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
EPHB2	2048	broad.mit.edu	37	1	23191471	23191471	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23191471G>A	uc009vqj.1	+	5	1214	c.1069G>A	c.(1069-1071)GTC>ATC	p.V357I	EPHB2_uc001bge.2_Missense_Mutation_p.V357I|EPHB2_uc001bgf.2_Missense_Mutation_p.V357I|EPHB2_uc010odu.1_Missense_Mutation_p.V357I|hsa-mir-4253|MI0015860_5'Flank	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	357	Extracellular (Potential).|Fibronectin type-III 1.				axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		AGAGGACCTCGTCTACAACAT	0.647									Hereditary_Prostate_Cancer				15	151	---	---	---	---	PASS
WDR63	126820	broad.mit.edu	37	1	85564293	85564293	+	Silent	SNP	A	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85564293A>G	uc001dkt.2	+	13	1622	c.1431A>G	c.(1429-1431)GGA>GGG	p.G477G	WDR63_uc009wcl.2_Silent_p.G438G	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	477	WD 2.									upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		TAGAAAATGGACATAAGAAAG	0.348													22	245	---	---	---	---	PASS
CHIA	27159	broad.mit.edu	37	1	111854861	111854861	+	Silent	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111854861G>A	uc001eas.2	+	4	208	c.105G>A	c.(103-105)CGG>CGA	p.R35R	CHIA_uc001ear.2_Intron|CHIA_uc001eaq.2_Intron|CHIA_uc009wgc.2_Intron|CHIA_uc001eat.2_Intron|CHIA_uc001eav.2_Intron|CHIA_uc001eau.2_Intron|CHIA_uc009wgd.2_Intron	NM_201653	NP_970615	Q9BZP6	CHIA_HUMAN	acidic chitinase isoform c	35					apoptosis|cell wall chitin metabolic process|chitin catabolic process|digestion|immune response|positive regulation of chemokine secretion|production of molecular mediator involved in inflammatory response|response to acid|response to fungus	cytoplasm|extracellular space	cation binding|chitin binding|chitinase activity|kinase binding|lysozyme activity|sugar binding			ovary(1)	1		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		CCCAGTACCGGCCAGGCCTGG	0.582													4	182	---	---	---	---	PASS
OLFML3	56944	broad.mit.edu	37	1	114522060	114522060	+	5'UTR	SNP	T	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114522060T>C	uc001eer.1	+	1					OLFML3_uc001ees.1_5'UTR|OLFML3_uc001eet.1_5'UTR	NM_020190	NP_064575	Q9NRN5	OLFL3_HUMAN	olfactomedin-like 3 precursor						multicellular organismal development	extracellular region					0	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCACCCCGCCTCCAAAGCTAA	0.602											OREG0013687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	26	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145359169	145359169	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145359169T>A	uc001end.3	+	74	9369	c.9334T>A	c.(9334-9336)TTG>ATG	p.L3112M	NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oyq.1_Intron|NBPF10_uc010oyr.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	3037											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCGTGTTGGCTTGGCTGTTGA	0.458													6	420	---	---	---	---	PASS
LHX9	56956	broad.mit.edu	37	1	197886895	197886895	+	5'UTR	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197886895C>T	uc001guk.1	+	1					LHX9_uc009wzc.1_Intron|LHX9_uc001gui.1_Intron|LHX9_uc001guj.1_Intron	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1						motor axon guidance|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						TACAGGGCAGCCCTCTCTGGT	0.577													36	77	---	---	---	---	PASS
OPTC	26254	broad.mit.edu	37	1	203472874	203472874	+	Splice_Site	SNP	G	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203472874G>C	uc001gzu.1	+	7	1140	c.1024_splice	c.e7+1			NM_014359	NP_055174	Q9UBM4	OPT_HUMAN	opticin precursor							proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.109)			CTCCTCCCAGGTAAGAACCCT	0.567													9	33	---	---	---	---	PASS
CAPN2	824	broad.mit.edu	37	1	223949937	223949937	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223949937C>T	uc001hob.3	+	14	1840	c.1616C>T	c.(1615-1617)GCC>GTC	p.A539V	CAPN2_uc010puy.1_Missense_Mutation_p.A461V|CAPN2_uc001hoc.2_Missense_Mutation_p.A120V	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1	539	Domain IV.				proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)		AGACTGTTTGCCCAGTTGGCA	0.483													3	86	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50779973	50779973	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50779973A>T	uc010fbq.2	-	9	3108	c.1631T>A	c.(1630-1632)ATA>AAA	p.I544K	NRXN1_uc002rxb.3_Missense_Mutation_p.I176K|NRXN1_uc002rxe.3_Missense_Mutation_p.I504K|NRXN1_uc002rxc.1_RNA	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	Error:Variant_position_missing_in_P58400_after_alignment					angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATCAAATGATATGGAGCCAGT	0.408													26	209	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179436709	179436709	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179436709G>A	uc010zfg.1	-	275	66670	c.66446C>T	c.(66445-66447)GCC>GTC	p.A22149V	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A15844V|TTN_uc010zfi.1_Missense_Mutation_p.A15777V|TTN_uc010zfj.1_Missense_Mutation_p.A15652V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23076							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)			GAGTTTGAAGGCTGGTGGAAT	0.468													12	63	---	---	---	---	PASS
CADM2	253559	broad.mit.edu	37	3	85961624	85961624	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85961624A>T	uc003dqj.2	+	5	1230	c.604A>T	c.(604-606)ATC>TTC	p.I202F	CADM2_uc003dqk.2_Missense_Mutation_p.I211F|CADM2_uc003dql.2_Missense_Mutation_p.I204F	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D	202	Ig-like C2-type 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		AGTGGCGGTCATCTGCAGAGT	0.473													6	37	---	---	---	---	PASS
ATP6V1A	523	broad.mit.edu	37	3	113499964	113499964	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113499964G>T	uc003eao.2	+	3	216	c.150G>T	c.(148-150)TTG>TTT	p.L50F	ATP6V1A_uc011bik.1_Missense_Mutation_p.L17F	NM_001690	NP_001681	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal V1 subunit A	50					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(2)|skin(1)	3						ACAGCGAATTGGTTGGAGAGA	0.438													24	178	---	---	---	---	PASS
FBXO40	51725	broad.mit.edu	37	3	121339403	121339403	+	5'UTR	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121339403C>T	uc003eeg.2	+	2						NM_016298	NP_057382	Q9UH90	FBX40_HUMAN	F-box protein 40						muscle cell differentiation	centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)		AGCTAAGAAGCAAGAAGAAAT	0.368													14	142	---	---	---	---	PASS
TRPC1	7220	broad.mit.edu	37	3	142509938	142509938	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142509938A>T	uc003evc.2	+	8	1511	c.1375A>T	c.(1375-1377)AGT>TGT	p.S459C	TRPC1_uc003evb.2_Missense_Mutation_p.S425C|TRPC1_uc011bni.1_Missense_Mutation_p.S26C	NM_003304	NP_003295	P48995	TRPC1_HUMAN	transient receptor potential cation channel,	459	Helical; (Potential).				axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	cytosol|integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						TAATCAACTCAGTTTTGTCAT	0.363													43	107	---	---	---	---	PASS
GPR171	29909	broad.mit.edu	37	3	150917067	150917067	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150917067G>A	uc003eyq.3	-	3	347	c.107C>T	c.(106-108)ACC>ATC	p.T36I	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_013308	NP_037440	O14626	GP171_HUMAN	G protein-coupled receptor 171	36	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AAAAGCCCAGGTTGCAAAACA	0.373													7	178	---	---	---	---	PASS
SERPINI2	5276	broad.mit.edu	37	3	167184993	167184993	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167184993C>A	uc003fer.1	-	2	386	c.328G>T	c.(328-330)GCC>TCC	p.A110S	SERPINI2_uc003fes.1_Missense_Mutation_p.A120S|SERPINI2_uc003fet.1_Missense_Mutation_p.A110S	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	110					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3						AGGTAGAGGGCATTGGCAAGA	0.343													18	165	---	---	---	---	PASS
SOX2	6657	broad.mit.edu	37	3	181430951	181430951	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181430951G>C	uc003fkx.2	+	1	1230	c.803G>C	c.(802-804)GGG>GCG	p.G268A	SOX2OT_uc003fkv.2_Intron|SOX2OT_uc003fkw.3_Intron	NM_003106	NP_003097	P48431	SOX2_HUMAN	sex-determining region Y-box 2	268					cell cycle arrest|chromatin organization|eye development|glial cell fate commitment|inner ear development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell proliferation|negative regulation of neuron differentiation|osteoblast differentiation|pituitary gland development|positive regulation of MAPKKK cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of caspase activity|response to growth factor stimulus|response to wounding|somatic stem cell maintenance	cytosol|transcription factor complex	miRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)			TGCCAGGCCGGGGACCTCCGG	0.672			A		NSCLC|oesophageal squamous carcinoma		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME						5	108	---	---	---	---	PASS
PSMD2	5708	broad.mit.edu	37	3	184019697	184019697	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184019697G>A	uc003fnn.1	+	5	575	c.542G>A	c.(541-543)CGG>CAG	p.R181Q	PSMD2_uc011brj.1_Missense_Mutation_p.R22Q|PSMD2_uc011brk.1_Missense_Mutation_p.R51Q	NM_002808	NP_002799	Q13200	PSMD2_HUMAN	proteasome 26S non-ATPase subunit 2	181					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding				0	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	AAGGTCCAGCGGGAGCCTCTG	0.542													22	120	---	---	---	---	PASS
CCDC96	257236	broad.mit.edu	37	4	7042970	7042970	+	3'UTR	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7042970G>A	uc003gjv.2	-	1					TADA2B_uc003gjw.3_5'Flank|TADA2B_uc010idi.2_5'Flank	NM_153376	NP_699207	Q2M329	CCD96_HUMAN	coiled-coil domain containing 96												0						AGGATGAAGTGTTTTGCAGAC	0.473													17	120	---	---	---	---	PASS
