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	16946438	16946438	+	RNA	SNP	G	C	C	rs28392876	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									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													3	21	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16956467	16956467	+	Intron	SNP	A	T	T	rs1762950	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16956467A>T	uc009vov.1	-						CROCCL1_uc001aze.2_Intron|CROCCL1_uc001azf.2_Intron|CROCCL1_uc001azg.1_Intron|CROCCL1_uc001azi.1_RNA	NR_026752				Homo sapiens mRNA for FLJ00313 protein.												0						gcaattttttaaatttttagt	0.214													6	15	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16956468	16956468	+	Intron	SNP	A	T	T	rs1762951	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16956468A>T	uc009vov.1	-						CROCCL1_uc001aze.2_Intron|CROCCL1_uc001azf.2_Intron|CROCCL1_uc001azg.1_Intron|CROCCL1_uc001azi.1_RNA	NR_026752				Homo sapiens mRNA for FLJ00313 protein.												0						caattttttaaatttttagta	0.219													6	16	---	---	---	---	PASS
CYP4A11	1579	broad.mit.edu	37	1	47395778	47395778	+	3'UTR	SNP	T	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47395778T>G	uc001cqp.3	-	12						NM_000778	NP_000769	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A,						long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|skin(2)	4					NADH(DB00157)	ggacggcaggTGGAGGCCCTC	0.259													11	29	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152277248	152277248	+	Missense_Mutation	SNP	C	T	T	rs149432670	byFrequency	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152277248C>T	uc001ezu.1	-	3	10150	c.10114G>A	c.(10114-10116)GCA>ACA	p.A3372T		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3372	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGGTCACGTGCGGACTCTTGG	0.587									Ichthyosis				9	717	---	---	---	---	PASS
OR10R2	343406	broad.mit.edu	37	1	158449980	158449980	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158449980C>G	uc010pik.1	+	1	313	c.313C>G	c.(313-315)CTA>GTA	p.L105V	uc001fso.1_RNA	NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	105	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)					GCTCATCAATCTACTTTCTGT	0.438													6	603	---	---	---	---	PASS
VSIG8	391123	broad.mit.edu	37	1	159827904	159827904	+	Missense_Mutation	SNP	G	A	A	rs112455697		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159827904G>A	uc001fuh.2	-	3	542	c.406C>T	c.(406-408)CGG>TGG	p.R136W	C1orf204_uc001fug.1_5'Flank	NM_001013661	NP_001013683	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8	136	Extracellular (Potential).|Ig-like V-type 1.					integral to membrane				central_nervous_system(1)	1	all_hematologic(112;0.0597)					ATGACCTTCCGGGTGGCCATG	0.557													32	75	---	---	---	---	PASS
FCGR2A	2212	broad.mit.edu	37	1	161488890	161488890	+	3'UTR	SNP	G	A	A	rs12562005	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161488890G>A	uc001gan.2	+	7					FCGR2A_uc001gam.2_3'UTR|FCGR2A_uc001gao.2_Intron	NM_001136219	NP_001129691	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor							integral to membrane|plasma membrane	IgG binding|receptor activity			ovary(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TGGGATTTGAGAAGAGAATTA	0.453													3	14	---	---	---	---	PASS
FMOD	2331	broad.mit.edu	37	1	203316790	203316790	+	Silent	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203316790C>T	uc001gzr.2	-	2	745	c.609G>A	c.(607-609)ACG>ACA	p.T203T	FMOD_uc010pqi.1_RNA	NM_002023	NP_002014	Q06828	FMOD_HUMAN	fibromodulin precursor	203	LRR 5.				transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)			GGTACAAGGCCGTGAGGTTCT	0.582													73	242	---	---	---	---	PASS
ZC3H11A	9877	broad.mit.edu	37	1	203819752	203819752	+	Silent	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203819752G>A	uc001hac.2	+	18	2665	c.2049G>A	c.(2047-2049)GTG>GTA	p.V683V	ZC3H11A_uc001had.2_Silent_p.V683V|ZC3H11A_uc001hae.2_Silent_p.V683V|ZC3H11A_uc001haf.2_Silent_p.V683V|ZC3H11A_uc010pqm.1_Silent_p.V629V	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	683							nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TTGCCGCTGTGAAGCCACTCA	0.498													5	52	---	---	---	---	PASS
SLC26A9	115019	broad.mit.edu	37	1	205884398	205884398	+	3'UTR	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205884398C>T	uc001hdq.2	-	21					SLC26A9_uc001hdm.2_Silent_p.S9S|SLC26A9_uc001hdn.2_Silent_p.S9S|SLC26A9_uc001hdo.2_3'UTR|SLC26A9_uc001hdp.2_Intron	NM_052934	NP_443166	Q7LBE3	S26A9_HUMAN	solute carrier family 26, member 9 isoform a							integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)|skin(1)	2	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			TTCCTCCGCCCGACACCCCCT	0.458													11	101	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	905786	905786	+	5'Flank	SNP	G	T	T	rs111964853		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:905786G>T	uc010ewg.2	-						uc010ewh.1_Silent_p.R54R					Homo sapiens cDNA FLJ46162 fis, clone TESTI4002520.																		ATTTCCTCCCGGCCTCCTCGC	0.617													10	523	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90259776	90259776	+	Intron	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90259776G>A	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		GACACAGCATGGACATGAGGG	0.537													5	348	---	---	---	---	PASS
TANC1	85461	broad.mit.edu	37	2	160031669	160031669	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160031669T>G	uc002uag.2	+	12	1983	c.1709T>G	c.(1708-1710)CTG>CGG	p.L570R	TANC1_uc010fol.1_Missense_Mutation_p.L464R|TANC1_uc010zcm.1_Missense_Mutation_p.L562R|TANC1_uc010fom.1_Missense_Mutation_p.L376R|TANC1_uc002uai.1_5'Flank	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	570						cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						AGGGGAGTGCTGGAGCCACTC	0.572													8	63	---	---	---	---	PASS
ITGB6	3694	broad.mit.edu	37	2	160994176	160994176	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160994176C>A	uc002ubh.2	-	10	1445	c.1429G>T	c.(1429-1431)GGG>TGG	p.G477W	ITGB6_uc010fou.2_Missense_Mutation_p.G477W|ITGB6_uc010zcq.1_Missense_Mutation_p.G435W|ITGB6_uc010fov.1_Missense_Mutation_p.G477W	NM_000888	NP_000879	P18564	ITB6_HUMAN	integrin, beta 6 precursor	477	Extracellular (Potential).|Cysteine-rich tandem repeats.|I.				cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3						GCACACACCCCACACTGGAAA	0.572													4	92	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179444120	179444120	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179444120A>T	uc010zfg.1	-	269	60157	c.59933T>A	c.(59932-59934)GTG>GAG	p.V19978E	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V13673E|TTN_uc010zfi.1_Missense_Mutation_p.V13606E|TTN_uc010zfj.1_Missense_Mutation_p.V13481E|uc002umv.1_3'UTR	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20905							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)			ATCAGGAGCCACTGTAAAATA	0.378													4	76	---	---	---	---	PASS
MARS2	92935	broad.mit.edu	37	2	198570300	198570300	+	Silent	SNP	G	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198570300G>T	uc002uuq.2	+	1	214	c.171G>T	c.(169-171)GCG>GCT	p.A57A	uc002uup.2_Intron	NM_138395	NP_612404	Q96GW9	SYMM_HUMAN	methionine-tRNA synthetase 2 precursor	57	HIGH region.				methionyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|methionine-tRNA ligase activity			ovary(1)|central_nervous_system(1)|skin(1)	3					L-Methionine(DB00134)	TGAACGCGGCGCCGCACATCG	0.647													5	47	---	---	---	---	PASS
AOX1	316	broad.mit.edu	37	2	201468741	201468741	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201468741C>A	uc002uvx.2	+	8	691	c.590C>A	c.(589-591)ACA>AAA	p.T197K		NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	197					inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TCTTTTTAGACAAGTCCAAAA	0.303													10	146	---	---	---	---	PASS
