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
KIF1B	23095	broad.mit.edu	37	1	10421772	10421772	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10421772C>T	uc001aqx.3	+	40	4395	c.4193C>T	c.(4192-4194)GCT>GTT	p.A1398V	KIF1B_uc001aqw.3_Missense_Mutation_p.A1352V|KIF1B_uc001aqy.2_Missense_Mutation_p.A1372V|KIF1B_uc001aqz.2_Missense_Mutation_p.A1398V|KIF1B_uc001ara.2_Missense_Mutation_p.A1358V|KIF1B_uc001arb.2_Missense_Mutation_p.A1384V	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	1398					anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		ATCCAGCCGGCTGTCATCACC	0.522													50	98	---	---	---	---	PASS
RNF186	54546	broad.mit.edu	37	1	20141319	20141319	+	Silent	SNP	G	C	C	rs138663359		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20141319G>C	uc001bcr.2	-	1	453	c.276C>G	c.(274-276)CCC>CCG	p.P92P		NM_019062	NP_061935	Q9NXI6	RN186_HUMAN	ring finger protein 186	92						integral to membrane	zinc ion binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;7.77e-05)|Kidney(64;0.000162)|GBM - Glioblastoma multiforme(114;0.00036)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGAGGCCCCCGGGGACGGCGG	0.667													20	33	---	---	---	---	PASS
PTPRU	10076	broad.mit.edu	37	1	29611375	29611375	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29611375G>T	uc001bru.2	+	14	2422	c.2312G>T	c.(2311-2313)CGC>CTC	p.R771L	PTPRU_uc001brv.2_Missense_Mutation_p.R771L|PTPRU_uc001brw.2_Missense_Mutation_p.R771L|PTPRU_uc009vtq.2_Missense_Mutation_p.R771L|PTPRU_uc009vtr.2_Missense_Mutation_p.R771L	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	771	Mediates interaction with CTNNB1 (By similarity).|Cytoplasmic (Potential).				canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GTCATCATCCGCAAAGGGTGA	0.597													11	53	---	---	---	---	PASS
ARTN	9048	broad.mit.edu	37	1	44401676	44401676	+	Intron	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44401676G>A	uc001cks.2	+						ARTN_uc001ckv.2_Intron|ARTN_uc001ckt.2_Intron|ARTN_uc001cku.2_Intron|ARTN_uc001ckw.2_Missense_Mutation_p.R8Q	NM_057091	NP_476432	Q5T4W7	ARTN_HUMAN	neurotrophic factor artemin isoform 1 precursor						axon guidance|neuroblast proliferation|signal transduction	extracellular region	growth factor activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				ATCTCAGCCCGAGGACAGCCC	0.637													9	5	---	---	---	---	PASS
LRIG2	9860	broad.mit.edu	37	1	113641369	113641369	+	Silent	SNP	T	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113641369T>A	uc001edf.1	+	9	1332	c.1134T>A	c.(1132-1134)GCT>GCA	p.A378A	LRIG2_uc009wgn.1_Silent_p.A275A	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	378	LRR 13.|Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TAGAAGATGCTAGTGAAGCCT	0.353													6	119	---	---	---	---	PASS
GUK1	2987	broad.mit.edu	37	1	228329472	228329472	+	Intron	SNP	C	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228329472C>G	uc001hsh.2	+						GUK1_uc001hsi.2_Intron|GUK1_uc001hsj.2_Intron|GUK1_uc010pvv.1_5'Flank	NM_000858	NP_000849	Q16774	KGUA_HUMAN	guanylate kinase 1 isoform b						nucleobase, nucleoside and nucleotide interconversion|purine nucleotide metabolic process	cytosol	ATP binding|guanylate kinase activity				0		Prostate(94;0.0405)				GGATCTGCGCCGGCGGCTCCC	0.627													3	14	---	---	---	---	PASS
FNDC4	64838	broad.mit.edu	37	2	27716993	27716993	+	Silent	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27716993A>G	uc002rkx.2	-	4	664	c.258T>C	c.(256-258)AAT>AAC	p.N86N	GCKR_uc002rky.2_5'Flank|GCKR_uc010ezd.2_5'Flank|GCKR_uc010ylu.1_5'Flank	NM_022823	NP_073734	Q9H6D8	FNDC4_HUMAN	fibronectin type III domain containing 4	86	Extracellular (Potential).|Fibronectin type-III.					integral to membrane					0	Acute lymphoblastic leukemia(172;0.155)					GCCCGGGGCCATTCTGCCGCT	0.632													9	18	---	---	---	---	PASS