C4orf40	401137	broad.mit.edu	37	4	71024217	71024217	+	Missense_Mutation	SNP	G	T	T	rs149016682	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71024217G>T	uc003hfa.3	+	4	321	c.248G>T	c.(247-249)GGA>GTA	p.G83V	C4orf40_uc003hfb.3_Missense_Mutation_p.G83V	NM_214711	NP_999876	Q6MZM9	CD040_HUMAN	hypothetical protein LOC401137 precursor	83						extracellular region					0						ACTTCTCCTGGATTCCCCTAT	0.488													76	466	---	---	---	---	PASS
C4orf36	132989	broad.mit.edu	37	4	87808950	87808950	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87808950C>G	uc003hqe.3	-	4	630	c.317G>C	c.(316-318)AGG>ACG	p.R106T		NM_144645	NP_653246	Q96KX1	CD036_HUMAN	hypothetical protein LOC132989	106											0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		ACCGGCTGGCCTTTCCCTCAG	0.433													13	115	---	---	---	---	PASS
ADH1B	125	broad.mit.edu	37	4	100232771	100232771	+	Missense_Mutation	SNP	C	T	T	rs140683864		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100232771C>T	uc003hus.3	-	7	955	c.871G>A	c.(871-873)GTC>ATC	p.V291I	ADH1A_uc011ceg.1_Intron|ADH1B_uc003hut.3_Missense_Mutation_p.V251I|ADH1B_uc011ceh.1_Missense_Mutation_p.V136I|ADH1B_uc011cei.1_Missense_Mutation_p.V251I	NM_000668	NP_000659	P00325	ADH1B_HUMAN	class I alcohol dehydrogenase, beta subunit	291					ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|zinc ion binding			ovary(1)|breast(1)	2				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Fomepizole(DB01213)|NADH(DB00157)	CCTACGATGACGCTTGTGCCA	0.478													52	254	---	---	---	---	PASS
C4orf17	84103	broad.mit.edu	37	4	100460359	100460359	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100460359C>T	uc003huw.2	+	7	991	c.668C>T	c.(667-669)GCC>GTC	p.A223V	C4orf17_uc003hux.2_RNA	NM_032149	NP_115525	Q53FE4	CD017_HUMAN	hypothetical protein LOC84103	223											0				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		TCTGAGCTTGCCGAGATAAAC	0.433													5	417	---	---	---	---	PASS
UBE2D3	7323	broad.mit.edu	37	4	103718447	103718447	+	3'UTR	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103718447C>A	uc003hwk.2	-	8					UBE2D3_uc003hwh.2_5'Flank|UBE2D3_uc003hwi.2_3'UTR|UBE2D3_uc003hwj.2_RNA|UBE2D3_uc003hwl.2_3'UTR|UBE2D3_uc011cet.1_3'UTR|UBE2D3_uc011ceu.1_3'UTR|UBE2D3_uc003hwo.2_3'UTR|UBE2D3_uc003hwp.2_3'UTR|UBE2D3_uc003hwq.2_3'UTR|UBE2D3_uc003hwr.2_3'UTR	NM_181887	NP_871616	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3 isoform 1						apoptosis|BMP signaling pathway|DNA repair|negative regulation of type I interferon production|proteasomal ubiquitin-dependent protein catabolic process|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein monoubiquitination|transforming growth factor beta receptor signaling pathway	endosome membrane|plasma membrane	ATP binding|protein binding|ubiquitin-protein ligase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.13e-08)		GGGAGGTAAACAAAAAATAAA	0.338													3	107	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113540750	113540750	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113540750T>C	uc003iau.2	-	6	659	c.448A>G	c.(448-450)ATT>GTT	p.I150V	C4orf21_uc003iaw.2_Missense_Mutation_p.I150V	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		GGAGAAAAAATAGTAGGGCCA	0.413													26	162	---	---	---	---	PASS
RAPGEF2	9693	broad.mit.edu	37	4	160275160	160275160	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160275160A>T	uc003iqg.3	+	22	4440	c.4130A>T	c.(4129-4131)CAC>CTC	p.H1377L		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	1377					cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		ATGCCTGCCCACATAGCTGTG	0.453													8	77	---	---	---	---	PASS
CCL28	56477	broad.mit.edu	37	5	43381809	43381809	+	3'UTR	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43381809C>A	uc003jnu.2	-	3					CCL28_uc003jns.2_Intron|CCL28_uc003jnt.2_Intron|CCL28_uc010ivn.2_3'UTR	NM_148672	NP_683513	Q9NRJ3	CCL28_HUMAN	chemokine (C-C motif) ligand 28 precursor						chemotaxis|immune response	extracellular space	chemokine activity			ovary(1)|kidney(1)	2						TTATTGGCTACATTTGCATAC	0.204													3	24	---	---	---	---	PASS
ESM1	11082	broad.mit.edu	37	5	54277917	54277917	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54277917C>T	uc003jpk.2	-	2	428	c.359G>A	c.(358-360)GGC>GAC	p.G120D	ESM1_uc010ivt.2_Intron	NM_007036	NP_008967	Q9NQ30	ESM1_HUMAN	endothelial cell-specific molecule 1 isoform a	120					angiogenesis|regulation of cell growth	extracellular region	growth factor activity|insulin-like growth factor binding				0		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.116)	Lung(15;0.23)			GTCACAGATGCCTGACTGGCA	0.507													50	123	---	---	---	---	PASS
ACTBL2	345651	broad.mit.edu	37	5	56777377	56777377	+	3'UTR	SNP	T	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56777377T>C	uc003jrm.2	-	1						NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2							cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		AAAGGGAAAATGTAAGCCCAC	0.438													20	98	---	---	---	---	PASS
PCDHB16	57717	broad.mit.edu	37	5	140564017	140564017	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564017G>T	uc003liv.2	+	1	3038	c.1883G>T	c.(1882-1884)AGG>ATG	p.R628M	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	628	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCACCGCCAGGCTGCTGAGC	0.692													18	69	---	---	---	---	PASS
GABRA1	2554	broad.mit.edu	37	5	161324440	161324440	+	3'UTR	SNP	A	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161324440A>T	uc010jiw.2	+	11					GABRA1_uc010jix.2_3'UTR|GABRA1_uc010jiy.2_3'UTR|GABRA1_uc003lyx.3_3'UTR|GABRA1_uc010jiz.2_3'UTR|GABRA1_uc010jja.2_3'UTR|GABRA1_uc010jjb.2_3'UTR	NM_000806	NP_000797	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)	TCTTTTACTCACATTCTGTTG	0.393													33	193	---	---	---	---	PASS
HLA-B	3106	broad.mit.edu	37	6	31323495	31323495	+	Intron	SNP	A	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31323495A>G	uc003nth.2	-						HLA-C_uc003ntb.2_5'Flank|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_5'Flank|HLA-B_uc011dnk.1_5'Flank|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Intron|HLA-B_uc003nti.1_5'Flank|HLA-B_uc010jsn.1_Intron|HLA-B_uc010jso.2_3'UTR	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						GAACCCAGACACCAGCCTGGA	0.572									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				3	38	---	---	---	---	PASS
HLA-B	3106	broad.mit.edu	37	6	31323507	31323507	+	Intron	SNP	G	A	A	rs41554617		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31323507G>A	uc003nth.2	-						HLA-C_uc003ntb.2_5'Flank|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_5'Flank|HLA-B_uc011dnk.1_5'Flank|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Intron|HLA-B_uc003nti.1_5'Flank|HLA-B_uc010jsn.1_Intron|HLA-B_uc010jso.2_3'UTR	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						CAGCCTGGACGCAGGCACCTG	0.562									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				3	32	---	---	---	---	PASS
HLA-DMA	3108	broad.mit.edu	37	6	32918330	32918330	+	Silent	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32918330C>T	uc003ocm.2	-	2	425	c.339G>A	c.(337-339)GGG>GGA	p.G113G	HLA-DMA_uc011dqm.1_Silent_p.G113G	NM_006120	NP_006111	Q31604	Q31604_HUMAN	major histocompatibility complex, class II, DM	113						integral to membrane|MHC class II protein complex					0						CAAGTTTTGGCCCTATTTGCT	0.502													6	363	---	---	---	---	PASS
NFYA	4800	broad.mit.edu	37	6	41065225	41065225	+	3'UTR	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41065225G>T	uc003opo.2	+	10					NFYA_uc003opp.2_3'UTR|NFYA_uc003opq.2_3'UTR	NM_002505	NP_002496	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha isoform 1						transcription from RNA polymerase II promoter	CCAAT-binding factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTTCCAATGGGACATTGATGA	0.438													10	42	---	---	---	---	PASS
SMOC2	64094	broad.mit.edu	37	6	168910644	168910644	+	Missense_Mutation	SNP	C	T	T	rs141002558	byFrequency	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168910644C>T	uc003qws.1	+	2	154	c.134C>T	c.(133-135)GCG>GTG	p.A45V	SMOC2_uc003qwr.1_Missense_Mutation_p.A45V	NM_022138	NP_071421	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	45	Kazal-like.				signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		TTGGACTGTGCGGGTTCGCCC	0.443													4	172	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	29773118	29773118	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29773118G>T	uc003tai.2	+	4	250	c.130G>T	c.(130-132)GAA>TAA	p.E44*						Homo sapiens DPY-19-like 2 pseudogene 3 (DPY19L2P3) pseudogene mRNA, complete sequence.																		ATCTGCCAAAGAAGTAAGAGA	0.289													5	316	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43351669	43351669	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43351669T>G	uc003tid.1	+	4	940	c.335T>G	c.(334-336)ATT>AGT	p.I112S	HECW1_uc011kbi.1_Missense_Mutation_p.I112S|HECW1_uc003tie.1_Missense_Mutation_p.I144S	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	112					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						GGGGACTGGATTGGCATGTAC	0.433													3	139	---	---	---	---	PASS
PMS2L11	441263	broad.mit.edu	37	7	76631555	76631555	+	RNA	SNP	C	T	T	rs61737188	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76631555C>T	uc003ufw.3	+	4		c.696C>T			PMS2L11_uc011kgn.1_RNA	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						GGCAATCGGGCCCCTGGCTGT	0.607													4	66	---	---	---	---	PASS
DOCK4	9732	broad.mit.edu	37	7	111517174	111517174	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111517174G>T	uc003vfx.2	-	17	1925	c.1656C>A	c.(1654-1656)TTC>TTA	p.F552L	DOCK4_uc003vfw.2_5'UTR|DOCK4_uc003vfy.2_Missense_Mutation_p.F552L|DOCK4_uc003vga.1_Missense_Mutation_p.F157L	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	552	DHR-1.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				TATTCCCAAGGAAAATGCCCT	0.348													6	33	---	---	---	---	PASS