PIKFYVE	200576	broad.mit.edu	37	2	209190217	209190217	+	Missense_Mutation	SNP	G	T	T	rs139157818	byFrequency	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209190217G>T	uc002vcz.2	+	20	2840	c.2682G>T	c.(2680-2682)GAG>GAT	p.E894D	PIKFYVE_uc010fun.1_Missense_Mutation_p.E575D|PIKFYVE_uc002vcy.1_Missense_Mutation_p.E838D	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	894					cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						CCCTGATTGAGGGACGAGGGC	0.493													5	262	---	---	---	---	PASS
SLC6A1	6529	broad.mit.edu	37	3	11078641	11078641	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11078641G>T	uc010hdq.2	+	16	2200	c.1789G>T	c.(1789-1791)GCC>TCC	p.A597S		NM_003042	NP_003033	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter	597	Cytoplasmic (Potential).|PDZ-binding.				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)|skin(1)	2		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Cocaine(DB00907)|Tiagabine(DB00906)	CAGCAAGGAGGCCTACATCTA	0.627													7	67	---	---	---	---	PASS
BTD	686	broad.mit.edu	37	3	15643299	15643299	+	5'UTR	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15643299C>A	uc003cah.2	+	1					HACL1_uc011avr.1_5'Flank|HACL1_uc011avs.1_5'Flank|HACL1_uc011avt.1_5'Flank|HACL1_uc003cag.2_5'Flank|HACL1_uc011avu.1_5'Flank|HACL1_uc010hep.2_5'Flank|HACL1_uc003caf.2_5'Flank|BTD_uc011avv.1_Intron|BTD_uc011avw.1_5'UTR|BTD_uc011avx.1_5'Flank	NM_000060	NP_000051	P43251	BTD_HUMAN	biotinidase precursor						central nervous system development|epidermis development|nitrogen compound metabolic process	extracellular space	biotin carboxylase activity|biotinidase activity				0						AACTCTGAGGCCTCTCGCCAT	0.602													6	37	---	---	---	---	PASS
LNX1	84708	broad.mit.edu	37	4	54424152	54424152	+	Intron	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54424152C>A	uc003hag.3	-						PDGFRA_uc003haa.2_Intron|LNX1_uc003haf.3_Translation_Start_Site|LNX1_uc003hah.3_Intron	NM_001126328	NP_001119800	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1 isoform a							cytoplasm	zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AGTGTGCTGCCTTCTCCCTGG	0.527													3	49	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113468559	113468559	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113468559T>C	uc003iau.2	-	24	5691	c.5480A>G	c.(5479-5481)GAG>GGG	p.E1827G	C4orf21_uc003iav.2_RNA|C4orf21_uc003iat.2_Missense_Mutation_p.E285G	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	649						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		CTTTTCACACTCAAACCTAAA	0.348													4	54	---	---	---	---	PASS
FBXO4	26272	broad.mit.edu	37	5	41934294	41934294	+	Missense_Mutation	SNP	G	T	T	rs139568068		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41934294G>T	uc003jmq.2	+	5	838	c.782G>T	c.(781-783)CGA>CTA	p.R261L	FBXO4_uc003jmp.2_Missense_Mutation_p.R261L|FBXO4_uc003jmr.2_Missense_Mutation_p.R261L	NM_012176	NP_036308	Q9UKT5	FBX4_HUMAN	F-box only protein 4 isoform 1	261					positive regulation of protein ubiquitination|protein polyubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|telomere maintenance|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	protein binding|protein homodimerization activity|ubiquitin-protein ligase activity			liver(1)	1		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				ATGTTCAGTCGACACAATGAA	0.368													3	115	---	---	---	---	PASS
MAP1B	4131	broad.mit.edu	37	5	71493006	71493006	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71493006G>A	uc003kbw.3	+	5	4065	c.3824G>A	c.(3823-3825)CGT>CAT	p.R1275H	MAP1B_uc010iyw.1_Missense_Mutation_p.R1292H|MAP1B_uc010iyx.1_Missense_Mutation_p.R1149H|MAP1B_uc010iyy.1_Missense_Mutation_p.R1149H	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1275						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CTGGGTGAACGTAGTGTGAAC	0.517													15	131	---	---	---	---	PASS
PPP2R2B	5521	broad.mit.edu	37	5	145969623	145969623	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145969623C>T	uc003loe.2	-	9	1744	c.1219G>A	c.(1219-1221)GAC>AAC	p.D407N	PPP2R2B_uc010jgm.2_Missense_Mutation_p.D396N|PPP2R2B_uc003log.3_Missense_Mutation_p.D407N|PPP2R2B_uc003lof.3_Missense_Mutation_p.D407N|PPP2R2B_uc003loi.3_Missense_Mutation_p.D410N|PPP2R2B_uc003loh.3_Missense_Mutation_p.D407N|PPP2R2B_uc003loj.3_Missense_Mutation_p.D387N|PPP2R2B_uc003lok.3_Missense_Mutation_p.D396N|PPP2R2B_uc011dbu.1_Missense_Mutation_p.D413N|PPP2R2B_uc011dbv.1_Missense_Mutation_p.D465N	NM_004576	NP_004567	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein	407					apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCAGACTGTCGACACTGATC	0.478													18	509	---	---	---	---	PASS
ZNF454	285676	broad.mit.edu	37	5	178392359	178392359	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178392359C>G	uc003mjo.1	+	5	1225	c.954C>G	c.(952-954)CAC>CAG	p.H318Q	ZNF454_uc010jkz.1_Missense_Mutation_p.H318Q	NM_182594	NP_872400	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	318	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		TTACCAAACACCAGAATATCC	0.393													4	142	---	---	---	---	PASS
HIST1H2BN	8341	broad.mit.edu	37	6	27806476	27806476	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27806476A>C	uc003njv.2	+	1	37	c.37A>C	c.(37-39)AAA>CAA	p.K13Q	HIST1H2AK_uc003njs.2_5'Flank|HIST1H2BN_uc003njt.1_RNA|HIST1H2BN_uc003nju.1_Missense_Mutation_p.K13Q	NM_003520	NP_003511	Q99877	H2B1N_HUMAN	histone cluster 1, H2bn	13					nucleosome assembly	nucleosome|nucleus	DNA binding				0						TGCCCCGAAGAAAGGCTCCAA	0.552													5	201	---	---	---	---	PASS
ABCC10	89845	broad.mit.edu	37	6	43403589	43403589	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43403589G>A	uc003ouy.1	+	5	1924	c.1709G>A	c.(1708-1710)CGG>CAG	p.R570Q	ABCC10_uc003ouz.1_Missense_Mutation_p.R527Q|ABCC10_uc010jyo.1_5'UTR	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10	570						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			TCCTTGGACCGGATCCAGCTT	0.567													5	177	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69348738	69348738	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69348738G>T	uc003pev.3	+	3	619	c.171G>T	c.(169-171)TGG>TGT	p.W57C	BAI3_uc010kak.2_Missense_Mutation_p.W57C	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	57	CUB.|Extracellular (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				ACTGCACTTGGACGCTGGAAA	0.393													5	226	---	---	---	---	PASS
MAP7	9053	broad.mit.edu	37	6	136687009	136687009	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136687009C>A	uc003qgz.2	-	10	1383	c.1137G>T	c.(1135-1137)GAG>GAT	p.E379D	MAP7_uc011edf.1_Missense_Mutation_p.E364D|MAP7_uc011edg.1_Missense_Mutation_p.E409D|MAP7_uc010kgu.2_Missense_Mutation_p.E401D|MAP7_uc011edh.1_Missense_Mutation_p.E364D|MAP7_uc010kgv.2_Missense_Mutation_p.E401D|MAP7_uc010kgs.2_Missense_Mutation_p.E233D|MAP7_uc011edi.1_Missense_Mutation_p.E233D|MAP7_uc010kgq.1_Missense_Mutation_p.E285D|MAP7_uc003qha.1_Missense_Mutation_p.E342D|MAP7_uc010kgr.2_Missense_Mutation_p.E233D	NM_003980	NP_003971	Q14244	MAP7_HUMAN	microtubule-associated protein 7	379	Pro-rich.				establishment or maintenance of cell polarity|microtubule cytoskeleton organization|protein localization in plasma membrane|response to osmotic stress	basolateral plasma membrane|microtubule|microtubule associated complex|nucleus|perinuclear region of cytoplasm	receptor binding|structural molecule activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		TCTTCTCAGGCTCCACTTTGA	0.557													4	207	---	---	---	---	PASS
DLGAP2	9228	broad.mit.edu	37	8	1616640	1616640	+	Silent	SNP	G	A	A	rs4565482	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1616640G>A	uc003wpl.2	+	6	1813	c.1716G>A	c.(1714-1716)CCG>CCA	p.P572P	DLGAP2_uc003wpm.2_Silent_p.P572P	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	651					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GGATGTCCCCGTGGCCCCAGG	0.672													3	3	---	---	---	---	PASS
EFCAB1	79645	broad.mit.edu	37	8	49641698	49641698	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49641698T>C	uc003xqo.2	-	5	639	c.479A>G	c.(478-480)GAC>GGC	p.D160G	EFCAB1_uc003xqn.3_Intron|EFCAB1_uc011ldj.1_Missense_Mutation_p.D108G|EFCAB1_uc010lxx.2_RNA|EFCAB1_uc011ldk.1_RNA	NM_024593	NP_078869	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1 isoform a	160	EF-hand 3.|3 (Potential).						calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				CCCATCATGGTCATGATCCTA	0.408													3	151	---	---	---	---	PASS
