	broad.mit.edu	37	6	29910622	29910622	+	Silent	SNP	C	T	T	rs143754376	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29910622C>T	uc003nol.2	+	2	162	c.162C>T	c.(160-162)GAC>GAT	p.D54D	HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_Intron|HLA-A_uc010jrq.2_5'UTR|HLA-A_uc003nok.2_5'UTR|HLA-A_uc003non.2_Silent_p.D54D|HLA-A_uc003noo.2_Silent_p.D54D|HLA-A_uc010jrr.2_Silent_p.D54D|HLA-A_uc003nom.2_5'UTR|HLA-A_uc010klp.2_Silent_p.D26D|HLA-A_uc011dmc.1_5'UTR|HLA-A_uc011dmd.1_5'Flank	NM_002116	NP_002107	P30443	1A01_HUMAN	major histocompatibility complex, class I, A	54	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2						ACGTGGACGACACGCAGTTCG	0.687									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			5	31	---	---	---	---	PASS
BTBD9	114781	broad.mit.edu	37	6	38548004	38548004	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38548004G>A	uc003ooa.3	-	6	1600	c.1024C>T	c.(1024-1026)CGA>TGA	p.R342*	BTBD9_uc003ony.3_Nonsense_Mutation_p.R274*|BTBD9_uc010jwv.2_Nonsense_Mutation_p.R274*|BTBD9_uc010jww.2_RNA|BTBD9_uc010jwx.2_Nonsense_Mutation_p.R342*	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a	342					cell adhesion						0						CGGCTATCTCGGTCCCACAAG	0.413													4	38	---	---	---	---	PASS
MOCS1	4337	broad.mit.edu	37	6	39880665	39880665	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39880665C>A	uc003opb.2	-	6	979	c.841G>T	c.(841-843)GTG>TTG	p.V281L	MOCS1_uc003opa.2_Missense_Mutation_p.V281L|MOCS1_uc003opc.2_Missense_Mutation_p.V281L|MOCS1_uc003opd.2_Missense_Mutation_p.V281L|MOCS1_uc003ope.2_Missense_Mutation_p.V194L	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	281	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					TCCTCTGGCACCTTCTCCAGC	0.577													136	185	---	---	---	---	PASS
CCNC	892	broad.mit.edu	37	6	100009259	100009259	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100009259A>C	uc003pqe.2	-	4	565	c.278T>G	c.(277-279)TTG>TGG	p.L93W	uc003pqc.2_Intron|CCNC_uc003pqd.2_Missense_Mutation_p.L8W|CCNC_uc010kcr.2_RNA|CCNC_uc010kcs.2_Missense_Mutation_p.L93W|CCNC_uc011eah.1_Missense_Mutation_p.L8W|CCNC_uc003pqf.2_Missense_Mutation_p.L93W	NM_005190	NP_005181	P24863	CCNC_HUMAN	cyclin C isoform a	93	Cyclin N-terminal.				regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	DNA-directed RNA polymerase II, holoenzyme	protein kinase binding				0		all_cancers(76;8.46e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.064)		TTTGGATGCCAAAAACACACA	0.323													4	75	---	---	---	---	PASS
HOXA3	3200	broad.mit.edu	37	7	27147490	27147490	+	3'UTR	SNP	T	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27147490T>G	uc011jzl.1	-	3					HOXA3_uc011jzk.1_3'UTR|HOXA3_uc003syk.2_3'UTR	NM_030661	NP_109377	O43365	HXA3_HUMAN	homeobox A3 isoform a						angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)	2						agaaaaaaGGTGGGTGGGGGG	0.493													10	56	---	---	---	---	PASS
EIF4H	7458	broad.mit.edu	37	7	73604629	73604629	+	Silent	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73604629C>T	uc003uad.1	+	5	470	c.462C>T	c.(460-462)TTC>TTT	p.F154F	RFC2_uc011kfa.1_Intron|EIF4H_uc010lbm.2_Intron|EIF4H_uc003uae.1_Intron|EIF4H_uc003uaf.1_Intron|MIR590_hsa-mir-590|MI0003602_5'Flank	NM_022170	NP_071496	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	154	HHV-1 Vhs binding site.				interspecies interaction between organisms|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex|perinuclear region of cytoplasm	nucleotide binding|protein binding|translation initiation factor activity				0						GGGATGACTTCAATTCTGGTA	0.453													14	26	---	---	---	---	PASS
NSUN5P1	155400	broad.mit.edu	37	7	75044432	75044432	+	5'Flank	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75044432G>A	uc003udh.1	+						NSUN5P1_uc003ude.1_5'UTR|NSUN5P1_uc003udf.1_5'UTR|NSUN5P1_uc003udg.1_5'UTR	NM_145645	NP_663620			NOL1/NOP2/Sun domain family, member 5B												0						CTGGACCCCCGCCAGGCTCCC	0.637													15	17	---	---	---	---	PASS
PMS2L11	441263	broad.mit.edu	37	7	76610478	76610478	+	RNA	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76610478C>T	uc003ufw.3	+	1		c.340C>T			PMS2L11_uc011kgn.1_RNA	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						TGGGACGCAGCTCCTCCTTCC	0.672													6	77	---	---	---	---	PASS
DPP6	1804	broad.mit.edu	37	7	154172163	154172163	+	Intron	SNP	T	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154172163T>C	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc010lqh.1_Silent_p.H104H|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CGCTTCCCCATGCCTCACCCC	0.488													17	26	---	---	---	---	PASS
NKX3-1	4824	broad.mit.edu	37	8	23539041	23539041	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23539041T>G	uc011kzx.1	-	2	446	c.398A>C	c.(397-399)CAC>CCC	p.H133P	NKX3-1_uc003xdv.1_Intron	NM_006167	NP_006158	Q99801	NKX31_HUMAN	NK3 homeobox 1	133	Homeobox.				negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding				0		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		CACCTGAGTGTGGGAGAAGGC	0.587													90	33	---	---	---	---	PASS