ZNF800	168850	broad.mit.edu	37	7	127014965	127014965	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127014965G>T	uc003vlx.1	-	5	688	c.425C>A	c.(424-426)GCA>GAA	p.A142E	ZNF800_uc003vlw.1_Missense_Mutation_p.A45E|ZNF800_uc003vly.1_Missense_Mutation_p.A142E|ZNF800_uc010lla.2_Missense_Mutation_p.A142E	NM_176814	NP_789784	Q2TB10	ZN800_HUMAN	zinc finger protein 800	142					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TTGAAATACTGCATTTTGATT	0.368													23	250	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	152143696	152143696	+	IGR	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152143696G>T								FABP5L3 (3598 upstream) : LOC100128822 (17513 downstream)																							GGTTCTCAGGGGAGCCACCAC	0.577													6	193	---	---	---	---	PASS
CTSB	1508	broad.mit.edu	37	8	11710851	11710851	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11710851T>G	uc003wum.2	-	4	437	c.113A>C	c.(112-114)AAT>ACT	p.N38T	CTSB_uc011kxl.1_Intron|CTSB_uc003wun.2_Missense_Mutation_p.N38T|CTSB_uc003wuo.2_Missense_Mutation_p.N38T|CTSB_uc003wup.2_Missense_Mutation_p.N38T|CTSB_uc003wuq.2_Missense_Mutation_p.N38T|CTSB_uc010lsc.2_5'UTR|CTSB_uc003wur.2_Missense_Mutation_p.N38T|CTSB_uc003wus.1_Missense_Mutation_p.N38T|CTSB_uc003wut.1_Missense_Mutation_p.N38T	NM_147780	NP_680090	P07858	CATB_HUMAN	cathepsin B preproprotein	38					proteolysis|regulation of apoptosis|regulation of catalytic activity	lysosome|melanosome	cysteine-type endopeptidase activity				0	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		CCACGTGGTATTCCGTTTGTT	0.602													26	140	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	11873857	11873857	+	3'UTR	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11873857G>A	uc003wuy.1	+	1										Homo sapiens cDNA FLJ33940 fis, clone CTONG2018069.																		gagaggccagggaagcagagg	0.264													3	1	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	11873862	11873862	+	3'UTR	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11873862C>T	uc003wuy.1	+	1										Homo sapiens cDNA FLJ33940 fis, clone CTONG2018069.																		gccagggaagcagaggaggcc	0.259													3	1	---	---	---	---	PASS
FAM66D	100132923	broad.mit.edu	37	8	12217042	12217042	+	Intron	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12217042G>T	uc011kxp.1	+						uc003wvm.1_Intron|uc010lsh.1_3'UTR|FAM66A_uc010lsi.2_5'Flank					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						GAACATATTCGGACTTTAGAT	0.373													5	5	---	---	---	---	PASS
PLAG1	5324	broad.mit.edu	37	8	57079203	57079203	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57079203G>A	uc003xsq.3	-	3	1553	c.1102C>T	c.(1102-1104)CCC>TCC	p.P368S	PLAG1_uc003xsr.3_Missense_Mutation_p.P368S|PLAG1_uc010lyi.2_Missense_Mutation_p.P368S|PLAG1_uc010lyj.2_Missense_Mutation_p.P286S	NM_001114635	NP_001108107	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1 isoform b	368	Activates transcription; Inhibition of nuclear import due to lack of NLS and KPNA2 interaction.|Repression domain; contains 3 sumoylation motifs and massively decrease transcription activity.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding		CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3)	salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1)	129		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			GATGAAGAGGGCACGCCACCT	0.463			T	TCEA1|LIFR|CTNNB1|CHCHD7	salivary adenoma								5	291	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113301593	113301593	+	Splice_Site	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113301593C>A	uc003ynu.2	-	57	9307	c.9148_splice	c.e57+1	p.G3050_splice	CSMD3_uc003yns.2_Splice_Site_p.G2252_splice|CSMD3_uc003ynt.2_Splice_Site_p.G3010_splice|CSMD3_uc011lhx.1_Splice_Site_p.G2881_splice	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						CCAAGTGGTACCTGAACAATG	0.378										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			94	191	---	---	---	---	PASS
TAF2	6873	broad.mit.edu	37	8	120770357	120770357	+	Silent	SNP	T	C	C	rs150316992		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120770357T>C	uc003you.2	-	21	2994	c.2724A>G	c.(2722-2724)CAA>CAG	p.Q908Q		NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2	908					G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TAAGTAGCCATTGCAGTTCTT	0.308													4	345	---	---	---	---	PASS
FAM83A	84985	broad.mit.edu	37	8	124204198	124204198	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124204198C>A	uc003ypv.2	+	3	2650	c.636C>A	c.(634-636)GAC>GAA	p.D212E	FAM83A_uc003ypw.2_Missense_Mutation_p.D212E|FAM83A_uc003ypy.2_Intron|FAM83A_uc003ypx.2_Missense_Mutation_p.D212E|FAM83A_uc003ypz.2_Missense_Mutation_p.D212E	NM_032899	NP_116288	Q86UY5	FA83A_HUMAN	hypothetical protein LOC84985 isoform a	212										ovary(3)|skin(1)	4	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			AGATCTCTGACAGTCACCTCA	0.398													34	300	---	---	---	---	PASS
TLN1	7094	broad.mit.edu	37	9	35698342	35698342	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35698342G>A	uc003zxt.2	-	55	7703	c.7349C>T	c.(7348-7350)TCG>TTG	p.S2450L		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	2450	I/LWEQ.				axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CATTGCCTCCGAGTCCTGGTC	0.552													14	83	---	---	---	---	PASS
HNRNPK	3190	broad.mit.edu	37	9	86586212	86586212	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86586212T>A	uc004ang.3	-	13	1292	c.1068A>T	c.(1066-1068)GAA>GAT	p.E356D	HNRNPK_uc011lsw.1_Missense_Mutation_p.E116D|HNRNPK_uc004and.3_Missense_Mutation_p.E116D|HNRNPK_uc004ank.3_Missense_Mutation_p.E356D|HNRNPK_uc004anf.3_Missense_Mutation_p.E356D|HNRNPK_uc004anh.3_Missense_Mutation_p.E332D|HNRNPK_uc011lsx.1_Missense_Mutation_p.E332D|HNRNPK_uc004ani.3_Missense_Mutation_p.E356D|HNRNPK_uc004anj.3_Missense_Mutation_p.E356D|HNRNPK_uc004ann.3_Missense_Mutation_p.E332D|HNRNPK_uc004anl.3_Missense_Mutation_p.E356D|HNRNPK_uc004anm.3_Missense_Mutation_p.E356D|uc004ano.1_5'Flank|MIR7-1_hsa-mir-7-1|MI0000263_5'Flank	NM_031262	NP_112552	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	356	5 X 4 AA repeats of G-X-G-G.|2 X 22 AA approximate repeats.				interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|single-stranded DNA binding			skin(1)	1						CCATCTGCCATTCTGATGGGC	0.383													49	222	---	---	---	---	PASS
COL27A1	85301	broad.mit.edu	37	9	116999978	116999978	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116999978G>A	uc011lxl.1	+	19	2710	c.2710G>A	c.(2710-2712)GGG>AGG	p.G904R	COL27A1_uc004bii.2_RNA	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	904	Collagen-like 5.|Pro-rich.|Triple-helical region.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						TGGGTTTCCCGGGCCCCCTGG	0.532													17	77	---	---	---	---	PASS
MYO3A	53904	broad.mit.edu	37	10	26417412	26417412	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26417412T>C	uc001isn.2	+	20	2567	c.2207T>C	c.(2206-2208)ATT>ACT	p.I736T	MYO3A_uc009xko.1_Missense_Mutation_p.I736T|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	736	Myosin head-like.				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						TGCATTAACATTGCAAATGAA	0.333													54	108	---	---	---	---	PASS
GDF10	2662	broad.mit.edu	37	10	48429220	48429220	+	Silent	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48429220G>A	uc001jfb.2	-	2	1122	c.666C>T	c.(664-666)TCC>TCT	p.S222S	GDF10_uc009xnp.2_Silent_p.S221S|GDF10_uc009xnq.1_Silent_p.S222S	NM_004962	NP_004953	P55107	BMP3B_HUMAN	growth differentiation factor 10 precursor	222					growth|skeletal system development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			lung(1)|central_nervous_system(1)	2						CCAGCTGGGCGGAGAGGAGCA	0.706													4	15	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73461858	73461858	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73461858T>C	uc001jrx.3	+	22	2854	c.2477T>C	c.(2476-2478)CTC>CCC	p.L826P	CDH23_uc001jry.2_Missense_Mutation_p.L442P|CDH23_uc001jrz.2_Missense_Mutation_p.L442P	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	826	Cadherin 8.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						TTCTACAGCCTCAACAGCACC	0.632													3	145	---	---	---	---	PASS
OR51B4	79339	broad.mit.edu	37	11	5323105	5323105	+	Silent	SNP	C	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5323105C>G	uc010qza.1	-	1	72	c.72G>C	c.(70-72)CGG>CGC	p.R24R	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_033179	NP_149419	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B,	24	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|skin(1)	2		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACATAGAGATCCGGTAGTGAA	0.473											OREG0003718	type=REGULATORY REGION|Gene=OR51B4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	25	164	---	---	---	---	PASS
CTR9	9646	broad.mit.edu	37	11	10785191	10785191	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10785191A>G	uc001mja.2	+	9	1108	c.959A>G	c.(958-960)GAA>GGA	p.E320G		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	320	TPR 6.				histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		ATTCTTTAGGAAGATTATGAC	0.294													18	159	---	---	---	---	PASS
NPAS4	266743	broad.mit.edu	37	11	66189623	66189623	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66189623T>A	uc001ohx.1	+	2	384	c.208T>A	c.(208-210)TCA>ACA	p.S70T	NPAS4_uc010rpc.1_5'UTR	NM_178864	NP_849195	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	70	PAS 1.				transcription, DNA-dependent		DNA binding|signal transducer activity				0						GGGGCTTCTCTCAGCTCAAGA	0.577											OREG0003368	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=NPAS4|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	24	73	---	---	---	---	PASS
P2RY2	5029	broad.mit.edu	37	11	72945224	72945224	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72945224C>A	uc001otj.2	+	3	353	c.20C>A	c.(19-21)CCC>CAC	p.P7H	P2RY2_uc001otk.2_Missense_Mutation_p.P7H|P2RY2_uc001otl.2_Missense_Mutation_p.P7H	NM_002564	NP_002555	P41231	P2RY2_HUMAN	purinergic receptor P2Y2	7	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(1)|skin(1)	4					Suramin(DB04786)	GACCTGGGCCCCTGGAATGAC	0.642													34	93	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2786435	2786435	+	Intron	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2786435G>T	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron|CACNA1C_uc010sea.1_Intron|uc001qkx.1_RNA|CACNA1C_uc001qky.1_5'Flank	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CCTGGTCATTGCCTCTGACCT	0.642													5	24	---	---	---	---	PASS