IFNA4	3441	broad.mit.edu	37	9	21186896	21186896	+	3'UTR	SNP	A	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21186896A>G	uc003zon.2	-	1						NM_021068	NP_066546	P05014	IFNA4_HUMAN	interferon, alpha 4 precursor						blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|interferon-alpha/beta receptor binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		TTGAAATGGAAGAACTCATGA	0.368													10	223	---	---	---	---	PASS
CREM	1390	broad.mit.edu	37	10	35500241	35500241	+	Intron	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35500241G>A	uc001iyb.2	+						CREM_uc001ixy.2_Intron|CREM_uc001ixz.2_Missense_Mutation_p.R68H|CREM_uc001iya.2_Missense_Mutation_p.R221H|CREM_uc001iyc.2_Intron|CREM_uc001iyd.2_Missense_Mutation_p.R272H|CREM_uc001iye.2_Missense_Mutation_p.R209H|CREM_uc001iyf.2_Intron|CREM_uc001iyg.2_Intron|CREM_uc001iyh.2_Intron|CREM_uc001iyi.2_Intron|CREM_uc001iyj.2_Intron|CREM_uc001iyk.2_Missense_Mutation_p.R151H|CREM_uc001iyl.2_Intron|CREM_uc001iym.2_Missense_Mutation_p.R93H|CREM_uc001iyn.2_Intron|CREM_uc001iyo.2_Missense_Mutation_p.R81H|CREM_uc001iyp.2_Missense_Mutation_p.R75H|CREM_uc001iyq.2_Intron|CREM_uc001iyr.2_Missense_Mutation_p.R85H|CREM_uc001iys.2_Intron|CREM_uc001iyt.2_Missense_Mutation_p.R68H	NM_181571	NP_853549	Q03060	CREM_HUMAN	cAMP responsive element modulator isoform a						cell differentiation|multicellular organismal development|signal transduction|spermatogenesis	nucleus	cAMP response element binding protein binding|protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CTTGAAAATCGTGTGGCTGTG	0.443													33	111	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093368	1093368	+	Silent	SNP	G	A	A	rs111440994		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093368G>A	uc001lsx.1	+	31	12300	c.12273G>A	c.(12271-12273)ACG>ACA	p.T4091T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4091						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccactacggtgaccccaa	0.000													3	6	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093410	1093410	+	Silent	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093410C>A	uc001lsx.1	+	31	12342	c.12315C>A	c.(12313-12315)ACC>ACA	p.T4105T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4105						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	agaccccaaccacgacaccca	0.000													3	12	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093424	1093424	+	Missense_Mutation	SNP	C	G	G	rs111642532		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093424C>G	uc001lsx.1	+	31	12356	c.12329C>G	c.(12328-12330)ACC>AGC	p.T4110S		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4110						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	acacccatcaccaccaccacc	0.000													3	10	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093452	1093452	+	Silent	SNP	G	A	A	rs34136803		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093452G>A	uc001lsx.1	+	31	12384	c.12357G>A	c.(12355-12357)CCG>CCA	p.P4119P		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4119						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccccaaccccgacacccaccg	0.000													4	6	---	---	---	---	PASS
NUP160	23279	broad.mit.edu	37	11	47800613	47800613	+	3'UTR	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47800613C>T	uc001ngm.2	-	36					NUP160_uc009ylw.2_RNA	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7						GTCTTAAGTCCTAAGAGGCAC	0.423													7	83	---	---	---	---	PASS
KRTAP5-9	3846	broad.mit.edu	37	11	71259894	71259894	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71259894C>T	uc001oqs.1	+	1	429	c.191C>T	c.(190-192)TCC>TTC	p.S64F		NM_005553	NP_005544	P26371	KRA59_HUMAN	keratin associated protein 5-9	64	8 X 4 AA repeats of C-C-X-P.				epidermis development	keratin filament					0						GGCTGTGGCTCCTGTGGGGGC	0.632													6	211	---	---	---	---	PASS
ACCN2	41	broad.mit.edu	37	12	50472357	50472357	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50472357C>T	uc001rvw.2	+	6	1220	c.991C>T	c.(991-993)CCA>TCA	p.P331S	ACCN2_uc001rvv.2_Missense_Mutation_p.P331S|ACCN2_uc009zln.2_Missense_Mutation_p.P122S|ACCN2_uc009zlo.2_Missense_Mutation_p.P331S	NM_001095	NP_001086	P78348	ACCN2_HUMAN	amiloride-sensitive cation channel 2, neuronal	331	Extracellular (By similarity).				calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)	GGTGCACATGCCAGGTCAGGC	0.587													5	221	---	---	---	---	PASS
R3HDM2	22864	broad.mit.edu	37	12	57662763	57662763	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57662763C>A	uc009zpm.1	-	15	1810	c.1775G>T	c.(1774-1776)AGC>ATC	p.S592I	R3HDM2_uc010srn.1_RNA|R3HDM2_uc001snu.2_Missense_Mutation_p.S287I|R3HDM2_uc001snr.2_Missense_Mutation_p.S319I|R3HDM2_uc001sns.2_Missense_Mutation_p.S592I|R3HDM2_uc001snt.2_Missense_Mutation_p.S606I|R3HDM2_uc009zpn.1_Intron	NM_014925	NP_055740	Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	592	Gln-rich.					nucleus	nucleic acid binding			ovary(2)	2						GCCCCCCATGCTGCTCCTCTG	0.587													5	255	---	---	---	---	PASS
RBM19	9904	broad.mit.edu	37	12	114260983	114260983	+	Intron	SNP	T	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114260983T>G	uc009zwi.2	-						RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_3'UTR	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19						multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GGAGCGGCTGTCCCGGTCCCC	0.706													4	5	---	---	---	---	PASS
SETD8	387893	broad.mit.edu	37	12	123875311	123875311	+	Silent	SNP	C	T	T	rs74356260		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123875311C>T	uc001uew.2	+	3	309	c.267C>T	c.(265-267)GCC>GCT	p.A89A	SETD8_uc001uex.2_Silent_p.A24A	NM_020382	NP_065115	Q9NQR1	SETD8_HUMAN	SET domain-containing 8	130					cell division|mitosis|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding|transcription corepressor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AACCATTAGCCGGAATCTACA	0.498													4	141	---	---	---	---	PASS
PABPC3	5042	broad.mit.edu	37	13	25672249	25672249	+	3'UTR	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25672249C>T	uc001upy.2	+	1						NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3						mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		TCAGAGACCACGAAAAGAAAT	0.358													19	234	---	---	---	---	PASS
TTC5	91875	broad.mit.edu	37	14	20764585	20764585	+	Silent	SNP	A	C	C	rs1953552	byFrequency	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20764585A>C	uc001vwt.2	-	6	717	c.660T>G	c.(658-660)GCT>GCG	p.A220A	TTC5_uc001vwu.2_Silent_p.A77A	NM_138376	NP_612385	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	220	TPR 3.				DNA repair	cytoplasm|nucleus	binding			ovary(1)	1	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		GATTGCTAGAAGCTTTTCTGT	0.438													6	454	---	---	---	---	PASS
METTL3	56339	broad.mit.edu	37	14	21969230	21969230	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21969230C>G	uc001wbc.2	-	5	1033	c.941G>C	c.(940-942)TGC>TCC	p.C314S	METTL3_uc001wbb.2_Missense_Mutation_p.C159S|METTL3_uc010tlw.1_RNA	NM_019852	NP_062826	Q86U44	MTA70_HUMAN	methyltransferase like 3	314					gene expression	nuclear speck	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity|RNA binding			pancreas(1)|skin(1)	2	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		AAGGAAAGAGCAGTCACCTAA	0.413													3	137	---	---	---	---	PASS
JUB	84962	broad.mit.edu	37	14	23451411	23451411	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23451411G>A	uc001whz.2	-	1	441	c.65C>T	c.(64-66)TCT>TTT	p.S22F		NM_032876	NP_116265	Q96IF1	JUB_HUMAN	ajuba isoform 1	22	PreLIM.				cell cycle|gene silencing by miRNA|positive regulation of protein complex assembly	cell-cell junction|cytoplasmic mRNA processing body|microtubule organizing center	alpha-catenin binding|zinc ion binding				0	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.0122)		AGACCGGCTAGATTCACCCTT	0.692													8	59	---	---	---	---	PASS