MRPL15	29088	broad.mit.edu	37	8	55049839	55049839	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55049839A>C	uc003xsa.2	+	3	338	c.275A>C	c.(274-276)CAG>CCG	p.Q92P		NM_014175	NP_054894	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15 precursor	92					translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome				0		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)			TTCAGACGCCAGTATAAGCCT	0.398													55	39	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113308235	113308235	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113308235G>A	uc003ynu.2	-	54	8600	c.8441C>T	c.(8440-8442)GCG>GTG	p.A2814V	CSMD3_uc003yns.2_Missense_Mutation_p.A2016V|CSMD3_uc003ynt.2_Missense_Mutation_p.A2774V|CSMD3_uc011lhx.1_Missense_Mutation_p.A2645V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2814	Extracellular (Potential).|Sushi 17.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ACAATGACCCGCTGAAATACG	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			27	28	---	---	---	---	PASS
WASH5P	375690	broad.mit.edu	37	9	14863	14863	+	Silent	SNP	A	G	G	rs141792353	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14863A>G	uc010mgm.1	-	11	1485	c.1342T>C	c.(1342-1344)TTG>CTG	p.L448L	WASH5P_uc003zfr.2_RNA	NM_182905	NP_878908			WAS protein family homolog 1												0						GGTGGCGGCAAAGGAGGGATG	0.647													3	34	---	---	---	---	PASS
TJP2	9414	broad.mit.edu	37	9	71844114	71844114	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71844114G>C	uc004ahe.2	+	10	1668	c.1468G>C	c.(1468-1470)GCA>CCA	p.A490P	TJP2_uc011lrs.1_Missense_Mutation_p.A467P|TJP2_uc011lrt.1_Missense_Mutation_p.A467P|TJP2_uc004ahd.2_Missense_Mutation_p.A490P|TJP2_uc004ahf.2_Missense_Mutation_p.A490P|TJP2_uc011lru.1_Missense_Mutation_p.A494P|TJP2_uc011lrv.1_Missense_Mutation_p.A512P	NM_004817	NP_004808	Q9UDY2	ZO2_HUMAN	tight junction protein 2 (zona occludens 2)	490					cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0						TCAACCAAAAGCAGCCCCGAG	0.388													7	141	---	---	---	---	PASS
ATP6V1G1	9550	broad.mit.edu	37	9	117359985	117359985	+	Silent	SNP	C	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117359985C>A	uc004bjc.2	+	3	444	c.319C>A	c.(319-321)CGG>AGG	p.R107R		NM_004888	NP_004879	O75348	VATG1_HUMAN	vacuolar H+ ATPase G1	107					cellular iron ion homeostasis|insulin receptor signaling pathway|proton transport|transferrin transport	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase complex	ATPase binding|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances				0						CTGTGACATTCGGCCAGAAAT	0.478													3	53	---	---	---	---	PASS
SCAI	286205	broad.mit.edu	37	9	127765792	127765792	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127765792C>G	uc004bpe.2	-	10	1000	c.919G>C	c.(919-921)GAG>CAG	p.E307Q	SCAI_uc004bpd.2_Missense_Mutation_p.E330Q|SCAI_uc010mwu.2_RNA	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2	307					negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						TTCATTGGCTCCCTTTCCAGA	0.413													20	56	---	---	---	---	PASS
ITIH2	3698	broad.mit.edu	37	10	7780658	7780658	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7780658A>G	uc001ijs.2	+	16	2194	c.2032A>G	c.(2032-2034)ATC>GTC	p.I678V		NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide	678					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3						AACGCCCGTGATCTCCATGCT	0.552													9	75	---	---	---	---	PASS
ARHGAP21	57584	broad.mit.edu	37	10	24884077	24884077	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24884077G>C	uc001isb.2	-	20	4242	c.3755C>G	c.(3754-3756)CCT>CGT	p.P1252R	ARHGAP21_uc010qdb.1_RNA	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1251	Rho-GAP.				signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding	p.P1251fs*2(1)		ovary(7)|pancreas(1)	8						ACGATCTAGAGGATCTTCTTT	0.299													4	25	---	---	---	---	PASS
TPH1	7166	broad.mit.edu	37	11	18062244	18062244	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18062244A>C	uc001mnp.2	-	1	92	c.66T>G	c.(64-66)TTT>TTG	p.F22L	TPH1_uc009yhe.2_RNA	NM_004179	NP_004170	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	22	ACT.				aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	TCTTTAAGGAAAAAATGAGAC	0.328													5	38	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20622883	20622883	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20622883A>G	uc001mqd.2	+	2	485	c.212A>G	c.(211-213)GAG>GGG	p.E71G	SLC6A5_uc009yic.2_5'UTR	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	71	Cytoplasmic (Potential).				synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	CGAGCCTGCGAGGCTGAGCGG	0.721													6	6	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20628637	20628637	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20628637C>T	uc001mqd.2	+	4	1037	c.764C>T	c.(763-765)GCC>GTC	p.A255V	SLC6A5_uc009yic.2_Missense_Mutation_p.A20V	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	255					synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	GGCCAGTTTGCCAGCCAGGGA	0.572													3	42	---	---	---	---	PASS