LMO3	55885	broad.mit.edu	37	12	16757832	16757832	+	Intron	SNP	T	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16757832T>A	uc001rdk.1	-						LMO3_uc001rdj.1_Translation_Start_Site|LMO3_uc010shy.1_Intron|LMO3_uc001rdl.1_Intron|LMO3_uc009zii.1_Intron|LMO3_uc010shz.1_Intron|LMO3_uc001rdm.1_Intron|LMO3_uc001rdo.1_Intron|LMO3_uc001rdp.1_Intron|LMO3_uc001rdn.1_Intron|LMO3_uc009zij.1_Intron|LMO3_uc009zik.1_Intron	NM_018640	NP_061110	Q8TAP4	LMO3_HUMAN	LIM domain only 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent		zinc ion binding				0		Hepatocellular(102;0.244)				ATGAGTTGACTTAGGCGTGTC	0.488													5	193	---	---	---	---	PASS
PRKAG1	5571	broad.mit.edu	37	12	49398646	49398646	+	Intron	SNP	C	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49398646C>G	uc001rsy.2	-						uc001rsw.2_Intron|PRKAG1_uc010smd.1_Intron|PRKAG1_uc001rsx.2_Intron|PRKAG1_uc001rsz.2_Intron|PRKAG1_uc009zlb.2_Intron|PRKAG1_uc010sme.1_3'UTR	NM_002733	NP_002724	P54619	AAKG1_HUMAN	AMP-activated protein kinase, noncatalytic						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|positive regulation of protein kinase activity|regulation of fatty acid oxidation|regulation of glycolysis|spermatogenesis	cytosol	cAMP-dependent protein kinase activity|cAMP-dependent protein kinase regulator activity|protein kinase binding			kidney(1)	1						gtgtgtgtgtCTTTTCTCTCT	0.244													6	79	---	---	---	---	PASS
KRT5	3852	broad.mit.edu	37	12	52908651	52908651	+	3'UTR	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52908651G>T	uc001san.2	-	9						NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5						epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		AACATGGCTTGAGCAACTGCC	0.527													7	40	---	---	---	---	PASS
KRT18	3875	broad.mit.edu	37	12	53342910	53342910	+	Intron	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53342910C>T	uc001sbe.2	+						KRT18_uc009zmn.1_Intron|KRT18_uc001sbf.1_5'UTR|KRT18_uc001sbg.2_5'UTR|KRT18_uc009zmo.2_5'UTR|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18						anatomical structure morphogenesis|cell cycle|Golgi to plasma membrane CFTR protein transport|interspecies interaction between organisms|negative regulation of apoptosis	centriolar satellite|keratin filament|perinuclear region of cytoplasm	protein binding|structural molecule activity			skin(1)	1						AGGCCGCCACCGTCGTCCGCA	0.682													25	81	---	---	---	---	PASS
ANKRD52	283373	broad.mit.edu	37	12	56647166	56647166	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56647166C>T	uc001skm.3	-	10	1096	c.1006G>A	c.(1006-1008)GAC>AAC	p.D336N		NM_173595	NP_775866	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	336							protein binding			ovary(2)	2						CCAAATTTGTCGGCACAATCA	0.552													4	185	---	---	---	---	PASS
TSPAN19	144448	broad.mit.edu	37	12	85421761	85421761	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85421761C>G	uc009zsj.2	-	4	281	c.180G>C	c.(178-180)TTG>TTC	p.L60F		NM_001100917	NP_001094387	P0C672	TSN19_HUMAN	tetraspanin 19	60	Helical; (Potential).					integral to membrane				ovary(1)	1						CCATTCCAATCAAAATTTGAG	0.299													6	34	---	---	---	---	PASS
ANKS1B	56899	broad.mit.edu	37	12	100206021	100206021	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100206021G>C	uc001tge.1	-	3	701	c.284C>G	c.(283-285)CCT>CGT	p.P95R	ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Missense_Mutation_p.P95R	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a	95	ANK 3.					Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CAGGTGAATAGGAAAATACCC	0.398													22	137	---	---	---	---	PASS
HPD	3242	broad.mit.edu	37	12	122281654	122281654	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122281654C>T	uc001ubj.2	-	12	956	c.916G>A	c.(916-918)GCC>ACC	p.A306T	HPD_uc001ubk.2_Missense_Mutation_p.A267T	NM_002150	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	306					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	TTGATCTTGGCCGTCTTCAGC	0.527													3	62	---	---	---	---	PASS
UBC	7316	broad.mit.edu	37	12	125397953	125397953	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125397953G>A	uc001ugs.3	-	2	813	c.365C>T	c.(364-366)GCC>GTC	p.A122V	UBC_uc001ugr.2_5'Flank|UBC_uc001ugu.1_Missense_Mutation_p.A122V|UBC_uc001ugt.2_Missense_Mutation_p.A122V|UBC_uc001ugv.2_Intron|UBC_uc001ugw.2_5'UTR	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	122	Ubiquitin-like 2.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		CTGCTTTCCGGCAAAGATCAA	0.547													6	375	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25161397	25161397	+	RNA	SNP	C	G	G	rs3874227	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25161397C>G	uc001upm.2	+	8		c.921C>G			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						TGAAACATCTCTACAACTGGA	0.343													3	104	---	---	---	---	PASS
ABCC4	10257	broad.mit.edu	37	13	95862961	95862961	+	Silent	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95862961C>A	uc001vmd.3	-	5	725	c.606G>T	c.(604-606)GTG>GTT	p.V202V	ABCC4_uc010afk.2_Silent_p.V202V|ABCC4_uc001vme.2_Silent_p.V202V|ABCC4_uc010tih.1_Silent_p.V127V|ABCC4_uc001vmf.2_Silent_p.V159V|ABCC4_uc010afl.1_Silent_p.V159V|ABCC4_uc010afm.1_Silent_p.V215V	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4	202	ABC transmembrane type-1 1.				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	CAAACTTGTTCACATCATTGG	0.378													13	70	---	---	---	---	PASS
OR4K14	122740	broad.mit.edu	37	14	20483200	20483200	+	Silent	SNP	A	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20483200A>T	uc010tky.1	-	1	153	c.153T>A	c.(151-153)TCT>TCA	p.S51S		NM_001004712	NP_001004712	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K,	51	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|large_intestine(1)	3	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		GGCAGGGATCAGAAATTACAG	0.463													13	79	---	---	---	---	PASS
GOLGA8DP	100132979	broad.mit.edu	37	15	22709152	22709152	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22709152G>T	uc010axw.2	-	11	1245	c.347C>A	c.(346-348)GCG>GAG	p.A116E	GOLGA8DP_uc010axx.2_Missense_Mutation_p.A116E|uc010tzw.1_5'Flank	NM_001012423	NP_001012423			golgi autoantigen, golgin subfamily a, 8E												0						GGCCTGGAGCGCTCCTGCCAC	0.607													4	55	---	---	---	---	PASS
RGS11	8786	broad.mit.edu	37	16	321411	321411	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:321411C>T	uc002cgj.1	-	11	739	c.736G>A	c.(736-738)GTC>ATC	p.V246I	RGS11_uc002cgi.1_Missense_Mutation_p.V225I|RGS11_uc010bqs.1_Missense_Mutation_p.V235I|RGS11_uc002cgk.1_Missense_Mutation_p.V62I	NM_183337	NP_899180	O94810	RGS11_HUMAN	regulator of G-protein signalling 11 isoform 1	246	G protein gamma.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			lung(1)|pancreas(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				TCAAGGCAGACGGAGGACTTC	0.652													8	69	---	---	---	---	PASS
PKD1	5310	broad.mit.edu	37	16	2147486	2147486	+	Silent	SNP	G	A	A	rs150310430	byFrequency	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2147486G>A	uc002cos.1	-	33	10448	c.10239C>T	c.(10237-10239)TCC>TCT	p.S3413S	PKD1_uc002cot.1_Silent_p.S3412S|PKD1_uc010bse.1_RNA	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	3413	Cytoplasmic (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3						TTCCCTCGCCGGAGGGCCAGC	0.682													3	80	---	---	---	---	PASS
ABCC11	85320	broad.mit.edu	37	16	48249248	48249248	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48249248A>C	uc002eff.1	-	7	1309	c.959T>G	c.(958-960)ATG>AGG	p.M320R	ABCC11_uc002efg.1_Missense_Mutation_p.M320R|ABCC11_uc002efh.1_Missense_Mutation_p.M320R|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	320	ABC transmembrane type-1 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				CATTCTTGTCATGAATACCTG	0.493									Cerumen_Type				3	135	---	---	---	---	PASS
PLEKHG4	25894	broad.mit.edu	37	16	67322104	67322104	+	Silent	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67322104G>A	uc002eso.3	+	19	5790	c.3255G>A	c.(3253-3255)CCG>CCA	p.P1085P	PLEKHG4_uc002esp.3_Silent_p.P892P|PLEKHG4_uc002esq.3_Silent_p.P1085P|PLEKHG4_uc010cef.2_Silent_p.P1085P|PLEKHG4_uc002ess.3_Silent_p.P1085P|PLEKHG4_uc010ceg.2_Silent_p.P1004P	NM_015432	NP_056247	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G	1085					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CCGTAGCCCCGTTTGACCATG	0.602													14	253	---	---	---	---	PASS
CAMKK1	84254	broad.mit.edu	37	17	3786739	3786739	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3786739C>A	uc002fwt.2	-	5	592	c.498G>T	c.(496-498)AAG>AAT	p.K166N	CAMKK1_uc002fwu.2_Missense_Mutation_p.K166N|CAMKK1_uc002fwv.2_Missense_Mutation_p.K166N	NM_172206	NP_757343	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase 1	166	Protein kinase.				synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		AGCCATACTGCTTCAGTAACT	0.507													8	91	---	---	---	---	PASS
ZNF594	84622	broad.mit.edu	37	17	5086795	5086795	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5086795C>G	uc010cla.1	-	2	913	c.757G>C	c.(757-759)GAT>CAT	p.D253H		NM_032530	NP_115919	Q96JF6	ZN594_HUMAN	zinc finger protein 594	253	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(1)	3						ATAATAAGATCTGTGCTTTGA	0.418													49	313	---	---	---	---	PASS
SUPT6H	6830	broad.mit.edu	37	17	27024072	27024072	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27024072T>G	uc002hby.2	+	30	4271	c.4181T>G	c.(4180-4182)CTG>CGG	p.L1394R	SUPT6H_uc010crt.2_Missense_Mutation_p.L1394R	NM_003170	NP_003161	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog	1394	SH2.				chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)					GCCTTCAGCCTGGGAGCCACT	0.577													5	53	---	---	---	---	PASS