ASB2	51676	broad.mit.edu	37	14	94401108	94401108	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94401108C>T	uc001ycc.1	-	8	2147	c.1658G>A	c.(1657-1659)CGA>CAA	p.R553Q	ASB2_uc001ycb.1_Missense_Mutation_p.R247Q|ASB2_uc001ycd.2_Missense_Mutation_p.R601Q	NM_016150	NP_057234	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box-containing protein	553	SOCS box.				intracellular signal transduction					ovary(1)|pancreas(1)	2		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		AACCCGCAGTCGGCAAAGGTG	0.488													46	109	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106206469	106206469	+	Intron	SNP	C	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106206469C>G	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Silent_p.T215T|uc001ysf.2_Silent_p.T215T					Parts of antibodies, mostly variable regions.												0						TGGTGATGGTCGTCCACAGCC	0.617													4	17	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106234188	106234188	+	Intron	SNP	A	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106234188A>G	uc010tyt.1	-						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						CACACGCTTAACAGGAAGAGT	0.592													6	10	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	25486926	25486926	+	Intron	SNP	G	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25486926G>T	uc001zae.2	+						SNORD115-39_uc001zah.1_RNA|SNORD115-40_uc001zai.1_5'Flank					Homo sapiens clone Rt-16 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																		TTGTCCTGAAGAGAGGTGATG	0.478													11	536	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28483865	28483865	+	Missense_Mutation	SNP	G	A	A	rs147946655	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28483865G>A	uc001zbj.2	-	24	3737	c.3631C>T	c.(3631-3633)CGC>TGC	p.R1211C		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1211	Cytochrome b5 heme-binding.				DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TCAGCTTTGCGTATAAGTGTC	0.388													11	161	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51758466	51758466	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51758466C>A	uc002abf.2	-	30	7657	c.7432G>T	c.(7432-7434)GAT>TAT	p.D2478Y	DMXL2_uc002abd.2_Missense_Mutation_p.D549Y|DMXL2_uc010ufy.1_Missense_Mutation_p.D2479Y|DMXL2_uc010bfa.2_Missense_Mutation_p.D1842Y	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2478						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		ATGCTTTCATCAGAATCATAT	0.264													4	234	---	---	---	---	PASS
ADAM10	102	broad.mit.edu	37	15	58902623	58902623	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58902623T>C	uc002afd.1	-	14	2342	c.1898A>G	c.(1897-1899)AAC>AGC	p.N633S	ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Missense_Mutation_p.N332S|ADAM10_uc002afe.1_Intron|ADAM10_uc002aff.1_Missense_Mutation_p.N170S	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor	633	Extracellular (Potential).|Cys-rich.				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		TCTAAAATCGTTGCAAGGGGA	0.478													5	161	---	---	---	---	PASS
KIAA1199	57214	broad.mit.edu	37	15	81234649	81234649	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81234649C>T	uc002bfw.1	+	26	3930	c.3670C>T	c.(3670-3672)CAC>TAC	p.H1224Y	KIAA1199_uc010unn.1_Missense_Mutation_p.H1224Y	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	1224										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						GCACTTCTTCCACCTCTGGAA	0.478													47	173	---	---	---	---	PASS
C15orf51	196968	broad.mit.edu	37	15	100340097	100340097	+	RNA	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100340097C>T	uc010urx.1	-	4		c.830G>A			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|uc002bvt.1_5'Flank	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						TGTCCCTACGCGAGTGCAGGT	0.592													5	43	---	---	---	---	PASS
WDR59	79726	broad.mit.edu	37	16	74922129	74922129	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74922129G>T	uc002fdh.1	-	22	2386	c.2284C>A	c.(2284-2286)CCA>ACA	p.P762T	WDR59_uc002fdf.1_Missense_Mutation_p.P207T|WDR59_uc002fdg.1_Missense_Mutation_p.P354T	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	762										ovary(1)|breast(1)	2						AAGGGGTTTGGTAGCCCCTGA	0.483													5	84	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11790187	11790187	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11790187G>A	uc002gne.2	+	57	11085	c.11017G>A	c.(11017-11019)GAG>AAG	p.E3673K	DNAH9_uc010coo.2_Missense_Mutation_p.E2967K|DNAH9_uc002gnf.2_5'UTR|DNAH9_uc010vvh.1_Missense_Mutation_p.E26K	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3673	Potential.				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CGAGGCCCGAGAGCACTACCG	0.527													7	180	---	---	---	---	PASS
LLGL1	3996	broad.mit.edu	37	17	18137336	18137336	+	Silent	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18137336C>T	uc002gsp.2	+	6	622	c.561C>T	c.(559-561)GAC>GAT	p.D187D		NM_004140	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1	187					cortical actin cytoskeleton organization|exocytosis|protein complex assembly	cortical actin cytoskeleton	protein kinase binding|structural molecule activity			breast(2)|skin(2)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)	6	all_neural(463;0.228)					GCGTGCCAGACGACTACCGCT	0.652													5	32	---	---	---	---	PASS
LRRC37A3	374819	broad.mit.edu	37	17	62856432	62856432	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62856432C>T	uc002jey.2	-	11	4363	c.3832G>A	c.(3832-3834)GCT>ACT	p.A1278T	LRRC37A3_uc010wqg.1_Missense_Mutation_p.A396T|LRRC37A3_uc002jex.1_Missense_Mutation_p.A255T|LRRC37A3_uc010wqf.1_Missense_Mutation_p.A316T|LRRC37A3_uc010dek.1_Missense_Mutation_p.A284T	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1278	Extracellular (Potential).					integral to membrane					0						ATGGAAATAGCGTGGGTTAAG	0.453													15	300	---	---	---	---	PASS
HGS	9146	broad.mit.edu	37	17	79668552	79668552	+	Silent	SNP	C	T	T	rs34897798	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79668552C>T	uc002kbg.2	+	22	2315	c.2238C>T	c.(2236-2238)GGC>GGT	p.G746G	MRPL12_uc002kbh.1_5'Flank|SLC25A10_uc010wut.1_5'Flank	NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	746	Interaction with NF2.|Gln-rich.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CACCCTCTGGCGGTCCCCCCC	0.682													4	5	---	---	---	---	PASS
KIAA0355	9710	broad.mit.edu	37	19	34818760	34818760	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34818760G>A	uc002nvd.3	+	5	1790	c.931G>A	c.(931-933)GCA>ACA	p.A311T		NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710	311										ovary(1)	1	Esophageal squamous(110;0.162)					GGCGATTGAAGCAAGTTTGCA	0.453													28	183	---	---	---	---	PASS
ZNF420	147923	broad.mit.edu	37	19	37618589	37618589	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37618589T>A	uc002ofl.2	+	5	911	c.696T>A	c.(694-696)TTT>TTA	p.F232L		NM_144689	NP_653290	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	232	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGAAAGCCTTTATTCGTAGCT	0.368													11	203	---	---	---	---	PASS
HNRNPUL1	11100	broad.mit.edu	37	19	41807592	41807592	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41807592C>T	uc002oqb.3	+	11	1959	c.1670C>T	c.(1669-1671)GCG>GTG	p.A557V	CYP2F1_uc010xvw.1_Intron|HNRNPUL1_uc002opz.3_Missense_Mutation_p.A457V|HNRNPUL1_uc002oqa.3_Missense_Mutation_p.A457V|HNRNPUL1_uc010ehm.2_Missense_Mutation_p.A557V|HNRNPUL1_uc002oqc.3_Missense_Mutation_p.A443V|HNRNPUL1_uc002oqe.3_Intron|HNRNPUL1_uc002oqd.3_Missense_Mutation_p.A457V|HNRNPUL1_uc010ehn.2_Missense_Mutation_p.A457V|HNRNPUL1_uc010eho.2_Missense_Mutation_p.A457V|HNRNPUL1_uc010xvy.1_Missense_Mutation_p.A457V|HNRNPUL1_uc010ehp.2_Missense_Mutation_p.A413V|HNRNPUL1_uc002oqf.3_5'Flank	NM_007040	NP_008971	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	557	Necessary for interaction with TP53.|Necessary for interaction with BRD7 and transcriptional activation.				nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	enzyme binding|RNA binding			central_nervous_system(1)|skin(1)	2						CCAGATCATGCGGTCTTAGAA	0.483													4	150	---	---	---	---	PASS