MCEE	84693	broad.mit.edu	37	2	71351338	71351338	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71351338C>A	uc002shs.2	-	2	421	c.376G>T	c.(376-378)GAG>TAG	p.E126*		NM_032601	NP_115990	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase precursor	126					fatty acid beta-oxidation|L-methylmalonyl-CoA metabolic process	mitochondrial matrix	methylmalonyl-CoA epimerase activity			ovary(1)	1						TAAAATACCTCGATGCAGATG	0.348													9	51	---	---	---	---	PASS
CDCA7	83879	broad.mit.edu	37	2	174223477	174223477	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174223477T>A	uc002uid.1	+	2	190	c.59T>A	c.(58-60)TTC>TAC	p.F20Y	CDCA7_uc002uic.1_Missense_Mutation_p.F20Y|CDCA7_uc010zej.1_Missense_Mutation_p.F20Y|CDCA7_uc010zek.1_Intron	NM_145810	NP_665809	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7 isoform 2	20					regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.116)			TTAAAGAAATTCAGATATGTG	0.368													15	106	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179435668	179435668	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179435668G>C	uc010zfg.1	-	275	67711	c.67487C>G	c.(67486-67488)ACT>AGT	p.T22496S	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T16191S|TTN_uc010zfi.1_Missense_Mutation_p.T16124S|TTN_uc010zfj.1_Missense_Mutation_p.T15999S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23423							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)			TTCAAAATGAGTGTCAATAAT	0.423													39	265	---	---	---	---	PASS
BZW1	9689	broad.mit.edu	37	2	201684787	201684787	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201684787A>C	uc010zhg.1	+	10	1197	c.1145A>C	c.(1144-1146)TAT>TCT	p.Y382S	BZW1_uc002uwc.2_Intron	NM_014670	NP_055485	Q7L1Q6	BZW1_HUMAN	basic leucine zipper and W2 domains 1	350	W2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	protein binding				0						GAGTATTGCTATGACAACATT	0.343													3	7	---	---	---	---	PASS
LAMB2	3913	broad.mit.edu	37	3	49169156	49169156	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49169156T>A	uc003cwe.2	-	5	759	c.460A>T	c.(460-462)ACA>TCA	p.T154S	LAMB2_uc003cwf.1_Missense_Mutation_p.T154S	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	154	Laminin N-terminal.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGGCGAAATGTCTGGGTAGGG	0.542													11	29	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52643828	52643828	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643828T>A	uc003des.2	-	16	2080	c.2068A>T	c.(2068-2070)AGA>TGA	p.R690*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.R690*|PBRM1_uc003der.2_Nonsense_Mutation_p.R658*|PBRM1_uc003det.2_Nonsense_Mutation_p.R705*|PBRM1_uc003deu.2_Nonsense_Mutation_p.R705*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.R690*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.R690*|PBRM1_uc003dey.2_Nonsense_Mutation_p.R690*|PBRM1_uc003dez.1_Nonsense_Mutation_p.R690*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.R603*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.R36*|PBRM1_uc003dfc.2_Nonsense_Mutation_p.R57*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	690	Bromo 5.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AACTCAGATCTAGAGGGAAGC	0.428			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								73	83	---	---	---	---	PASS
ACTR8	93973	broad.mit.edu	37	3	53908276	53908276	+	Silent	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53908276G>A	uc003dhd.2	-	8	1086	c.1027C>T	c.(1027-1029)CTG>TTG	p.L343L	ACTR8_uc003dhb.2_Intron|ACTR8_uc003dhc.2_Silent_p.L232L	NM_022899	NP_075050	Q9H981	ARP8_HUMAN	actin-related protein 8	343					cell division|DNA recombination|DNA repair|mitosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex	protein binding			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		AGGTGTTGCAGAAGAAGACAA	0.358													27	63	---	---	---	---	PASS