MEOX1	4222	broad.mit.edu	37	17	41719182	41719182	+	3'UTR	SNP	C	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41719182C>G	uc002idz.2	-	3					MEOX1_uc002iea.2_3'UTR|MEOX1_uc002ieb.2_3'UTR	NM_004527	NP_004518	P50221	MEOX1_HUMAN	mesenchyme homeobox 1 isoform 1							nucleus	sequence-specific DNA binding				0		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)		GGAGAGGCTGCCCTGGCTGGG	0.527													9	25	---	---	---	---	PASS
SPATA20	64847	broad.mit.edu	37	17	48629019	48629019	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48629019C>T	uc002irf.2	+	12	1817	c.1676C>T	c.(1675-1677)CCT>CTT	p.P559L	SPATA20_uc002irc.2_Missense_Mutation_p.P226L|SPATA20_uc002ire.2_Missense_Mutation_p.P515L|SPATA20_uc002ird.2_Missense_Mutation_p.P575L|SPATA20_uc002irg.2_RNA	NM_022827	NP_073738	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	559					cell differentiation|mannose metabolic process|multicellular organismal development|spermatogenesis	extracellular region	mannose-6-phosphate isomerase activity|protein binding				0	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TACACCGGCCCTGGGGGGACT	0.637													16	90	---	---	---	---	PASS
ANKFN1	162282	broad.mit.edu	37	17	54403670	54403670	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54403670C>A	uc002iun.1	+	3	186	c.151C>A	c.(151-153)CAA>AAA	p.Q51K		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	51										large_intestine(1)|ovary(1)	2						AAGCACTGGACAATTACCAAC	0.398													24	184	---	---	---	---	PASS
TBC1D3P2	440452	broad.mit.edu	37	17	60342234	60342234	+	RNA	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60342234C>T	uc010woz.1	-	14		c.1895G>A				NR_027486				Homo sapiens cDNA FLJ60189 complete cds, highly similar to TBC1 domain family member 3.												0						GTCTGGTGTGCTCCATCTCTG	0.498													4	99	---	---	---	---	PASS
EPB41L3	23136	broad.mit.edu	37	18	5410602	5410602	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5410602G>A	uc002kmt.1	-	14	2170	c.2084C>T	c.(2083-2085)ACG>ATG	p.T695M	EPB41L3_uc010wzh.1_Missense_Mutation_p.T526M|EPB41L3_uc002kmu.1_Missense_Mutation_p.T526M|EPB41L3_uc010dkq.1_Missense_Mutation_p.T417M|EPB41L3_uc002kms.1_Translation_Start_Site|EPB41L3_uc010wze.1_Translation_Start_Site|EPB41L3_uc010wzf.1_Translation_Start_Site|EPB41L3_uc010wzg.1_Translation_Start_Site|EPB41L3_uc010dkr.2_Missense_Mutation_p.T87M	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	695	Spectrin--actin-binding (Potential).				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						TGCGGTGTCCGTGCGCTCACT	0.557													8	37	---	---	---	---	PASS
IMPA2	3613	broad.mit.edu	37	18	11999109	11999109	+	Silent	SNP	A	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11999109A>T	uc002kqp.1	+	2	367	c.153A>T	c.(151-153)GCA>GCT	p.A51A	IMPA2_uc002kqo.1_5'UTR|IMPA2_uc010dlb.1_5'UTR|IMPA2_uc002kqq.1_5'UTR	NM_014214	NP_055029	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	51					inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)	CATCAGCTGCAGATCTTGTGA	0.408													21	151	---	---	---	---	PASS
CTAGE1	64693	broad.mit.edu	37	18	19996969	19996969	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19996969G>A	uc002ktv.1	-	1	910	c.806C>T	c.(805-807)TCG>TTG	p.S269L		NM_172241	NP_758441	Q96RT6	CTGE2_HUMAN	cutaneous T-cell lymphoma-associated antigen 1	269						integral to membrane				ovary(1)	1	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					ACCATCTTCCGATTCACTGTT	0.378													29	168	---	---	---	---	PASS
FARSA	2193	broad.mit.edu	37	19	13041068	13041068	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13041068C>G	uc002mvs.2	-	4	520	c.472G>C	c.(472-474)GAG>CAG	p.E158Q	FARSA_uc002mvt.2_RNA|FARSA_uc010xmv.1_Missense_Mutation_p.E158Q|FARSA_uc010dyy.1_Missense_Mutation_p.E79Q	NM_004461	NP_004452	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	158					phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)	TTCCTCAGCTCGCTCCTCTCC	0.652													26	175	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41533022	41533022	+	Intron	SNP	G	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41533022G>C	uc002opo.2	-						uc002ops.1_RNA	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTTGAAGAGCCAGTCGAAG	0.662													4	54	---	---	---	---	PASS
ZNF226	7769	broad.mit.edu	37	19	44680770	44680770	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44680770G>C	uc002oyp.2	+	6	1499	c.1355G>C	c.(1354-1356)TGT>TCT	p.C452S	ZNF226_uc002oyq.2_Missense_Mutation_p.C335S|ZNF226_uc002oyr.2_Missense_Mutation_p.C335S|ZNF226_uc010ejg.2_3'UTR|ZNF226_uc002oys.2_Missense_Mutation_p.C452S|ZNF226_uc002oyt.2_Missense_Mutation_p.C452S	NM_001032373	NP_001027545	Q9NYT6	ZN226_HUMAN	zinc finger protein 226 isoform a	452	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)|all_neural(266;0.202)				TGTGAGGAATGTGGTAAAGGC	0.428													5	120	---	---	---	---	PASS
PRR12	57479	broad.mit.edu	37	19	50099582	50099582	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50099582G>A	uc002poo.3	+	4	1990	c.1990G>A	c.(1990-1992)GAG>AAG	p.E664K		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CTTGGTGGGCGAGGACGGGGC	0.682													9	22	---	---	---	---	PASS
ZNF415	55786	broad.mit.edu	37	19	53612395	53612395	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53612395T>A	uc002qax.2	-	7	1396	c.1047A>T	c.(1045-1047)AAA>AAT	p.K349N	ZNF415_uc002qat.2_Missense_Mutation_p.K313N|ZNF415_uc002qaw.2_Missense_Mutation_p.K301N|ZNF415_uc010yds.1_Missense_Mutation_p.K301N|ZNF415_uc010ydt.1_Missense_Mutation_p.K301N|ZNF415_uc002qau.2_Missense_Mutation_p.K288N|ZNF415_uc002qav.2_Missense_Mutation_p.K313N|ZNF415_uc002qba.2_Missense_Mutation_p.K71N|ZNF415_uc002qay.2_Missense_Mutation_p.K288N|ZNF415_uc002qaz.2_Missense_Mutation_p.K349N	NR_028343		Q09FC8	ZN415_HUMAN	RecName: Full=Zinc finger protein 415;	349	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.0191)		ACTCATAACATTTGTAAGGTT	0.408													8	168	---	---	---	---	PASS
TGM3	7053	broad.mit.edu	37	20	2312728	2312728	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2312728A>G	uc002wfx.3	+	10	1511	c.1414A>G	c.(1414-1416)ATG>GTG	p.M472V		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	472					cell envelope organization|hair follicle morphogenesis|keratinization|peptide cross-linking|protein tetramerization	cytoplasm|extrinsic to internal side of plasma membrane	acyltransferase activity|calcium ion binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(4)|ovary(3)|breast(1)|skin(1)	9					L-Glutamine(DB00130)	GACGTCTTCAATGGGTTTGGA	0.522													6	116	---	---	---	---	PASS
CST5	1473	broad.mit.edu	37	20	23858157	23858157	+	Silent	SNP	C	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23858157C>T	uc002wtr.1	-	2	397	c.330G>A	c.(328-330)CAG>CAA	p.Q110Q		NM_001900	NP_001891	P28325	CYTD_HUMAN	cystatin D precursor	110						extracellular region	cysteine-type endopeptidase inhibitor activity|protein binding				0						TCAGTTTTGGCTGGTCATTGA	0.438													4	163	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29614275	29614275	+	5'UTR	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29614275G>A	uc010ztk.1	+	1					FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA					RecName: Full=Protein FRG1B;												0						aagaaaaagagcaaagataag	0.234													3	56	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29614288	29614288	+	5'UTR	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29614288G>A	uc010ztk.1	+	1					FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA					RecName: Full=Protein FRG1B;												0						aagataagaagagaaaaagag	0.229													3	65	---	---	---	---	PASS
NCOA6	23054	broad.mit.edu	37	20	33334716	33334716	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33334716G>A	uc002xav.2	-	11	5380	c.2809C>T	c.(2809-2811)CCA>TCA	p.P937S	NCOA6_uc002xaw.2_Missense_Mutation_p.P937S	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	937	NCOA1-binding region.|Gln-rich.|CREBBP-binding region.				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7						AGACCAGCTGGGCGAGTATCT	0.408													8	115	---	---	---	---	PASS
SERPIND1	3053	broad.mit.edu	37	22	21141257	21141257	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21141257G>A	uc002ztb.1	+	5	1470	c.1403G>A	c.(1402-1404)CGC>CAC	p.R468H	PI4KA_uc002zsz.3_Intron|SERPIND1_uc002ztc.2_Missense_Mutation_p.R496H	NM_000185	NP_000176	P05546	HEP2_HUMAN	heparin cofactor II precursor	468					blood coagulation|chemotaxis|regulation of proteolysis	extracellular region	heparin binding|serine-type endopeptidase inhibitor activity				0	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)	ACCCAAGTCCGCTTCACTGTC	0.582													4	192	---	---	---	---	PASS
NF2	4771	broad.mit.edu	37	22	30067836	30067836	+	Nonsense_Mutation	SNP	C	T	T	rs74315499		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30067836C>T	uc003age.3	+	11	1464	c.1021C>T	c.(1021-1023)CGA>TGA	p.R341*	NF2_uc003afy.3_Nonsense_Mutation_p.R341*|NF2_uc003afz.3_Nonsense_Mutation_p.R258*|NF2_uc003agf.3_Nonsense_Mutation_p.R341*|NF2_uc003agb.3_Nonsense_Mutation_p.R264*|NF2_uc003agc.3_Nonsense_Mutation_p.R303*|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Nonsense_Mutation_p.R341*|NF2_uc003aga.3_Nonsense_Mutation_p.R299*|NF2_uc003agh.3_Nonsense_Mutation_p.R300*|NF2_uc003agi.3_Nonsense_Mutation_p.R258*|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Nonsense_Mutation_p.R303*|NF2_uc010gvp.2_Intron|NF2_uc011akq.1_5'Flank	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1	341	Glu-rich.				actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.R341*(20)|p.L127_D382del(1)|p.M334fs*4(1)|p.?(1)|p.M334_Q362del(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						GCGCCTCGCTCGAGAGAAGCA	0.567			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				36	49	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38097437	38097437	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38097437G>T	uc003atr.2	+	3	336	c.65G>T	c.(64-66)CGC>CTC	p.R22L	TRIOBP_uc003atu.2_5'UTR|TRIOBP_uc003atq.1_Missense_Mutation_p.R22L|TRIOBP_uc003ats.1_5'UTR	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	22					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					ACCCAGAACCGCTGTCAAAAC	0.567													10	18	---	---	---	---	PASS