SHANK1	50944	broad.mit.edu	37	19	51219979	51219979	+	Silent	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51219979G>A	uc002psx.1	-	1	217	c.198C>T	c.(196-198)GAC>GAT	p.D66D		NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	66					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		AGTGGGCGTCGTCTGGGACGG	0.672													4	141	---	---	---	---	PASS
ZNF600	162966	broad.mit.edu	37	19	53270592	53270592	+	Nonsense_Mutation	SNP	A	C	C			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53270592A>C	uc002qab.3	-	3	703	c.417T>G	c.(415-417)TAT>TAG	p.Y139*		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	139					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		AATTATTCCCATAGTTATTAG	0.373													5	390	---	---	---	---	PASS
MCM8	84515	broad.mit.edu	37	20	5965622	5965622	+	Silent	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5965622G>A	uc002wmi.2	+	15	2306	c.1929G>A	c.(1927-1929)GAG>GAA	p.E643E	MCM8_uc002wmj.2_Silent_p.E627E|MCM8_uc002wmk.2_Silent_p.E683E|MCM8_uc002wml.2_Silent_p.E643E|MCM8_uc010gbp.2_Silent_p.E596E|MCM8_uc002wmm.2_Silent_p.E181E	NM_032485	NP_115874	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	643					cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1						TAGTTTCTGAGAAGCCATTAT	0.378													10	94	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16338592	16338592	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16338592G>T	uc002yjx.2	-	4	2520	c.1922C>A	c.(1921-1923)TCA>TAA	p.S641*		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	641	Repression domain 2.				androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TGACATGGATGACTGCATTCC	0.438													8	316	---	---	---	---	PASS
ADAMTS1	9510	broad.mit.edu	37	21	28211980	28211980	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28211980C>T	uc002ymf.2	-	7	2409	c.1954G>A	c.(1954-1956)GTC>ATC	p.V652I		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	652	Cys-rich.				integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)		TTTGGTGAGACGCCAGCGTAC	0.468													20	299	---	---	---	---	PASS
TBC1D10A	83874	broad.mit.edu	37	22	30688748	30688748	+	Silent	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30688748G>A	uc011akt.1	-	11	1167	c.1143C>T	c.(1141-1143)TGC>TGT	p.C381C	GATSL3_uc003ahf.2_Intron|GATSL3_uc003ahg.2_Intron|GATSL3_uc003ahh.2_Intron|GATSL3_uc010gvq.2_Intron|GATSL3_uc003ahi.2_Intron|TBC1D10A_uc003ahj.3_Silent_p.C293C|TBC1D10A_uc010gvu.2_Silent_p.C388C|TBC1D10A_uc003ahk.3_Silent_p.C381C	NM_031937	NP_114143	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	381						intracellular|microvillus	guanyl-nucleotide exchange factor activity|PDZ domain binding|Rab GTPase activator activity			ovary(1)	1						GCGGGGAGCGGCACTGCAGCT	0.657													4	55	---	---	---	---	PASS
SYN3	8224	broad.mit.edu	37	22	33260926	33260926	+	Silent	SNP	T	C	C			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33260926T>C	uc003amx.2	-	5	846	c.687A>G	c.(685-687)ACA>ACG	p.T229T	SYN3_uc003amy.2_Silent_p.T229T|SYN3_uc003amz.2_Silent_p.T228T	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa	229	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						TGGGGAAAAATGTTTGCTCCA	0.438													15	371	---	---	---	---	PASS
PLXNB2	23654	broad.mit.edu	37	22	50720835	50720835	+	Intron	SNP	A	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50720835A>T	uc003bkv.3	-						PLXNB2_uc003bkt.1_5'Flank|PLXNB2_uc003bku.1_5'UTR	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor						regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCCTGACCACACGGGGCTTCC	0.721													7	17	---	---	---	---	PASS
ZMYM3	9203	broad.mit.edu	37	X	70472907	70472907	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70472907C>A	uc004dzh.1	-	2	286	c.199G>T	c.(199-201)GAA>TAA	p.E67*	BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Nonsense_Mutation_p.E67*|ZMYM3_uc004dzj.1_Nonsense_Mutation_p.E67*|ZMYM3_uc011mpu.1_5'Flank|ZMYM3_uc004dzk.3_Nonsense_Mutation_p.E67*|ZMYM3_uc004dzl.3_Nonsense_Mutation_p.E67*|ZMYM3_uc004dzm.3_Nonsense_Mutation_p.E67*	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	67					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)					GGGTCTTTTTCCAGGCCAGCA	0.642													3	30	---	---	---	---	PASS
POF1B	79983	broad.mit.edu	37	X	84561266	84561266	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84561266G>T	uc004eer.2	-	12	1384	c.1238C>A	c.(1237-1239)TCA>TAA	p.S413*	POF1B_uc004ees.2_Nonsense_Mutation_p.S413*	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	413	Potential.						actin binding				0						TTCCATGTCTGATAGTGTATG	0.343													50	155	---	---	---	---	PASS
GABRQ	55879	broad.mit.edu	37	X	151821286	151821286	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151821286G>A	uc004ffp.1	+	9	1461	c.1441G>A	c.(1441-1443)GAA>AAA	p.E481K		NM_018558	NP_061028	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) receptor, theta	481						cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|neurotransmitter transporter activity			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TTTTCCTACCGAAATCCGCAA	0.547													4	161	---	---	---	---	PASS
MAGEA6	4105	broad.mit.edu	37	X	151869832	151869832	+	Silent	SNP	C	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151869832C>T	uc004ffq.1	+	3	716	c.522C>T	c.(520-522)CAC>CAT	p.H174H	MAGEA6_uc004ffr.1_Silent_p.H174H|MAGEA2_uc010nto.2_Intron	NM_005363	NP_005354	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	174	MAGE.						protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)					CCATCGGCCACGTGTACATCT	0.532													13	143	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	4274160	4274163	+	IGR	DEL	CTTT	-	-	rs11801817		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4274160_4274163delCTTT								LOC100133612 (440283 upstream) : LOC284661 (197948 downstream)																							tccttccttcctttcttccttcct	0.078													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31128558	31128559	+	IGR	INS	-	TGG	TGG	rs150361136	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31128558_31128559insTGG								None (None upstream) : MATN1 (55567 downstream)																							ggtggtggtgatggtggtgatg	0.069													6	3	---	---	---	---	
AK2	204	broad.mit.edu	37	1	33486746	33486747	+	Intron	INS	-	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33486746_33486747insA	uc001bwp.1	-						uc001bwn.2_Intron|AK2_uc001bwo.1_Intron|AK2_uc010ohq.1_Intron|AK2_uc009vud.1_Intron|AK2_uc010ohr.1_Intron|AK2_uc001bwq.1_Intron	NM_001625	NP_001616	P54819	KAD2_HUMAN	adenylate kinase 2 isoform a						nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				gactcccatctaaaaaaaaaaa	0.064													4	2	---	---	---	---	
DNTTIP2	30836	broad.mit.edu	37	1	94341489	94341490	+	Intron	INS	-	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94341489_94341490insA	uc001dqf.2	-						DNTTIP2_uc010otm.1_Intron	NM_014597	NP_055412	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal,						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		AGGAATTCCTGAAAAAAAACTC	0.158													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199130136	199130137	+	IGR	INS	-	G	G	rs142603788	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199130136_199130137insG								MIR181A1 (301854 upstream) : NR5A2 (866633 downstream)																							gaaggaaggaagaaggaaggaa	0.149													3	4	---	---	---	---	
ADI1	55256	broad.mit.edu	37	2	3504893	3504894	+	Intron	INS	-	A	A	rs144556875	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3504893_3504894insA	uc002qxp.3	-						ADI1_uc010yiq.1_Intron	NM_018269	NP_060739	Q9BV57	MTND_HUMAN	acireductone dioxygenase 1						L-methionine salvage from methylthioadenosine	cytoplasm|nucleus|plasma membrane	acireductone dioxygenase (Ni2+-requiring) activity|metal ion binding|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		CCATAAAAATGAAACTACACTT	0.455													4	3	---	---	---	---	