ACTR8	93973	broad.mit.edu	37	3	53908279	53908279	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53908279G>A	uc003dhd.2	-	8	1083	c.1024C>T	c.(1024-1026)CTT>TTT	p.L342F	ACTR8_uc003dhb.2_Intron|ACTR8_uc003dhc.2_Missense_Mutation_p.L231F	NM_022899	NP_075050	Q9H981	ARP8_HUMAN	actin-related protein 8	342					cell division|DNA recombination|DNA repair|mitosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex	protein binding			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		TGTTGCAGAAGAAGACAATCC	0.358													27	65	---	---	---	---	PASS
RAB7A	7879	broad.mit.edu	37	3	128516883	128516883	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128516883A>T	uc003eks.1	+	3	383	c.151A>T	c.(151-153)ATG>TTG	p.M51L	RAB7A_uc010hsv.1_Missense_Mutation_p.M51L|RAB7A_uc003ekt.2_Missense_Mutation_p.M27L	NM_004637	NP_004628	P51149	RAB7A_HUMAN	RAB7, member RAS oncogene family	51					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)		CAAGGAGGTGATGGTGGATGA	0.443													37	84	---	---	---	---	PASS
ACPL2	92370	broad.mit.edu	37	3	141011820	141011820	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141011820G>T	uc003etu.2	+	8	1515	c.1216G>T	c.(1216-1218)GAG>TAG	p.E406*	ACPL2_uc003etv.2_Nonsense_Mutation_p.E406*|ACPL2_uc011bna.1_Nonsense_Mutation_p.E368*|ACPL2_uc011bnb.1_Nonsense_Mutation_p.E389*	NM_152282	NP_689495	Q8TE99	ACPL2_HUMAN	acid phosphatase-like 2 precursor	406						extracellular region	acid phosphatase activity			skin(1)	1						GTTGATCTTTGAGCTTTGGCA	0.507													73	170	---	---	---	---	PASS
TIPARP	25976	broad.mit.edu	37	3	156421359	156421359	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156421359T>A	uc003fav.2	+	5	1642	c.1394T>A	c.(1393-1395)GTC>GAC	p.V465D	TIPARP_uc003faw.2_Missense_Mutation_p.V465D	NM_015508	NP_056323	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	465	PARP catalytic.						NAD+ ADP-ribosyltransferase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|breast(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TTCATCCAAGTCCCTGTTTCT	0.383													21	141	---	---	---	---	PASS
FYTTD1	84248	broad.mit.edu	37	3	197476818	197476818	+	5'UTR	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197476818C>T	uc003fyi.2	+	1					KIAA0226_uc003fyd.3_5'Flank|KIAA0226_uc003fyf.2_5'Flank|FYTTD1_uc011bui.1_Intron|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_5'Flank	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1						mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		TGTCCGCGCCCGCTCTCGGCG	0.726													6	14	---	---	---	---	PASS
WDR19	57728	broad.mit.edu	37	4	39245924	39245924	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39245924C>A	uc003gtv.2	+	22	2632	c.2478C>A	c.(2476-2478)GAC>GAA	p.D826E	WDR19_uc011byi.1_Missense_Mutation_p.D666E|WDR19_uc003gtw.1_Missense_Mutation_p.D423E	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	826					cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						GAATGGGAGACATACGTCGAG	0.468													8	172	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69870535	69870535	+	3'UTR	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69870535C>A	uc011cao.1	-	9					UGT2B10_uc011can.1_3'UTR			P36537	UDB10_HUMAN	RecName: Full=UDP-glucuronosyltransferase 2B28;          Short=UDPGT 2B28;          EC=2.4.1.17; Flags: Precursor;						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5						TGAAGTATCCCTATCTATCAG	0.333													18	28	---	---	---	---	PASS
HMGB2	3148	broad.mit.edu	37	4	174253220	174253220	+	3'UTR	SNP	A	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174253220A>T	uc011ckc.1	-	4					HMGB2_uc003ita.3_3'UTR|HMGB2_uc003itb.2_3'UTR|HMGB2_uc003itc.2_3'UTR	NM_001130689	NP_001124161	P26583	HMGB2_HUMAN	high-mobility group box 2						base-excision repair, DNA ligation|cell chemotaxis|cellular response to lipopolysaccharide|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|negative regulation of transcription, DNA-dependent|nucleosome assembly|phosphatidylinositol-mediated signaling|positive regulation of DNA binding|positive regulation of endothelial cell proliferation|positive regulation of erythrocyte differentiation|positive regulation of megakaryocyte differentiation|positive regulation of nuclease activity|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	condensed chromosome|extracellular space|nucleolus|nucleoplasm|perinuclear region of cytoplasm|protein complex	chemoattractant activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding|transcription regulatory region DNA binding				0		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		GCATCATTAAAGGATAGCCAT	0.214													20	213	---	---	---	---	PASS