CD82	3732	broad.mit.edu	37	11	44626916	44626916	+	Silent	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44626916C>T	uc001myc.2	+	6	521	c.273C>T	c.(271-273)TTC>TTT	p.F91F	CD82_uc001myd.2_Intron	NM_002231	NP_002222	P27701	CD82_HUMAN	CD82 antigen isoform 1	91	Helical; (Potential).					integral to plasma membrane	protein binding			ovary(1)	1						ACTTTGCTTTCCTGCTCCTGA	0.617													27	32	---	---	---	---	PASS
ADAMTS15	170689	broad.mit.edu	37	11	130343148	130343148	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130343148C>T	uc010scd.1	+	8	2285	c.2285C>T	c.(2284-2286)ACG>ATG	p.T762M		NM_139055	NP_620686	Q8TE58	ATS15_HUMAN	a disintegrin-like and metalloprotease	762	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|pancreas(1)|lung(1)|skin(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		TACAGCGGCACGGGCACAGCG	0.672													4	90	---	---	---	---	PASS
PRB2	653247	broad.mit.edu	37	12	11546067	11546067	+	Silent	SNP	A	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11546067A>G	uc010shk.1	-	3	980	c.945T>C	c.(943-945)CCT>CCC	p.P315P		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGGGACCTTGAGGCTGGTTGC	0.607													5	441	---	---	---	---	PASS
PFDN5	5204	broad.mit.edu	37	12	53689395	53689395	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53689395T>C	uc001scl.2	+	1	161	c.44T>C	c.(43-45)CTA>CCA	p.L15P	PFDN5_uc001scm.2_Missense_Mutation_p.L15P|PFDN5_uc001scn.2_RNA|PFDN5_uc001sco.2_RNA	NM_002624	NP_002615	Q99471	PFD5_HUMAN	prefoldin subunit 5 isoform alpha	15					'de novo' posttranslational protein folding|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent	nucleus|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)	1						CTGCCGCAGCTAGAAATGCTC	0.592													3	93	---	---	---	---	PASS
TBX3	6926	broad.mit.edu	37	12	115110035	115110035	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115110035A>C	uc001tvt.1	-	8	2807	c.1843T>G	c.(1843-1845)TCC>GCC	p.S615A	TBX3_uc001tvu.1_Missense_Mutation_p.S595A	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	615	Transcription repression.				anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GCCGCAGAGGAGGCGGCCGCC	0.662													3	7	---	---	---	---	PASS
LHFP	10186	broad.mit.edu	37	13	40175053	40175053	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40175053G>A	uc001uxf.2	-	2	812	c.301C>T	c.(301-303)CTC>TTC	p.L101F		NM_005780	NP_005771	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner precursor	101	Helical; (Potential).					integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		AGGGCAGTGAGCGCCACCAGG	0.587			T	HMGA2	lipoma								12	136	---	---	---	---	PASS
DGKH	160851	broad.mit.edu	37	13	42761271	42761271	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42761271C>T	uc001uyl.1	+	14	1646	c.1625C>T	c.(1624-1626)GCC>GTC	p.A542V	DGKH_uc010tfh.1_Missense_Mutation_p.A542V|DGKH_uc001uym.1_Missense_Mutation_p.A542V|DGKH_uc010tfi.1_Missense_Mutation_p.A297V|DGKH_uc010tfj.1_Missense_Mutation_p.A397V|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.A397V|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	542					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		GTAGCTGATGCCGTGGCCAGT	0.423													4	170	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106237609	106237609	+	RNA	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106237609G>A	uc010tyt.1	-	3611		c.57274C>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA					Parts of antibodies, mostly variable regions.												0						CGCTGGTCAGGGCGCCTGAGT	0.672													3	34	---	---	---	---	PASS
BBS4	585	broad.mit.edu	37	15	73015166	73015166	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73015166T>A	uc002avb.2	+	7	480	c.437T>A	c.(436-438)ATA>AAA	p.I146K	BBS4_uc010ukv.1_Missense_Mutation_p.I134K|BBS4_uc002avc.2_5'UTR|BBS4_uc002avd.2_Missense_Mutation_p.I154K|BBS4_uc010bja.2_5'UTR	NM_033028	NP_149017	Q96RK4	BBS4_HUMAN	Bardet-Biedl syndrome 4	146	Interaction with PCM1.|TPR 3.				adult behavior|brain morphogenesis|cell cycle cytokinesis|centrosome organization|cerebral cortex development|convergent extension involved in gastrulation|dendrite development|fat cell differentiation|heart looping|hippocampus development|intracellular transport|maintenance of protein location in nucleus|melanosome transport|microtubule anchoring at centrosome|neural tube closure|nonmotile primary cilium assembly|photoreceptor cell maintenance|pigment granule aggregation in cell center|positive regulation of flagellum assembly|regulation of cilium beat frequency involved in ciliary motility|regulation of cytokinesis|regulation of lipid metabolic process|retina homeostasis|retinal rod cell development|sensory perception of smell|sensory processing|spermatid development|striatum development	BBSome|centriolar satellite|centriole|cilium membrane|microtubule basal body|motile cilium|nonmotile primary cilium|nucleus|pericentriolar material	alpha-tubulin binding|beta-tubulin binding|dynactin binding|microtubule motor activity				0						GTTTGCTACATATACCTGAAG	0.373									Bardet-Biedl_syndrome				18	46	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15122780	15122780	+	Missense_Mutation	SNP	G	C	C	rs148363540	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15122780G>C	uc002dda.3	+	15	1474	c.1250G>C	c.(1249-1251)GGA>GCA	p.G417A	PDXDC1_uc010uzl.1_Missense_Mutation_p.G402A|PDXDC1_uc010uzm.1_Missense_Mutation_p.G326A|PDXDC1_uc002dcz.2_Missense_Mutation_p.G394A|PDXDC1_uc002ddb.3_Missense_Mutation_p.G390A|PDXDC1_uc010uzn.1_Missense_Mutation_p.G389A|PDXDC1_uc002ddc.2_Missense_Mutation_p.G417A	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain	417					carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	ACACCTTCAGGAGTCGGCCGG	0.567													3	57	---	---	---	---	PASS