PKDREJ	10343	broad.mit.edu	37	22	46654878	46654878	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46654878A>G	uc003bhh.2	-	1	4342	c.4342T>C	c.(4342-4344)TTC>CTC	p.F1448L		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1448	Helical; (Potential).				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		GAACAGGTGAACAAAAAAGTT	0.383													3	183	---	---	---	---	PASS
GEMIN8	54960	broad.mit.edu	37	X	14038611	14038611	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14038611C>A	uc004cwb.2	-	4	401	c.58G>T	c.(58-60)GTA>TTA	p.V20L	GEMIN8_uc004cwc.2_Missense_Mutation_p.V20L|GEMIN8_uc004cwd.2_Missense_Mutation_p.V20L	NM_017856	NP_060326	Q9NWZ8	GEMI8_HUMAN	gem (nuclear organelle) associated protein 8	20					spliceosomal snRNP assembly	Cajal body|cytoplasm|SMN complex|spliceosomal complex	protein binding				0						CTTGCATATACCGGATGAGAA	0.448													38	130	---	---	---	---	PASS
SPEN	23013	broad.mit.edu	37	1	16203144	16203144	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16203144delC	uc001axk.1	+	3	1056	c.852delC	c.(850-852)ATCfs	p.I284fs	SPEN_uc010obp.1_Frame_Shift_Del_p.I243fs	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	284	Ser-rich.|By similarity.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GTGATTCAATCAGCAGCAGCA	0.473													130	65	---	---	---	---	
ARHGEF19	128272	broad.mit.edu	37	1	16528470	16528483	+	Intron	DEL	CCTACCCTAGGGAC	-	-	rs58225172		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16528470_16528483delCCTACCCTAGGGAC	uc001ayc.1	-						ARHGEF19_uc009voo.1_Intron|ARHGEF19_uc001ayb.1_Intron	NM_153213	NP_694945	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19						regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		AGGACCCAGGCCTACCCTAGGGACCCATGTCTGC	0.621													3	6	---	---	---	---	
FOXJ3	22887	broad.mit.edu	37	1	42693774	42693783	+	Intron	DEL	AACTGAGAAA	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42693774_42693783delAACTGAGAAA	uc001che.2	-						FOXJ3_uc001chf.2_Intron|FOXJ3_uc001chg.2_Intron|FOXJ3_uc001chh.1_Intron	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ACTTGTTTTGAACTGAGAAAAAGATTATAT	0.271													7	8	---	---	---	---	
CCDC30	728621	broad.mit.edu	37	1	43010889	43010889	+	Intron	DEL	A	-	-	rs141597374		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43010889delA	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron|CCDC30_uc010oju.1_Intron|CCDC30_uc001chp.2_Intron	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30												0						TGCCTATGGTAAAAAAAAAAT	0.279													2	4	---	---	---	---	
DNAJB4	11080	broad.mit.edu	37	1	78471050	78471050	+	Intron	DEL	T	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78471050delT	uc001dij.2	+						DNAJB4_uc010orn.1_Intron	NM_007034	NP_008965	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4						protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding				0						gctctgtctcttttttttttt	0.199													11	5	---	---	---	---	
INTS3	65123	broad.mit.edu	37	1	153731751	153731751	+	Intron	DEL	A	-	-	rs71584136		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153731751delA	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron|INTS3_uc010peb.1_Intron|INTS3_uc001fcw.2_Intron|INTS3_uc010pec.1_Intron	NM_023015	NP_075391	Q68E01	INT3_HUMAN	integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ccctgtctggaaaaaaaaaaa	0.219													2	6	---	---	---	---	
MAEL	84944	broad.mit.edu	37	1	166973742	166973742	+	Intron	DEL	A	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166973742delA	uc001gdy.1	+						MAEL_uc001gdz.1_Intron|MAEL_uc009wvf.1_Intron	NM_032858	NP_116247	Q96JY0	MAEL_HUMAN	maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1						TGAAGACTGCAAAAGCTAAAC	0.313													1	5	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215814187	215814187	+	Intron	DEL	A	-	-	rs138417166		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215814187delA	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CAATCCaaacaaaaaaaaaaa	0.318										HNSCC(13;0.011)			8	4	---	---	---	---	
FBXO11	80204	broad.mit.edu	37	2	48067087	48067087	+	Intron	DEL	T	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48067087delT	uc010fbl.2	-						FBXO11_uc002rwe.2_Intron|FBXO11_uc002rwf.2_Intron|FBXO11_uc002rwg.1_Intron	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1						ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATGTGGAAGAttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133018715	133018715	+	IGR	DEL	T	-	-	rs66735050		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133018715delT								NCRNA00164 (3173 upstream) : GPR39 (155432 downstream)																							GGCGGGGTGGTGGGGGGTGCC	0.532													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75264910	75264913	+	IGR	DEL	AAAA	-	-	rs35563675		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75264910_75264913delAAAA								CNTN3 (694567 upstream) : FAM86D (205792 downstream)																							TGATGACCCCaaaaaaaaaaaaaa	0.294													5	3	---	---	---	---	
RUVBL1	8607	broad.mit.edu	37	3	127823955	127823955	+	Intron	DEL	T	-	-	rs71615963		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127823955delT	uc003ekh.2	-						RUVBL1_uc003ekf.2_Intron|RUVBL1_uc010hss.2_Intron	NM_003707	NP_003698	Q9Y265	RUVB1_HUMAN	RuvB-like 1						cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)		GAAATGCAACttttttttttt	0.169													4	2	---	---	---	---	
RAB7A	7879	broad.mit.edu	37	3	128517689	128517689	+	Intron	DEL	G	-	-	rs35124528		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128517689delG	uc003eks.1	+						RAB7A_uc010hsv.1_Intron|RAB7A_uc003ekt.2_Intron	NM_004637	NP_004628	P51149	RAB7A_HUMAN	RAB7, member RAS oncogene family						endocytosis|endosome to lysosome transport|epidermal growth factor catabolic process|protein transport|small GTPase mediated signal transduction	Golgi apparatus|late endosome|lysosome|melanosome|phagocytic vesicle	GDP binding|GTP binding|GTPase activity|protein binding				0				GBM - Glioblastoma multiforme(114;0.231)		aaaaaaaaaagaATCCCAGGA	0.209													6	5	---	---	---	---	
ZNF876P	642280	broad.mit.edu	37	4	247254	247255	+	Intron	DEL	TA	-	-	rs34738994		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:247254_247255delTA	uc010iba.2	+							NR_027481				Homo sapiens cDNA clone IMAGE:4828836.												0						TTTGTATAAGTATATATATATT	0.134													2	5	---	---	---	---	
IDUA	3425	broad.mit.edu	37	4	997672	997672	+	Intron	DEL	G	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:997672delG	uc003gby.2	+						IDUA_uc003gbz.2_Intron|IDUA_uc003gca.2_Intron	NM_000203	NP_000194	P35475	IDUA_HUMAN	alpha-L-iduronidase precursor						disaccharide metabolic process	lysosome	cation binding|L-iduronidase activity				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)		Laronidase(DB00090)	AGAGTGCCCAGGGGCTGGGGA	0.677													25	15	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20544485	20544486	+	Intron	DEL	GC	-	-	rs68143710		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20544485_20544486delGC	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						gtgtgtgtgtgCGctataagat	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	38253858	38253858	+	IGR	DEL	T	-	-	rs71954573		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38253858delT								TBC1D1 (113065 upstream) : FLJ13197 (360464 downstream)																							CTGCCCCCGCttttttttttg	0.249													4	5	---	---	---	---	
TNIP3	79931	broad.mit.edu	37	4	122082481	122082482	+	Intron	INS	-	T	T	rs149582125	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122082481_122082482insT	uc010ing.2	-						TNIP3_uc010inh.2_Intron|TNIP3_uc011cgj.1_Intron|TNIP3_uc010ini.2_Intron	NM_024873	NP_079149	Q96KP6	TNIP3_HUMAN	TNFAIP3 interacting protein 3											ovary(1)	1						GTTGCGATTTAAAAAATACCTG	0.361													6	6	---	---	---	---	
PET112L	5188	broad.mit.edu	37	4	152625232	152625232	+	Intron	DEL	C	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152625232delC	uc003iml.2	-						PET112L_uc003imm.3_Intron	NM_004564	NP_004555	O75879	GATB_HUMAN	PET112-like precursor							mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	ACAGAATGATCTTTTTTTTTT	0.343													6	3	---	---	---	---	
HSD17B4	3295	broad.mit.edu	37	5	118861408	118861409	+	Intron	INS	-	T	T	rs12659452		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118861408_118861409insT	uc003ksj.2	+						HSD17B4_uc011cwg.1_Intron|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Intron|HSD17B4_uc003ksk.3_Intron|HSD17B4_uc011cwj.1_Intron|HSD17B4_uc010jcn.1_Intron|HSD17B4_uc010jco.1_Intron	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)	ttcctgttttgttttttttttt	0.213													4	2	---	---	---	---	
MRS2	57380	broad.mit.edu	37	6	24416484	24416484	+	Intron	DEL	T	-	-	rs35657958		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24416484delT	uc003neb.2	+						MRS2_uc003nea.2_Intron|MRS2_uc011djl.1_Intron|MRS2_uc011djm.1_Intron|MRS2_uc011djn.1_Intron|MRS2_uc003nec.2_Intron	NM_020662	NP_065713	Q9HD23	MRS2_HUMAN	MRS2-like, magnesium homeostasis factor						ion transport	integral to membrane|mitochondrial inner membrane					0						AATACTCAACttttttttttt	0.139													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27237169	27237169	+	IGR	DEL	A	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27237169delA								PRSS16 (12920 upstream) : POM121L2 (39673 downstream)																							aaacaaaaacaaaaaaaaaCC	0.303													3	3	---	---	---	---	
MACC1	346389	broad.mit.edu	37	7	20229372	20229373	+	Intron	DEL	AA	-	-	rs72309121		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20229372_20229373delAA	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						acaaacacataaacacacacac	0.163													6	4	---	---	---	---	