ZNF512	84450	broad.mit.edu	37	2	27824511	27824512	+	Intron	INS	-	TTTTG	TTTTG	rs143396334	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27824511_27824512insTTTTG	uc002rla.2	+						ZNF512_uc010ylv.1_Intron|ZNF512_uc010ylw.1_Intron|ZNF512_uc002rlb.2_Intron|ZNF512_uc010ylx.1_Intron|ZNF512_uc002rlc.2_Intron|ZNF512_uc010yly.1_Intron|ZNF512_uc010ylz.1_Intron	NM_032434	NP_115810	Q96ME7	ZN512_HUMAN	zinc finger protein 512						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					tggctaattttttttgttttgt	0.000													4	2	---	---	---	---	
MTIF2	4528	broad.mit.edu	37	2	55464785	55464786	+	Intron	INS	-	T	T	rs72103107		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55464785_55464786insT	uc002ryn.2	-						MTIF2_uc010yox.1_Intron|MTIF2_uc002ryo.2_Intron	NM_001005369	NP_001005369	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2						regulation of translational initiation	mitochondrion	GTP binding|GTPase activity|ribosomal small subunit binding|translation initiation factor activity			ovary(1)	1						ttctttttttcttttttttttt	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107176067	107176067	+	IGR	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107176067delT								RGPD3 (91266 upstream) : ST6GAL2 (241991 downstream)																							cttccatttctttttttttcc	0.100													4	2	---	---	---	---	
TMEM87B	84910	broad.mit.edu	37	2	112834615	112834616	+	Intron	INS	-	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112834615_112834616insA	uc002thm.2	+						TMEM87B_uc010fkg.2_Intron|TMEM87B_uc010fkh.2_Intron	NM_032824	NP_116213	Q96K49	TM87B_HUMAN	transmembrane protein 87B precursor							integral to membrane					0						acccccatctcaaaaaaaaaaa	0.089													4	3	---	---	---	---	
RGPD5	84220	broad.mit.edu	37	2	113127926	113127926	+	Intron	DEL	G	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113127926delG	uc002ths.1	-						RGPD8_uc010fkk.1_Intron	NM_005054	NP_005045	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5 isoform						intracellular transport	cytoplasm	binding				0						CTTTTTTGGTGGGGGGGGGGG	0.189													9	4	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223512162	223512163	+	Intron	INS	-	A	A	rs147059558	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223512162_223512163insA	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron|FARSB_uc002vng.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	GACCAGCTTTCAGTTTTACTGA	0.450													8	4	---	---	---	---	
MTMR14	64419	broad.mit.edu	37	3	9739752	9739753	+	Intron	INS	-	C	C			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9739752_9739753insC	uc003brz.2	+						MTMR14_uc003bsa.2_Intron|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993	Q8NCE2	MTMRE_HUMAN	jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)					TGTTCACTCTGCAGCCTCTAAA	0.540													4	2	---	---	---	---	
SACM1L	22908	broad.mit.edu	37	3	45755733	45755733	+	Intron	DEL	G	-	-	rs79483400		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45755733delG	uc003cos.2	+						SACM1L_uc011bag.1_Intron|SACM1L_uc011bah.1_Intron	NM_014016	NP_054735	Q9NTJ5	SAC1_HUMAN	suppressor of actin 1							Golgi apparatus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		TATTTTGTTTGTTTTTTTTTT	0.299													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12637717	12637717	+	IGR	DEL	T	-	-	rs142332040		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12637717delT								None (None upstream) : HSP90AB2P (697320 downstream)																							ATAGGCTAGCTTTTTTTTTTT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14562532	14562533	+	Intron	INS	-	GAAG	GAAG	rs28546830		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14562532_14562533insGAAG	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																		gagggagggaagaaggaaggaa	0.158													2	4	---	---	---	---	
RASL11B	65997	broad.mit.edu	37	4	53730662	53730662	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53730662delC	uc003gzt.2	+	3	397	c.217delC	c.(217-219)CAAfs	p.Q73fs		NM_023940	NP_076429	Q9BPW5	RSLBB_HUMAN	RAS-like family 11 member B	73	Small GTPase-like.				small GTPase mediated signal transduction	membrane	GTP binding|GTPase activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0302)			CTATACTAGACAAGTTCAGAT	0.378													785	7	---	---	---	---	
UTP3	57050	broad.mit.edu	37	4	71554620	71554622	+	In_Frame_Del	DEL	GAG	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71554620_71554622delGAG	uc003hfo.2	+	1	425_427	c.226_228delGAG	c.(226-228)GAGdel	p.E81del		NM_020368	NP_065101	Q9NQZ2	SAS10_HUMAN	UTP3, small subunit processome component	81	Glu-rich.				brain development|chromatin modification|gene silencing	nucleolus					0			Lung(101;0.235)			ggaggatggcgaggaggaggagg	0.291													67	7	---	---	---	---	
ADH1C	126	broad.mit.edu	37	4	100265826	100265827	+	Intron	INS	-	AACTC	AACTC	rs138852664	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100265826_100265827insAACTC	uc003huu.2	-							NM_000669	NP_000660	P00326	ADH1G_HUMAN	class I alcohol dehydrogenase, gamma subunit						ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)	TACATTTTCTTAACAAGTTTTT	0.297									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185832046	185832046	+	IGR	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185832046delT								ACSL1 (84831 upstream) : HELT (107949 downstream)																							GCTCTACATCTTTCCTGGAAA	0.303													4	2	---	---	---	---	
SLC9A3	6550	broad.mit.edu	37	5	474946	474946	+	Intron	DEL	G	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:474946delG	uc003jbe.2	-						SLC9A3_uc011clx.1_Intron|LOC25845_uc003jbd.2_5'Flank|LOC25845_uc010itb.1_5'Flank	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen							cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			gagacctggagggagaggAGC	0.348													4	3	---	---	---	---	
RNASEN	29102	broad.mit.edu	37	5	31405874	31405874	+	Intron	DEL	C	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31405874delC	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						TTTCAAGAttctttttttttt	0.303													9	4	---	---	---	---	
CENPK	64105	broad.mit.edu	37	5	64838464	64838465	+	Intron	INS	-	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64838464_64838465insA	uc003jts.2	-						CENPK_uc003jtt.2_Intron|CENPK_uc003jtu.2_Intron	NM_022145	NP_071428	Q9BS16	CENPK_HUMAN	SoxLZ/Sox6 leucine zipper binding protein						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)		actccgtttccaaaaaaaaaaa	0.104													4	2	---	---	---	---	
ZFYVE16	9765	broad.mit.edu	37	5	79746634	79746635	+	Intron	DEL	TT	-	-	rs72398531		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79746634_79746635delTT	uc003kgr.3	+						ZFYVE16_uc003kgp.2_Intron|ZFYVE16_uc003kgq.3_Intron|ZFYVE16_uc003kgs.3_Intron|ZFYVE16_uc003kgt.3_Intron	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16						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)		CTTATATCCAtttttttttttt	0.119													6	3	---	---	---	---	
PPP2R2B	5521	broad.mit.edu	37	5	145969962	145969962	+	Intron	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145969962delT	uc003loe.2	-						PPP2R2B_uc010jgm.2_Intron|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			tttttttgtgttttttttttt	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174170410	174170413	+	IGR	DEL	CCTT	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174170410_174170413delCCTT								MSX2 (12509 upstream) : DRD1 (697263 downstream)																							ccttccttccccttccttccttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	834408	834411	+	IGR	DEL	CCTA	-	-	rs72349013		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:834408_834411delCCTA								EXOC2 (141299 upstream) : LOC285768 (126831 downstream)																							ttccttccttcctaccttccttcc	0.123													4	2	---	---	---	---	