TAOK2	9344	broad.mit.edu	37	16	29996717	29996717	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29996717G>T	uc002dva.1	+	14	2389	c.1606G>T	c.(1606-1608)GGG>TGG	p.G536W	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TAOK2_uc002dvb.1_Missense_Mutation_p.G536W|TAOK2_uc002dvc.1_Missense_Mutation_p.G536W|TAOK2_uc010bzm.1_Missense_Mutation_p.G543W|TAOK2_uc002dvd.1_Missense_Mutation_p.G363W	NM_016151	NP_057235	Q9UL54	TAOK2_HUMAN	TAO kinase 2 isoform 2	536	Potential.				actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1						GGCTGGCTTTGGGGCAGAGGC	0.672													8	10	---	---	---	---	PASS
FUK	197258	broad.mit.edu	37	16	70508758	70508758	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70508758C>T	uc002eyy.2	+	18	2279	c.2221C>T	c.(2221-2223)CGA>TGA	p.R741*	FUK_uc010cft.2_Nonsense_Mutation_p.R773*|FUK_uc002eyz.2_Nonsense_Mutation_p.R232*	NM_145059	NP_659496	Q8N0W3	FUK_HUMAN	fucokinase	741						cytoplasm	ATP binding|fucokinase activity			ovary(1)	1		Ovarian(137;0.0694)				CCTGGCTGTGCGAGTGGACGG	0.677													4	13	---	---	---	---	PASS
FBXW10	10517	broad.mit.edu	37	17	18682505	18682505	+	Missense_Mutation	SNP	T	C	C	rs117160613	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18682505T>C	uc002guk.2	+	14	3285	c.3053T>C	c.(3052-3054)GTC>GCC	p.V1018A	FBXW10_uc002guj.2_Missense_Mutation_p.V1017A|FBXW10_uc002gul.2_Missense_Mutation_p.V1027A|FBXW10_uc010cqh.1_Missense_Mutation_p.V965A|FAM18B_uc002gum.2_5'Flank	NM_031456	NP_113644	Q5XX13	FBW10_HUMAN	F-box and WD-40 domain protein 10	1018										ovary(1)	1						CCAGGAAAAGTCAGCAAAGCT	0.488													3	34	---	---	---	---	PASS
MED1	5469	broad.mit.edu	37	17	37566711	37566711	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37566711G>A	uc002hrv.3	-	17	1975	c.1763C>T	c.(1762-1764)TCG>TTG	p.S588L	MED1_uc010wee.1_Missense_Mutation_p.S416L|MED1_uc002hru.2_Intron	NM_004774	NP_004765	Q15648	MED1_HUMAN	mediator complex subunit 1	588	Interaction with ESR1.|Interaction with THRA.|Interaction with VDR.|Interaction with the Mediator complex and THRA.				androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		ATGGCCCACCGACTCATGCCG	0.512										HNSCC(31;0.082)			33	82	---	---	---	---	PASS
NPEPPS	9520	broad.mit.edu	37	17	45664677	45664677	+	Silent	SNP	C	T	T	rs149817839	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45664677C>T	uc002ilr.3	+	9	1285	c.1062C>T	c.(1060-1062)CTC>CTT	p.L354L	NPEPPS_uc010wkt.1_Silent_p.L350L|NPEPPS_uc010wku.1_Silent_p.L318L|NPEPPS_uc010wkv.1_5'UTR	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	354					proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						GACATGAACTCGCCCATCAAT	0.358													3	21	---	---	---	---	PASS
BZRAP1	9256	broad.mit.edu	37	17	56385061	56385061	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56385061C>A	uc002ivx.3	-	24	5765	c.4894G>T	c.(4894-4896)GCT>TCT	p.A1632S	BZRAP1_uc002ivv.2_5'Flank|BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Missense_Mutation_p.A1572S|BZRAP1_uc010wnt.1_Missense_Mutation_p.A1632S	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	1632	SH3 2.					mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCAAACAGAGCCACAAAGATC	0.567													7	64	---	---	---	---	PASS
CSH1	1442	broad.mit.edu	37	17	61972640	61972640	+	Intron	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61972640C>T	uc002jcs.1	-						CSH2_uc002jck.2_Intron|CSH1_uc002jcp.1_Intron|CSH1_uc002jcq.1_Intron|CSH1_uc002jcr.1_3'UTR|CSH1_uc002jct.1_Intron|CSH1_uc002jcu.1_Missense_Mutation_p.E217K|CSH1_uc002jcv.1_Intron|CSH1_uc002jcw.2_Intron|CSH1_uc002jcy.2_3'UTR	NM_001317	NP_001308	P01243	CSH_HUMAN	chorionic somatomammotropin hormone 1 isoform 1						female pregnancy|signal transduction	extracellular region	hormone activity|metal ion binding			skin(1)	1						CTCCCTCTCTCATTTATCCAT	0.557									Russell-Silver_syndrome				47	57	---	---	---	---	PASS
CBX4	8535	broad.mit.edu	37	17	77808784	77808784	+	Silent	SNP	A	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77808784A>C	uc002jxe.2	-	5	820	c.657T>G	c.(655-657)GGT>GGG	p.G219G		NM_003655	NP_003646	O00257	CBX4_HUMAN	chromobox homolog 4	219	Interaction with BMI1.				anti-apoptosis|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|PcG protein complex	enzyme binding|transcription corepressor activity			skin(2)	2			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TGCCTGGAGCACCCGCCGCAC	0.692											OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	26	---	---	---	---	PASS