WBSCR27	155368	broad.mit.edu	37	7	73249451	73249456	+	Intron	DEL	CTCTCC	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73249451_73249456delCTCTCC	uc003tzj.2	-						RFC2_uc011kfa.1_Intron	NM_152559	NP_689772	Q8N6F8	WBS27_HUMAN	Williams-Beuren syndrome chromosome region 27											central_nervous_system(1)	1		Lung NSC(55;0.159)				TGGGGACGCTctctccctctccctct	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141479343	141479344	+	IGR	DEL	TT	-	-	rs3840580		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141479343_141479344delTT								TAS2R4 (155 upstream) : TAS2R5 (10673 downstream)																							CATTCTGTAATTTTTTTTTTTT	0.337													6	5	---	---	---	---	
RP1L1	94137	broad.mit.edu	37	8	10479845	10479846	+	Intron	INS	-	A	A	rs34315849		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10479845_10479846insA	uc003wtc.2	-							NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1						intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)		aaaacaaagccaaaaaaaaaaa	0.173													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	11778296	11778296	+	IGR	DEL	G	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11778296delG								CTSB (52650 upstream) : DEFB136 (53152 downstream)																							CTAGAAAAGAGGGTTGAAAAA	0.418													2	4	---	---	---	---	
STAU2	27067	broad.mit.edu	37	8	74585136	74585137	+	Intron	INS	-	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74585136_74585137insA	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_Intron|STAU2_uc003xzp.2_Intron|STAU2_uc011lfi.1_Intron|STAU2_uc003xzq.2_Intron|STAU2_uc010lzk.2_Intron|STAU2_uc010lzl.1_Intron|STAU2_uc003xzs.2_Intron|STAU2_uc003xzr.2_Intron	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			TGGGGTAGGGGAAAAAAAAAAA	0.356													4	3	---	---	---	---	
LAPTM4B	55353	broad.mit.edu	37	8	98817905	98817906	+	Intron	INS	-	A	A	rs145779188	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98817905_98817906insA	uc003yia.2	+						LAPTM4B_uc010mbg.2_Intron	NM_018407	NP_060877	Q86VI4	LAP4B_HUMAN	lysosomal associated transmembrane protein 4						transport	endomembrane system|integral to membrane	protein binding			skin(1)	1	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)			CTTACCCACTTAAAAATGATTG	0.381													4	2	---	---	---	---	
HAUS6	54801	broad.mit.edu	37	9	19056596	19056596	+	Intron	DEL	T	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19056596delT	uc003znk.2	-						HAUS6_uc011lmz.1_Intron	NM_017645	NP_060115	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2						CCCAGAGTACttttttttttt	0.169													4	2	---	---	---	---	
IARS	3376	broad.mit.edu	37	9	95055581	95055585	+	Intron	DEL	AATAA	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95055581_95055585delAATAA	uc004art.1	-						IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron|SNORA84_uc010mqv.2_5'Flank	NM_013417	NP_038203	P41252	SYIC_HUMAN	isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)	acggtacatcaataaaataagtatc	0.078													9	5	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101150902	101150905	+	Intron	DEL	TGTG	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101150902_101150905delTGTG	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	GCCTGGCCTCtgtgtgtgtgtgtg	0.230													6	3	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119748439	119748440	+	Intron	INS	-	C	C	rs150523837	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119748439_119748440insC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						TGTCCAGGCTGCCCCCCCCCAC	0.584													4	2	---	---	---	---	
RC3H2	54542	broad.mit.edu	37	9	125667592	125667594	+	5'Flank	DEL	CCT	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125667592_125667594delCCT	uc010mwc.1	-						RC3H2_uc004bnc.2_5'Flank|RC3H2_uc004bne.3_5'Flank|RC3H2_uc011lzg.1_5'Flank	NM_001100588	NP_001094058	Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type zinc finger domains 2							cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(2)|lung(2)	4						tccacctccgcctcctcctcctc	0.488													4	2	---	---	---	---	
FBXO18	84893	broad.mit.edu	37	10	5945294	5945295	+	Intron	INS	-	T	T			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5945294_5945295insT	uc001iis.2	+						FBXO18_uc001iir.2_Intron|FBXO18_uc009xig.2_Intron|FBXO18_uc001iit.2_Intron	NM_178150	NP_835363	Q8NFZ0	FBX18_HUMAN	F-box only protein, helicase, 18 isoform 2						DNA repair	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(2)|skin(1)	3						TTTCCATGAAGttttttttttt	0.163													4	2	---	---	---	---	
ACTR1A	10121	broad.mit.edu	37	10	104241138	104241139	+	Intron	INS	-	A	A	rs138360884	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104241138_104241139insA	uc001kvv.2	-						ACTR1A_uc010qqn.1_Intron|ACTR1A_uc010qqo.1_Intron	NM_005736	NP_005727	P61163	ACTZ_HUMAN	ARP1 actin-related protein 1 homolog A,						G2/M transition of mitotic cell cycle|vesicle-mediated transport	centrosome|cytosol|dynactin complex	ATP binding			central_nervous_system(1)	1		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)		GGGACTATTGGGGGGGGCAGGG	0.589													2	4	---	---	---	---	
NRAP	4892	broad.mit.edu	37	10	115355171	115355172	+	Intron	INS	-	C	C	rs140708526	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115355171_115355172insC	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		gtttagctcagcccattaccat	0.223													4	4	---	---	---	---	
C10orf84	63877	broad.mit.edu	37	10	120095476	120095476	+	Intron	DEL	T	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120095476delT	uc001ldo.2	-						C10orf84_uc010qss.1_Intron	NM_022063	NP_071346	Q9H8W3	F204A_HUMAN	hypothetical protein LOC63877												0		Colorectal(252;0.101)		all cancers(201;0.0244)		GTGGTTTGGGTTTTTTTTTTT	0.353													5	4	---	---	---	---	
DEAF1	10522	broad.mit.edu	37	11	680002	680003	+	Intron	INS	-	ACCAGGATG	ACCAGGATG	rs138147673	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:680002_680003insACCAGGATG	uc001lqq.1	-						DEAF1_uc009ycf.1_Intron	NM_021008	NP_066288	O75398	DEAF1_HUMAN	deformed epidermal autoregulatory factor 1						embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CACAGGAGAAAACCAGGATGGC	0.520													4	2	---	---	---	---	
EIF3M	10480	broad.mit.edu	37	11	32609935	32609942	+	Intron	DEL	AAAAAAAA	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32609935_32609942delAAAAAAAA	uc001mtu.2	+						EIF3M_uc010ref.1_Intron	NM_006360	NP_006351	Q7L2H7	EIF3M_HUMAN	eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)|breast(1)|skin(1)	3	Breast(20;0.109)					acttcatctgaaaaaaaaaaaaaaaaaa	0.125													5	3	---	---	---	---	
KDM5A	5927	broad.mit.edu	37	12	459613	459613	+	Intron	DEL	G	-	-	rs72516305		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:459613delG	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						aaaaaaaaaaGAGTTAAATAA	0.119			T 	NUP98	AML								3	4	---	---	---	---	
ACSM4	341392	broad.mit.edu	37	12	7459444	7459444	+	Intron	DEL	A	-	-	rs140474774		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7459444delA	uc001qsx.1	+							NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0						TACAGAAGACAAAAAAAAAAA	0.214													3	3	---	---	---	---	
ABCC9	10060	broad.mit.edu	37	12	21982125	21982125	+	Intron	DEL	C	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21982125delC	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	AAATAGATTTCtttttttttt	0.179													8	5	---	---	---	---	
PRKAB1	5564	broad.mit.edu	37	12	120110460	120110461	+	Intron	DEL	AG	-	-	rs150497180		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120110460_120110461delAG	uc009zwu.2	+						PRKAB1_uc001txg.2_Intron	NM_006253	NP_006244	Q9Y478	AAKB1_HUMAN	AMP-activated protein kinase beta 1						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol					0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Adenosine monophosphate(DB00131)|Metformin(DB00331)	TACAGAAGAAAGAGAATATTTC	0.342													5	5	---	---	---	---	
DNAH10	196385	broad.mit.edu	37	12	124315343	124315343	+	Intron	DEL	T	-	-	rs7976816		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124315343delT	uc001uft.3	+							NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		aaaaaaaaaattagctgagcg	0.100													4	5	---	---	---	---	
CCNA1	8900	broad.mit.edu	37	13	37007495	37007498	+	Intron	DEL	TTGA	-	-	rs67424671		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37007495_37007498delTTGA	uc001uvr.3	+						CCNA1_uc010teo.1_Intron|CCNA1_uc010abq.2_Intron|CCNA1_uc010abp.2_Intron|CCNA1_uc001uvs.3_Intron|CCNA1_uc010abr.2_Intron	NM_003914	NP_003905	P78396	CCNA1_HUMAN	cyclin A1 isoform a						cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding			lung(2)|skin(2)|ovary(1)	5		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		TACAGGAAAGTTGATTGATTTATt	0.255													4	3	---	---	---	---	
SLC15A1	6564	broad.mit.edu	37	13	99336799	99336800	+	3'UTR	INS	-	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99336799_99336800insA	uc001vno.2	-	23						NM_005073	NP_005064	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide						digestion|protein transport	integral to plasma membrane|membrane fraction	peptide:hydrogen symporter activity			ovary(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Cefadroxil(DB01140)|Ceftibuten(DB01415)|Cyclacillin(DB01000)	aactctgtctcaaaaaaaaaaa	0.124													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22979847	22979848	+	Intron	INS	-	A	A	rs113534338		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22979847_22979848insA	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001weh.1_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wen.1_Intron|uc001weo.2_Intron|uc001wep.2_Intron|uc001weq.2_Intron|uc001wer.2_Intron|uc001wet.2_Intron|uc001weu.2_Intron|uc001wev.2_Intron|uc001wew.2_Intron|uc010tmv.1_Intron|uc001wez.2_Intron|uc010ajx.1_Intron|uc001wfb.1_Intron|uc001wfd.1_Intron|uc001wfe.2_Intron|uc001wfg.2_Intron|uc001wfh.1_5'Flank|uc001wfi.2_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																		aaaaaaaaaggaaaaaaaaaaa	0.371													8	6	---	---	---	---	