MTO1	25821	broad.mit.edu	37	6	74175898	74175898	+	Intron	DEL	A	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74175898delA	uc003pgy.3	+						MTO1_uc010kav.2_Intron|MTO1_uc003pgz.3_Intron|MTO1_uc003pha.3_Intron|MTO1_uc003phb.3_Intron|MTO1_uc003phc.1_Intron	NM_133645	NP_598400	Q9Y2Z2	MTO1_HUMAN	mitochondrial translation optimization 1 homolog						tRNA processing	mitochondrion	flavin adenine dinucleotide binding			ovary(3)|skin(2)|pancreas(1)	6						CAAGGTGCTCATATATTTATT	0.323													218	12	---	---	---	---	
ECHDC1	55862	broad.mit.edu	37	6	127652297	127652297	+	Intron	DEL	T	-	-	rs66884305		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127652297delT	uc003qax.2	-						ECHDC1_uc003qaz.3_Intron|ECHDC1_uc010key.2_Intron|ECHDC1_uc003qay.3_Intron|ECHDC1_uc010kez.2_Intron|ECHDC1_uc010kex.2_5'Flank	NM_001139510	NP_001132982	Q9NTX5	ECHD1_HUMAN	enoyl Coenzyme A hydratase domain containing 1								catalytic activity				0				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)		TCCCCAtttcttttttttttt	0.189													13	9	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	148112872	148112873	+	3'UTR	INS	-	A	A	rs145619519		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148112872_148112873insA	uc003weu.1	+	24					CNTNAP2_uc003wev.1_3'UTR	NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			AGACTGATCACAAAAAAAAAAA	0.332										HNSCC(39;0.1)			5	3	---	---	---	---	
SLC7A2	6542	broad.mit.edu	37	8	17412801	17412801	+	Intron	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17412801delT	uc011kyc.1	+						SLC7A2_uc011kyd.1_Intron|SLC7A2_uc011kye.1_Intron|SLC7A2_uc011kyf.1_Intron	NM_001008539	NP_001008539	P52569	CTR2_HUMAN	solute carrier family 7, member 2 isoform 2						cellular amino acid metabolic process|ion transport	cytoplasm|integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity			ovary(2)|skin(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	CCCTTTGGGATTTTTTTTTTA	0.294													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142723811	142723813	+	IGR	DEL	TGA	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142723811_142723813delTGA								FLJ43860 (206481 upstream) : MIR1302-7 (143790 downstream)																							gtggtggtggtgatggtggtgat	0.020													4	2	---	---	---	---	
C9orf72	203228	broad.mit.edu	37	9	27558227	27558227	+	Intron	DEL	A	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27558227delA	uc003zqq.2	-							NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a											ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		AGCATGTGTTAAAAAAAAAAA	0.299													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66960593	66960597	+	IGR	DEL	CCACC	-	-	rs143953537		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66960593_66960597delCCACC								LOC442421 (457566 upstream) : AQP7P1 (293670 downstream)																							ATACAGGTTTCCACCCCCCCCCCAC	0.405													4	3	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72659303	72659308	+	Intron	DEL	GGGGTG	-	-	rs10559392		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72659303_72659308delGGGGTG	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						GGCCAAGCCTggggtgggggtggggg	0.631													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42596908	42596910	+	IGR	DEL	TCA	-	-	rs74210869		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42596908_42596910delTCA								None (None upstream) : LOC441666 (230405 downstream)																							ggaatcatcttcaaatggaaagg	0.000													208	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42600053	42600053	+	IGR	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42600053delT								None (None upstream) : LOC441666 (227262 downstream)																							ttgaacggaattgaatggaat	0.000													108	7	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95095461	95095462	+	Intron	INS	-	TTTCC	TTTCC	rs148769270	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95095461_95095462insTTTCC	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						CCCCTCCCCCTTTTCCTTTCTG	0.574													11	8	---	---	---	---	
ABCC8	6833	broad.mit.edu	37	11	17453720	17453720	+	Intron	DEL	C	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17453720delC	uc001mnc.2	-						ABCC8_uc010rcy.1_Intron	NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	CTCCACCCTACCCCCAAGAGA	0.557													4	2	---	---	---	---	
PACS1	55690	broad.mit.edu	37	11	66000448	66000449	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66000448_66000449insA	uc001oha.1	+	15	1883_1884	c.1749_1750insA	c.(1747-1752)CTCCAGfs	p.L583fs	PACS1_uc010rou.1_Frame_Shift_Ins_p.L119fs	NM_018026	NP_060496	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	583_584					interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6						CTGAGCTGCTCCAGGACCAGCG	0.624													423	35	---	---	---	---	
XRRA1	143570	broad.mit.edu	37	11	74631052	74631052	+	Intron	DEL	A	-	-	rs112064551		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74631052delA	uc009yub.2	-						XRRA1_uc001ovm.2_Intron|XRRA1_uc001ovo.2_Intron|XRRA1_uc001ovq.3_Intron|XRRA1_uc001ovp.3_Intron|XRRA1_uc001ovr.2_Intron	NM_182969	NP_892014	Q6P2D8	XRRA1_HUMAN	X-ray radiation resistance associated 1						response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1						ATAAAACTGCAAAAAAAAAAA	0.333													4	2	---	---	---	---	
SLC39A5	283375	broad.mit.edu	37	12	56629508	56629510	+	Intron	DEL	CTT	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56629508_56629510delCTT	uc010sqj.1	+						SLC39A5_uc010sqi.1_In_Frame_Del_p.F215del|SLC39A5_uc010sqk.1_Intron	NM_173596	NP_775867	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (metal ion						zinc ion transport	basolateral plasma membrane|integral to membrane	metal ion transmembrane transporter activity			ovary(1)|skin(1)	2						TTTTCTCCTCCTTCTGCTGAGAC	0.399													359	9	---	---	---	---	
YEATS4	8089	broad.mit.edu	37	12	69759837	69759837	+	Intron	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69759837delT	uc001sux.2	+							NM_006530	NP_006521	O95619	YETS4_HUMAN	glioma-amplified sequence-41						histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			TTCAAAATCCTTTTTTTTTTC	0.284													4	2	---	---	---	---	
RNF10	9921	broad.mit.edu	37	12	121011389	121011389	+	Intron	DEL	A	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121011389delA	uc001typ.3	+						RNF10_uc010szk.1_Intron|RNF10_uc001tyq.3_Intron	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10						negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					gtcatttatcaaaaaaaaaaa	0.025													4	2	---	---	---	---	
SLC7A7	9056	broad.mit.edu	37	14	23244438	23244442	+	Intron	DEL	CTTAT	-	-	rs71421155		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23244438_23244442delCTTAT	uc001wgr.3	-						SLC7A7_uc001wgs.3_Intron|SLC7A7_uc001wgt.3_Intron|SLC7A7_uc001wgu.3_Intron|SLC7A7_uc001wgv.3_Intron	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		TACTTTTTGCCTTATCTTAGAGCAG	0.429													2	4	---	---	---	---	
FAM177A1	283635	broad.mit.edu	37	14	35546674	35546674	+	Intron	DEL	C	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35546674delC	uc001wsp.2	+						FAM177A1_uc001wsq.2_Intron	NM_001079519	NP_001072987	Q8N128	F177A_HUMAN	hypothetical protein LOC283635 isoform 2												0						TTTTCAAGttctttttttttt	0.129													4	2	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	47669738	47669738	+	Intron	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47669738delT	uc001wwj.3	-						MDGA2_uc001wwi.3_Intron|MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						ttttcttttcttttttttttt	0.274													6	3	---	---	---	---	
RTL1	388015	broad.mit.edu	37	14	101350670	101350671	+	In_Frame_Ins	INS	-	TCT	TCT	rs138109406	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101350670_101350671insTCT	uc010txj.1	-	1	514_515	c.455_456insAGA	c.(454-456)GAG>GAAGAG	p.152_152E>EE	MIR432_hsa-mir-432|MI0003133_5'Flank|uc010txk.1_5'Flank|MIR136_hsa-mir-136|MI0000475_5'Flank	NM_001134888	NP_001128360	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	152										pancreas(1)	1						TCTGGTTTTGCTCTTGAGGAGT	0.520													8	6	---	---	---	---	