SIRT7	51547	broad.mit.edu	37	17	79873382	79873382	+	Silent	SNP	G	A	A	rs146448282	byFrequency	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79873382G>A	uc002kcj.1	-	5	447	c.414C>T	c.(412-414)GCC>GCT	p.A138A	SIRT7_uc002kck.1_5'UTR|SIRT7_uc002kcl.1_Silent_p.A56A	NM_016538	NP_057622	Q9NRC8	SIRT7_HUMAN	sirtuin 7	138	Deacetylase sirtuin-type.				chromatin silencing|positive regulation of transcription on exit from mitosis|protein deacetylation|rRNA transcription	cytoplasm|nucleolus organizer region	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ binding|protein binding|zinc ion binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CGCTCAGGTCGGCAGCACTGC	0.652													3	28	---	---	---	---	PASS
PIP5K1C	23396	broad.mit.edu	37	19	3651957	3651957	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3651957C>T	uc002lyj.1	-	8	1051	c.994G>A	c.(994-996)GAG>AAG	p.E332K	PIP5K1C_uc010xhq.1_Missense_Mutation_p.E332K|PIP5K1C_uc010xhr.1_Missense_Mutation_p.E332K	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	332	PIPK.				axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GCCTGCCGCTCGCGCTCGTGC	0.652													15	37	---	---	---	---	PASS
UHRF1	29128	broad.mit.edu	37	19	4950688	4950688	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4950688G>A	uc002mbo.2	+	12	1751	c.1583G>A	c.(1582-1584)CGG>CAG	p.R528Q	UHRF1_uc010xik.1_RNA|UHRF1_uc010duf.2_RNA|UHRF1_uc002mbp.2_Missense_Mutation_p.R541Q	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains	528	YDG.|Methyl-CpG binding and interaction with HDAC1.				cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		AAGGACTGGCGGTCGGGGAAG	0.607													22	30	---	---	---	---	PASS
MAP2K7	5609	broad.mit.edu	37	19	7975046	7975046	+	Intron	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7975046G>A	uc002mit.2	+						MAP2K7_uc002miv.2_Intron|MAP2K7_uc010xka.1_Intron|MAP2K7_uc010xkb.1_Intron|MAP2K7_uc010dvv.2_5'UTR	NM_145185	NP_660186	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7						activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|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	cytosol|nucleus	ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1)	11					Etoposide(DB00773)	GGAGAGGGAGGAGGCCCAGCC	0.672													5	4	---	---	---	---	PASS
MRI1	84245	broad.mit.edu	37	19	13875456	13875456	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13875456G>T	uc002mxe.2	+	1	120	c.54G>T	c.(52-54)CAG>CAT	p.Q18H	MRI1_uc002mxf.2_Missense_Mutation_p.Q18H	NM_001031727	NP_001026897	Q9BV20	MTNA_HUMAN	translation initiation factor eIF-2B subunit	18					L-methionine salvage from methylthioadenosine	cell projection|cytoplasm|nucleus	identical protein binding|S-methyl-5-thioribose-1-phosphate isomerase activity			ovary(1)	1						TCCTAGACCAGCTGCTGCTGC	0.612													6	52	---	---	---	---	PASS
HNRNPL	3191	broad.mit.edu	37	19	39334540	39334540	+	Silent	SNP	A	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39334540A>G	uc010xul.1	-	6	833	c.822T>C	c.(820-822)AAT>AAC	p.N274N	HNRNPL_uc002ojk.2_5'Flank|HNRNPL_uc002ojl.2_5'Flank|HNRNPL_uc010xum.1_Silent_p.N141N|HNRNPL_uc010xun.1_5'UTR	NM_001533	NP_001524	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	274					nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TCTTGAACACATTCAAGCGTG	0.507													31	60	---	---	---	---	PASS
PSG6	5675	broad.mit.edu	37	19	43585093	43585093	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43585093T>C	uc002ovi.2	-	2	463	c.370A>G	c.(370-372)ATC>GTC	p.I124V	PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Missense_Mutation_p.I124V|PSG2_uc002ovq.3_Missense_Mutation_p.I124V|PSG2_uc010eiq.1_Missense_Mutation_p.I124V|PSG2_uc002ovs.3_Missense_Mutation_p.I124V|PSG2_uc002ovt.3_Missense_Mutation_p.I124V			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;	123	Ig-like V-type.				female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				CGCTTTATGATGTGTAAGGTG	0.493													16	160	---	---	---	---	PASS
CD37	951	broad.mit.edu	37	19	49842785	49842785	+	Intron	SNP	A	C	C			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49842785A>C	uc002pnd.2	+						uc002pnb.1_Intron|CD37_uc002pnc.2_Intron|CD37_uc010yam.1_3'UTR|CD37_uc010yan.1_3'UTR|CD37_uc002pnf.3_3'UTR|CD37_uc002pne.2_Intron	NM_001774	NP_001765	P11049	CD37_HUMAN	CD37 antigen isoform A							integral to membrane					0		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)		AGCGCAGCCCACCCCGGCCCT	0.687													4	12	---	---	---	---	PASS
SIGLEC5	8778	broad.mit.edu	37	19	52130800	52130800	+	Silent	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52130800G>A	uc002pxe.2	-	6	1336	c.1197C>T	c.(1195-1197)CAC>CAT	p.H399H		NM_003830	NP_003821	O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5 precursor	399	Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			skin(2)|breast(1)|central_nervous_system(1)	4		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGAGCCCCCCGTGGAGGATCA	0.627													20	39	---	---	---	---	PASS