NOVA1	4857	broad.mit.edu	37	14	27066713	27066713	+	5'UTR	DEL	C	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27066713delC	uc001wpy.2	-	1					NOVA1_uc001wpz.2_5'UTR|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_5'UTR	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1						locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)		tttcttttttctttttttttt	0.353													3	3	---	---	---	---	
PPM1A	5494	broad.mit.edu	37	14	60756378	60756379	+	Intron	INS	-	T	T	rs75155276		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60756378_60756379insT	uc010apn.2	+						PPM1A_uc001xew.3_Intron|PPM1A_uc001xey.3_Intron	NM_021003	NP_066283	P35813	PPM1A_HUMAN	protein phosphatase 1A isoform 1						cell cycle arrest|insulin receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein dephosphorylation|Wnt receptor signaling pathway	cytosol|nucleus|protein serine/threonine phosphatase complex	magnesium ion binding|manganese ion binding|protein serine/threonine phosphatase activity|signal transducer activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.046)		GGTCAACCTGATTTTTTTTTTT	0.243													4	2	---	---	---	---	
PDIA2	64714	broad.mit.edu	37	16	332559	332559	+	Intron	DEL	G	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:332559delG	uc002cgn.1	+						ARHGDIG_uc002cgm.1_Intron|PDIA2_uc010bqt.1_5'Flank|PDIA2_uc002cgo.1_5'Flank	NM_006849	NP_006840	Q13087	PDIA2_HUMAN	protein disulfide isomerase A2 precursor						apoptosis|cell redox homeostasis|glycerol ether metabolic process|protein folding|protein retention in ER lumen|response to hypoxia	endoplasmic reticulum lumen	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity|steroid binding			central_nervous_system(1)|skin(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GGAACGGGGCGGGGGGGGGAA	0.692													3	3	---	---	---	---	
NOMO2	283820	broad.mit.edu	37	16	18549712	18549712	+	Intron	DEL	A	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18549712delA	uc002dfe.2	-						NOMO2_uc002dff.2_Intron|NOMO2_uc010bvx.2_Intron	NM_001004060	NP_001004060	Q5JPE7	NOMO2_HUMAN	nodal modulator 2 isoform 1							endoplasmic reticulum membrane|integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			skin(1)	1						tctgtctctcaaaaaaaaaaa	0.174													8	5	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	21092702	21092703	+	Intron	INS	-	A	A	rs143126523		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21092702_21092703insA	uc010vbe.1	-							NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		CAAAGAACATTAAAAAAAAAAA	0.198													5	5	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2888574	2888574	+	Intron	DEL	T	-	-	rs71377564		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2888574delT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						AACAGTGATGTTTTTTTTTTT	0.398													6	3	---	---	---	---	
SUZ12	23512	broad.mit.edu	37	17	30325566	30325568	+	Intron	DEL	ATC	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30325566_30325568delATC	uc002hgs.2	+						SUZ12_uc002hgt.2_Intron	NM_015355	NP_056170	Q15022	SUZ12_HUMAN	joined to JAZF1						negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				TGCTTCTTTAATCATCTTTTATT	0.256			T	JAZF1	endometrial stromal tumours								5	6	---	---	---	---	
CACNG4	27092	broad.mit.edu	37	17	64961302	64961305	+	Intron	DEL	ATAT	-	-	rs144703660	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64961302_64961305delATAT	uc002jft.1	+							NM_014405	NP_055220	Q9UBN1	CCG4_HUMAN	voltage-dependent calcium channel gamma-4						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane	voltage-gated calcium channel activity			central_nervous_system(1)	1	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			acacacacacatatacacacgcgc	0.471													5	3	---	---	---	---	
CLUL1	27098	broad.mit.edu	37	18	626917	626918	+	Intron	INS	-	AG	AG			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:626917_626918insAG	uc002kkp.2	+						CLUL1_uc010wys.1_Intron|CLUL1_uc002kkq.2_Intron	NM_014410	NP_055225	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal) precursor						cell death	extracellular region				ovary(2)	2						gaaagaaagaaagaaagaaaga	0.000													2	4	---	---	---	---	
ZCCHC2	54877	broad.mit.edu	37	18	60212014	60212015	+	Intron	DEL	TG	-	-	rs150177822		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60212014_60212015delTG	uc002lip.3	+						ZCCHC2_uc002lio.2_Intron	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2						cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding			lung(1)|prostate(1)	2						CCATATAATATGTGTGTTTTTT	0.332													5	6	---	---	---	---	
PIP5K1C	23396	broad.mit.edu	37	19	3642656	3642657	+	Intron	INS	-	A	A	rs139835481	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3642656_3642657insA	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type						axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		TGTTTTAAGTTAAAAAAAAAAC	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	9324429	9324431	+	IGR	DEL	AAC	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9324429_9324431delAAC								OR7D2 (24936 upstream) : OR7D4 (144 downstream)																							caataacaataacaacaacaaaC	0.158													6	4	---	---	---	---	
GIPC1	10755	broad.mit.edu	37	19	14590164	14590165	+	Intron	INS	-	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14590164_14590165insA	uc002myt.2	-						GIPC1_uc002myu.2_Intron|GIPC1_uc002myv.2_Intron|GIPC1_uc002myw.2_Intron|GIPC1_uc002myx.2_Intron|GIPC1_uc002myy.2_Intron	NM_005716	NP_005707	O14908	GIPC1_HUMAN	regulator of G-protein signalling 19 interacting						endothelial cell migration|G-protein coupled receptor protein signaling pathway|glutamate secretion|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|protein targeting|regulation of protein stability|regulation of synaptic plasticity|synaptic transmission	cell cortex|dendritic shaft|dendritic spine|membrane fraction|soluble fraction|synaptic vesicle|vesicle membrane	actin binding|myosin binding|protein homodimerization activity|receptor binding				0						gactctgtctcaaaaaaaaaaa	0.292													4	2	---	---	---	---	
ZNF99	7652	broad.mit.edu	37	19	22952563	22952563	+	Intron	DEL	A	-	-	rs78722239		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22952563delA	uc010xrh.1	-							NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				actctgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36913800	36913800	+	IGR	DEL	A	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36913800delA								ZFP82 (4250 upstream) : ZNF566 (22222 downstream)																							CTTTGTCATTAAAAAAAAAAA	0.194													10	5	---	---	---	---	
ISOC2	79763	broad.mit.edu	37	19	55964546	55964547	+	3'UTR	INS	-	C	C	rs139098245	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55964546_55964547insC	uc002qlb.2	-	6					ISOC2_uc002qla.2_3'UTR|ISOC2_uc002qlc.2_3'UTR	NM_001136201	NP_001129673	Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2 isoform 1						protein destabilization	mitochondrion|nucleus	catalytic activity|protein binding			ovary(1)	1	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		GCAGCACCCTGCCCCCCCCACA	0.639													2	5	---	---	---	---	
DPM1	8813	broad.mit.edu	37	20	49565355	49565355	+	Intron	DEL	A	-	-	rs76899294		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49565355delA	uc002xvw.1	-						DPM1_uc002xvv.1_5'Flank|DPM1_uc002xvx.1_Intron	NM_003859	NP_003850	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase 1						C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding			ovary(1)	1						TTGCCAAAAGAAAAAAAAAAG	0.189													12	6	---	---	---	---	
C21orf81	391267	broad.mit.edu	37	21	15347257	15347258	+	Intron	INS	-	A	A	rs80199214		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15347257_15347258insA	uc002yji.2	-							NR_027270				Homo sapiens C21orf81 protein (C21orf81) mRNA, complete cds.												0						ACCCTGCACAGAAAAAAAGTTG	0.307													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44756088	44756096	+	IGR	DEL	CACCACCAA	-	-	rs72268009	by1000genomes	TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44756088_44756096delCACCACCAA								CRYAA (163175 upstream) : SIK1 (78302 downstream)																							tcaccaccaccaccaccaacaccaccacc	0.000													4	2	---	---	---	---	
POLR2F	5435	broad.mit.edu	37	22	38355725	38355725	+	Intron	DEL	A	-	-	rs72332168		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38355725delA	uc003aul.2	+						POLR2F_uc010gxi.2_Intron|POLR2F_uc003aum.2_Intron	NM_021974	NP_068809	P61218	RPAB2_HUMAN	DNA directed RNA polymerase II polypeptide F						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex|nucleolus	DNA binding|DNA-directed RNA polymerase activity			breast(1)	1	Melanoma(58;0.045)					GAAAAACGATAAAAAAAAAAA	0.189													3	6	---	---	---	---	
CXorf59	286464	broad.mit.edu	37	X	36163179	36163180	+	3'UTR	DEL	TA	-	-	rs112151442		TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36163179_36163180delTA	uc004ddk.1	+	11						NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464							integral to membrane				central_nervous_system(1)	1						aattcccgtttatatatatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	82130968	82130969	+	IGR	INS	-	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82130968_82130969insA								None (None upstream) : POU3F4 (632300 downstream)																							CATTATAAACTAAAAAAAAAAa	0.139													3	3	---	---	---	---	
CXorf66	347487	broad.mit.edu	37	X	139047824	139047824	+	5'Flank	DEL	T	-	-			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139047824delT	uc004fbb.2	-							NM_001013403	NP_001013421	Q5JRM2	CX066_HUMAN	hypothetical protein LOC347487 precursor							integral to membrane					0						ACCAAATGACttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13538862	13538863	+	IGR	INS	-	A	A			TCGA-CJ-4901-01A-01D-1429-08	TCGA-CJ-4901-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13538862_13538863insA								None (None upstream) : None (None downstream)																							aacaatacaccaaaatggggtt	0.089													4	2	---	---	---	---	