HERC2	8924	broad.mit.edu	37	15	28517836	28517837	+	Intron	INS	-	G	G			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28517836_28517837insG	uc001zbj.2	-						HERC2_uc001zbl.1_Intron	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		AGAAAAAAAAAAAGAACAGTTC	0.361													5	3	---	---	---	---	
CAPN3	825	broad.mit.edu	37	15	42677730	42677731	+	Intron	DEL	AG	-	-	rs79988905	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42677730_42677731delAG	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		ATACACACACagagagagagag	0.347											OREG0023085	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	5	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14700252	14700252	+	Intron	DEL	G	-	-	rs62037478		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14700252delG	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						aagaccctgagggaaaaaaaa	0.139													3	3	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74394379	74394380	+	Intron	INS	-	A	A	rs142790741	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74394379_74394380insA	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						TAGTCATCCTTAAACAAAATTC	0.327													8	5	---	---	---	---	
PFAS	5198	broad.mit.edu	37	17	8171691	8171691	+	Intron	DEL	A	-	-	rs76845148		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8171691delA	uc002gkr.2	+						PFAS_uc010vuv.1_Intron|PFAS_uc002gks.2_Intron	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase						'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	attccatctcaaaaaaaaaaa	0.065													6	3	---	---	---	---	
CLTC	1213	broad.mit.edu	37	17	57762167	57762168	+	Intron	INS	-	AA	AA	rs137920746	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57762167_57762168insAA	uc002ixq.1	+						CLTC_uc002ixp.2_Intron|CLTC_uc002ixr.1_Intron	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					gactccatctcaaaaaaaaaga	0.144			T	ALK|TFE3	ALCL|renal 								4	2	---	---	---	---	
RECQL5	9400	broad.mit.edu	37	17	73626922	73626923	+	Intron	INS	-	T	T	rs56158987		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73626922_73626923insT	uc010dgl.2	-						RECQL5_uc010dgk.2_Intron|RECQL5_uc002jot.3_5'Flank|LOC643008_uc002jow.2_5'Flank	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1						DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			TCTCATCTGTGGGGGGGGGGGG	0.649								Other_identified_genes_with_known_or_suspected_DNA_repair_function					7	5	---	---	---	---	
C19orf59	199675	broad.mit.edu	37	19	7744076	7744077	+	3'UTR	DEL	CC	-	-	rs112807024		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7744076_7744077delCC	uc002mhh.1	+	7					TRAPPC5_uc002mhi.1_5'Flank|TRAPPC5_uc002mhj.1_5'Flank|TRAPPC5_uc002mhk.1_5'Flank	NM_174918	NP_777578	Q8IX19	MCEM1_HUMAN	mast cell-expressed membrane protein 1							integral to membrane				skin(1)	1						CGGGAAATGACCCCCCCCCCCC	0.520											OREG0025208	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21749584	21749585	+	IGR	INS	-	A	A	rs140005343	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21749584_21749585insA								ZNF429 (10516 upstream) : ZNF100 (157259 downstream)																							CGATGACCAAGAAAAAACTAAA	0.446													5	3	---	---	---	---	
ZNF235	9310	broad.mit.edu	37	19	44807360	44807361	+	Intron	DEL	AT	-	-	rs147186620		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44807360_44807361delAT	uc002oza.3	-						ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF235_uc002ozb.3_Intron|ZNF235_uc010xwx.1_Intron	NM_004234	NP_004225	Q14590	ZN235_HUMAN	zinc finger protein 93 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)				AAATTAACAGATATATATATAT	0.158													5	5	---	---	---	---	
C20orf7	79133	broad.mit.edu	37	20	13769224	13769224	+	Intron	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13769224delT	uc002wom.2	+						C20orf7_uc002wol.1_Intron|C20orf7_uc002won.2_Intron|C20orf7_uc002woo.2_Intron	NM_024120	NP_077025	Q5TEU4	CT007_HUMAN	hypothetical protein LOC79133 isoform 1						mitochondrial respiratory chain complex I assembly	extrinsic to mitochondrial inner membrane	methyltransferase activity				0		Myeloproliferative disorder(85;0.00878)				CCTCTGTGTCTTTTTTTTTAG	0.313													216	7	---	---	---	---	
TPX2	22974	broad.mit.edu	37	20	30382558	30382559	+	Intron	INS	-	GTGT	GTGT	rs10638647		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30382558_30382559insGTGT	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			tctgtcgcatagtgtgtgtgtg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	41899705	41899706	+	IGR	INS	-	A	A	rs111467855		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41899705_41899706insA								PTPRT (81148 upstream) : SFRS6 (186798 downstream)																							gattccatctcaaaaaaaaaag	0.000													2	4	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45192255	45192256	+	Intron	DEL	GA	-	-	rs33976933		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45192255_45192256delGA	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron|SLC13A3_uc002xse.1_Splice_Site|SLC13A3_uc010ghm.1_Intron|SLC13A3_uc010zxv.1_Intron	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CAGCAagagggagagagagaga	0.292													41	8	---	---	---	---	
BACH1	571	broad.mit.edu	37	21	30693966	30693967	+	Intron	INS	-	T	T			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30693966_30693967insT	uc002ynj.2	+						BACH1_uc002ynk.2_Intron|BACH1_uc002ynl.2_Intron	NM_001186	NP_001177	O14867	BACH1_HUMAN	BTB and CNC homology 1 transcription factor							nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|liver(1)	2						TGTGCAACCCCttttttttttt	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	33157611	33157613	+	IGR	DEL	CAT	-	-	rs62221574		TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33157611_33157613delCAT								SFRS15 (53180 upstream) : HUNK (88015 downstream)																							tcaccaccaccatcaccatcacc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20151725	20151726	+	IGR	INS	-	ACC	ACC	rs138268702	by1000genomes	TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20151725_20151726insACC								ZDHHC8 (16196 upstream) : LOC150197 (42129 downstream)																							ccaccatcactaccaccaccac	0.025													4	2	---	---	---	---	
FRMPD4	9758	broad.mit.edu	37	X	12725041	12725042	+	Intron	DEL	TC	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12725041_12725042delTC	uc004cuz.1	+						FRMPD4_uc011mij.1_Intron	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4						positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						AGTGGTAATTTCTTTTTTTTTT	0.431													158	7	---	---	---	---	
ACE2	59272	broad.mit.edu	37	X	15613301	15613302	+	Intron	DEL	CT	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15613301_15613302delCT	uc004cxa.1	-						ACE2_uc004cxb.2_Intron	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor						angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)	CTTTTGACCActctctctctct	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	48307150	48307150	+	IGR	DEL	T	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48307150delT								SSX4 (54365 upstream) : SLC38A5 (9778 downstream)																							ccggtcTGGATTTTTTTTTTT	0.209													25	7	---	---	---	---	
WDR13	64743	broad.mit.edu	37	X	48457035	48457035	+	Intron	DEL	C	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48457035delC	uc004dkh.1	+						WDR13_uc010nif.1_Intron|WDR13_uc004dki.1_Intron|WDR13_uc004dkj.1_Intron|WDR13_uc004dkk.1_Intron|WDR13_uc004dkl.3_5'UTR|WDR13_uc011mme.1_5'Flank	NM_017883	NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13 protein							cytoplasm|nucleus				ovary(2)	2						TCCTGCCGTACCCCCCCCCCC	0.602													7	5	---	---	---	---	
HCFC1	3054	broad.mit.edu	37	X	153223804	153223806	+	Intron	DEL	TCC	-	-			TCGA-CH-5738-01A-11D-1576-08	TCGA-CH-5738-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153223804_153223806delTCC	uc004fjp.2	-							NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1						cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACACTCACCTTCCTCCTCCTCCT	0.596													4	2	---	---	---	---	