SIRPB1	10326	broad.mit.edu	37	20	1552430	1552430	+	Missense_Mutation	SNP	T	C	C	rs2253427	byFrequency	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1552430T>C	uc010gai.2	-	3	786	c.687A>G	c.(685-687)ATA>ATG	p.I229M	SIRPB1_uc002wfk.3_Intron	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1	229	Ig-like C1-type 1.|Extracellular (Potential).				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1						TGATGTGGGCTATCTCGCAGA	0.607													3	119	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29624093	29624093	+	Splice_Site	SNP	G	T	T	rs75468660		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29624093G>T	uc010ztl.1	+	1	58	c.26_splice	c.e1+1	p.R9_splice	FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CTGATTCCAGGTGAGCTTATG	0.289													3	19	---	---	---	---	PASS
TSHZ2	128553	broad.mit.edu	37	20	51870363	51870363	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51870363G>A	uc002xwo.2	+	2	1322	c.366G>A	c.(364-366)ATG>ATA	p.M122I		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	122					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			ACAATTGCATGGATAAAATGA	0.522													24	32	---	---	---	---	PASS
CCT8L2	150160	broad.mit.edu	37	22	17072407	17072407	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17072407C>T	uc002zlp.1	-	1	1294	c.1034G>A	c.(1033-1035)GGC>GAC	p.G345D		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	345					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTGGCACTTGCCTGGCCTCTG	0.547													4	137	---	---	---	---	PASS
SLC7A4	6545	broad.mit.edu	37	22	21384286	21384286	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21384286C>T	uc002zud.2	-	3	1405	c.1337G>A	c.(1336-1338)GGC>GAC	p.G446D	SLC7A4_uc002zue.2_Missense_Mutation_p.G446D	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid	446					cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GTGTACAGTGCCCACCAGCTG	0.657													6	19	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19474752	19474752	+	Intron	DEL	A	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19474752delA	uc001bbi.2	-						UBR4_uc001bbk.1_Intron	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CTGCAAAGAGAAAAAAAAAAA	0.448													3	3	---	---	---	---	
TINAGL1	64129	broad.mit.edu	37	1	32044601	32044602	+	Intron	DEL	GT	-	-	rs28555101		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32044601_32044602delGT	uc001bta.2	+						TINAGL1_uc001bsz.2_Intron|TINAGL1_uc010ogi.1_Intron|TINAGL1_uc010ogj.1_Intron|TINAGL1_uc010ogk.1_Intron	NM_022164	NP_071447	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1						endosome transport|immune response|proteolysis	extracellular region	cysteine-type endopeptidase activity|extracellular matrix structural constituent|polysaccharide binding|scavenger receptor activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		GTGACAGCTGgtgtgtgtgtgt	0.233													2	4	---	---	---	---	
BMP8A	353500	broad.mit.edu	37	1	39988318	39988319	+	Intron	INS	-	TTG	TTG	rs139401553	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39988318_39988319insTTG	uc001cdi.2	+						PPIEL_uc001cdj.1_Intron|PPIEL_uc001cdk.2_Intron	NM_181809	NP_861525	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8A precursor						cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GAGAAAGGGTTTTGTTGTTGTT	0.356													6	3	---	---	---	---	
INADL	10207	broad.mit.edu	37	1	62327531	62327532	+	Intron	INS	-	TC	TC	rs145278086	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62327531_62327532insTC	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						TAATCCTCCtttctctctctct	0.173													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143391923	143391924	+	IGR	DEL	AT	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143391923_143391924delAT								None (None upstream) : LOC100286793 (255715 downstream)																							TATTTTGGAGATATATATATAT	0.262													6	3	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179563644	179563644	+	Intron	DEL	A	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179563644delA	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTGGTAACTaaaaaaaaaaa	0.269													4	2	---	---	---	---	
GADL1	339896	broad.mit.edu	37	3	30769526	30769526	+	3'UTR	DEL	A	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30769526delA	uc003cep.2	-	15						NM_207359	NP_997242	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)	TTTTTTTTTTAAACTTTCTTC	0.393													4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195538502	195538503	+	Intron	DEL	TC	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195538502_195538503delTC	uc011bto.1	-						MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzv.2_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		tttcccctattctctctctctc	0.317													7	4	---	---	---	---	
TNPO1	3842	broad.mit.edu	37	5	72146952	72146953	+	Intron	INS	-	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72146952_72146953insA	uc003kck.3	+						TNPO1_uc011csi.1_Intron|TNPO1_uc011csj.1_Intron|TNPO1_uc003kch.2_Intron|TNPO1_uc003kci.3_Intron|TNPO1_uc003kcg.3_Intron	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1						interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		ATTCTTAGTTTAAAAAAAAAAC	0.317													4	2	---	---	---	---	
SERAC1	84947	broad.mit.edu	37	6	158564362	158564385	+	Intron	DEL	TCTCTCTCTCTCTCTCTCTATATA	-	-	rs10594921		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158564362_158564385delTCTCTCTCTCTCTCTCTCTATATA	uc003qrc.2	-						SERAC1_uc003qrb.2_Intron	NM_032861	NP_116250	Q96JX3	SRAC1_HUMAN	serine active site containing 1						GPI anchor metabolic process|intracellular protein transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	binding|hydrolase activity, acting on ester bonds				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		tctctctctctctctctctctctctctctatatatatatatata	0.183													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	33977125	33977126	+	Intron	INS	-	GTGT	GTGT			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33977125_33977126insGTGT	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						GGAGAAGTAGGgtgtgtgtgtg	0.391													3	3	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76796901	76796901	+	Intron	DEL	A	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76796901delA	uc003uga.2	+						CCDC146_uc003ufz.1_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GTTTATTTTTATTATTTTCCA	0.264													4	2	---	---	---	---	
KIAA1797	54914	broad.mit.edu	37	9	20995373	20995374	+	Intron	INS	-	AC	AC	rs150489586		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20995373_20995374insAC	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)		AAAAAAAAAAAAAACAACTTTC	0.267													3	3	---	---	---	---	
ZNF143	7702	broad.mit.edu	37	11	9549036	9549036	+	Intron	DEL	T	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9549036delT	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		TGACTGTGGCTTTTGAATTGT	0.398													39	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56098812	56098813	+	IGR	INS	-	G	G			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56098812_56098813insG								OR8K3 (12093 upstream) : OR8K1 (14702 downstream)																							ATCAGGGCTTTGGGGGCATCAT	0.411													4	3	---	---	---	---	
PAN2	9924	broad.mit.edu	37	12	56726385	56726386	+	Intron	DEL	AA	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56726385_56726386delAA	uc001skx.2	-						PAN2_uc001skz.2_Intron|PAN2_uc001sky.2_Intron	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						ccctgtctcgaaaaaaaaaaaa	0.193													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21677698	21677699	+	IGR	INS	-	A	A			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21677698_21677699insA								LATS2 (41976 upstream) : SAP18 (36954 downstream)																							actcggtttccaaaaaaaaaGG	0.218													6	3	---	---	---	---	
KIAA0564	23078	broad.mit.edu	37	13	42465337	42465338	+	Intron	INS	-	A	A	rs11422492		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42465337_42465338insA	uc001uyj.2	-						KIAA0564_uc001uyk.2_Intron	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		ttagactgaccaaaaaaaaaaa	0.144													5	3	---	---	---	---	
UGGT2	55757	broad.mit.edu	37	13	96600473	96600478	+	Intron	DEL	ACACAC	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96600473_96600478delACACAC	uc001vmt.2	-							NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3						TCTAAGGAATacacacacacacacac	0.209													4	2	---	---	---	---	
DOCK9	23348	broad.mit.edu	37	13	99567413	99567414	+	Intron	DEL	GT	-	-	rs150790463		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99567413_99567414delGT	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tis.1_Intron|DOCK9_uc010tit.1_Intron|DOCK9_uc010afu.1_Intron	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TGTCAGGGAAGTAAGTTATAAT	0.252													4	2	---	---	---	---	
PNMA1	9240	broad.mit.edu	37	14	74179051	74179057	+	3'UTR	DEL	TGGCATT	-	-	rs1305033		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74179051_74179057delTGGCATT	uc001xor.1	-	1						NM_006029	NP_006020	Q8ND90	PNMA1_HUMAN	paraneoplastic antigen MA1						apoptosis|central nervous system development|inflammatory response to antigenic stimulus|spermatogenesis	cytoplasm|focal adhesion|nucleolus	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00331)|KIRC - Kidney renal clear cell carcinoma(182;0.0797)		ACCCTTTACCTGGCATTTTAGCCAGCA	0.473													1	5	---	---	---	---	
CATSPERB	79820	broad.mit.edu	37	14	92176033	92176034	+	Intron	INS	-	A	A	rs143282961	by1000genomes	TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92176033_92176034insA	uc001xzs.1	-							NM_024764	NP_079040	Q9H7T0	CTSRB_HUMAN	cation channel, sperm-associated, beta						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|skin(2)|ovary(1)	5		all_cancers(154;0.0663)|all_epithelial(191;0.236)				gactccatctcaaaaaaacaaa	0.134													4	2	---	---	---	---	
CYFIP1	23191	broad.mit.edu	37	15	22958073	22958073	+	Intron	DEL	C	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22958073delC	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_Intron|CYFIP1_uc001yuu.2_Intron	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TGCTGCATGGCTTGGGGCTGA	0.562													4	2	---	---	---	---	
CATSPER2	117155	broad.mit.edu	37	15	43950663	43950663	+	Intron	DEL	C	-	-	rs67805714		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43950663delC	uc001zsl.1	-									Q96P56	CTSR2_HUMAN	Homo sapiens putative ion channel protein CATSPER2 variant 1 mRNA, complete cds.						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|protein binding|voltage-gated ion channel activity			ovary(1)	1		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		aaaaaaaaaacaaaaCACAGT	0.234													9	4	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44168003	44168003	+	Intron	DEL	T	-	-	rs34063043		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44168003delT	uc001ztl.2	-						FRMD5_uc001ztj.1_Intron|FRMD5_uc001ztk.1_Intron|FRMD5_uc010uef.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		CTGGGCCTAGttttttttttt	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	8102780	8102780	+	IGR	DEL	T	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8102780delT								C17orf59 (9216 upstream) : AURKB (5270 downstream)																							CCCTGGCCTATTTTTTTTTTT	0.358													4	2	---	---	---	---	
ULK2	9706	broad.mit.edu	37	17	19684555	19684555	+	Intron	DEL	C	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19684555delC	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082	Q8IYT8	ULK2_HUMAN	unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					TCtttcttttctttttttttt	0.159													4	2	---	---	---	---	
ABCA6	23460	broad.mit.edu	37	17	67081660	67081661	+	Intron	INS	-	A	A	rs35438104		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67081660_67081661insA	uc002jhw.1	-							NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					TATCCAAAGGCaaaaaaaaaaa	0.277													2	4	---	---	---	---	
TSPAN16	26526	broad.mit.edu	37	19	11422999	11422999	+	Intron	DEL	A	-	-	rs149530459		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11422999delA	uc002mqv.1	+						TSPAN16_uc002mqu.1_Intron|uc002mqw.1_Intron	NM_012466	NP_036598	Q9UKR8	TSN16_HUMAN	transmembrane 4 superfamily member 16							integral to membrane				skin(1)	1						gaacaaaactaaaaaaaAAAA	0.090													3	3	---	---	---	---	
CHERP	10523	broad.mit.edu	37	19	16640581	16640583	+	In_Frame_Del	DEL	TGC	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16640581_16640583delTGC	uc002nei.1	-	8	1079_1081	c.1005_1007delGCA	c.(1003-1008)CAGCAA>CAA	p.335_336QQ>Q	MED26_uc002nee.2_Intron	NM_006387	NP_006378	Q8IWX8	CHERP_HUMAN	calcium homeostasis endoplasmic reticulum	335_336	Gln-rich.				cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding			ovary(2)	2						ctgctgctgttgctgctgctgct	0.552													50	8	---	---	---	---	
CHD6	84181	broad.mit.edu	37	20	40118655	40118656	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40118655_40118656insT	uc002xka.1	-	12	1620_1621	c.1442_1443insA	c.(1441-1443)AACfs	p.N481fs	CHD6_uc002xkd.2_Frame_Shift_Ins_p.N459fs	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	481	Helicase ATP-binding.				chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				CCAAAATACAGTTTTTTCTGCA	0.376													126	73	---	---	---	---	
EDN3	1908	broad.mit.edu	37	20	57899654	57899654	+	Intron	DEL	C	-	-	rs111992101		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57899654delC	uc002yap.2	+						EDN3_uc002yaq.2_3'UTR|EDN3_uc002yar.2_3'UTR|EDN3_uc002yas.2_3'UTR	NM_000114	NP_000105	P14138	EDN3_HUMAN	endothelin 3 isoform 1 preproprotein						cell surface receptor linked signaling pathway|inositol phosphate-mediated signaling|neutrophil chemotaxis|peptide hormone secretion|positive regulation of heart rate|positive regulation of hormone secretion|positive regulation of leukocyte chemotaxis|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction	extracellular space|soluble fraction	endothelin B receptor binding|hormone activity			skin(1)	1	all_lung(29;0.0115)					CTTAACAATACCCCCCCCCCA	0.507													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11085940	11085942	+	Intron	DEL	CAC	-	-			TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11085940_11085942delCAC	uc002yit.1	-						BAGE_uc002yix.2_Intron	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)		ccaccaccatcaccaccaccacc	0.158													3	3	---	---	---	---	
OTUD5	55593	broad.mit.edu	37	X	48791593	48791593	+	Intron	DEL	T	-	-	rs10715761		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48791593delT	uc004dlu.2	-						OTUD5_uc004dlt.3_Intron|OTUD5_uc004dlv.2_Intron|OTUD5_uc011mmp.1_Intron	NM_017602	NP_060072	Q96G74	OTUD5_HUMAN	OTU domain containing 5 isoform a						negative regulation of type I interferon production		cysteine-type peptidase activity			pancreas(1)	1						TAACTCCCTATTTTTTTTTTT	0.443													4	3	---	---	---	---	
NXF4	55999	broad.mit.edu	37	X	101804817	101804818	+	5'Flank	INS	-	C	C	rs112443744		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101804817_101804818insC	uc004ejf.1	+							NR_002216				Homo sapiens cDNA FLJ42710 fis, clone BRAMY3007609, moderately similar to Homo sapiens nuclear RNA export factor 2 (NXF2).												0						GTGTGGCAGCACCCCCCCCCCA	0.535													4	2	---	---	---	---	
IL13RA1	3597	broad.mit.edu	37	X	117910551	117910551	+	Intron	DEL	G	-	-	rs74983654		TCGA-CH-5767-01	TCGA-CH-5767-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117910551delG	uc004eqs.2	+						IL13RA1_uc004eqt.1_Intron	NM_001560	NP_001551	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0						ttttaaaaaagtgtggtaagg	0.149													4	2	---	---	---	---	