IL6ST	3572	broad.mit.edu	37	5	55259325	55259325	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55259325T>C	uc003jqq.2	-	7	923	c.668A>G	c.(667-669)AAT>AGT	p.N223S	IL6ST_uc010iwb.2_Missense_Mutation_p.N223S|IL6ST_uc010iwc.2_Missense_Mutation_p.N57S|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_5'UTR|IL6ST_uc003jqr.2_Missense_Mutation_p.N223S	NM_002184	NP_002175	P40189	IL6RB_HUMAN	interleukin 6 signal transducer isoform 1	223	Extracellular (Potential).|Fibronectin type-III 2.				interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ATGTGGCGGATTGGGCTTCAC	0.294			O		hepatocellular ca								30	68	---	---	---	---	PASS
MAST4	375449	broad.mit.edu	37	5	66448561	66448561	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66448561C>G	uc003jut.1	+	24	2893	c.2825C>G	c.(2824-2826)TCC>TGC	p.S942C	MAST4_uc003juw.2_Missense_Mutation_p.S870C	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	1134	Ser-rich.					cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGCCGAGATTCCTCAGCAGCT	0.542													14	115	---	---	---	---	PASS
CD180	4064	broad.mit.edu	37	5	66479404	66479404	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66479404C>T	uc003juy.2	-	3	1415	c.1267G>A	c.(1267-1269)GAA>AAA	p.E423K		NM_005582	NP_005573	Q99467	CD180_HUMAN	CD180 molecule precursor	423	LRR 14.|Extracellular (Potential).				inflammatory response|innate immune response	integral to membrane|plasma membrane	receptor activity			ovary(1)	1		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		TCGAGGAGTTCTAGCTGAGGA	0.453													80	186	---	---	---	---	PASS
APBB3	10307	broad.mit.edu	37	5	139941387	139941387	+	Intron	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139941387G>A	uc003lgd.1	-						APBB3_uc003lgb.1_5'UTR|APBB3_uc003lgc.1_5'UTR|APBB3_uc003lge.1_Intron|APBB3_uc003lgf.1_Intron|APBB3_uc010jfp.1_Intron|APBB3_uc011czi.1_5'UTR|APBB3_uc010jfq.1_5'Flank	NM_133172	NP_573418	O95704	APBB3_HUMAN	amyloid beta precursor protein-binding, family							actin cytoskeleton|cytoplasm				ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGGAGTAGGGACATCAGGG	0.582													13	35	---	---	---	---	PASS
PCDHB7	56129	broad.mit.edu	37	5	140553926	140553926	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140553926G>A	uc003lit.2	+	1	1684	c.1510G>A	c.(1510-1512)GTC>ATC	p.V504I		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	504	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCCTCCCTGGTCTCCATCAA	0.682													13	124	---	---	---	---	PASS
TCERG1	10915	broad.mit.edu	37	5	145878250	145878250	+	Splice_Site	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145878250G>A	uc003lob.2	+	16	2422	c.2382_splice	c.e16+1	p.K794_splice	TCERG1_uc003loc.2_Splice_Site_p.K773_splice	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGTGAGAAGGTAAGATGGTT	0.403													6	62	---	---	---	---	PASS
SLC6A7	6534	broad.mit.edu	37	5	149583511	149583511	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149583511G>C	uc003lrr.2	+	10	1613	c.1242G>C	c.(1240-1242)GAG>GAC	p.E414D		NM_014228	NP_055043	Q99884	SC6A7_HUMAN	solute carrier family 6, member 7	414						integral to plasma membrane|membrane fraction	neurotransmitter:sodium symporter activity|proline:sodium symporter activity				0		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	TGACAGATGAGTTCCCATACT	0.512													8	64	---	---	---	---	PASS
GABRG2	2566	broad.mit.edu	37	5	161520982	161520982	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161520982G>T	uc003lyz.3	+	2	614	c.256G>T	c.(256-258)GGA>TGA	p.G86*	GABRG2_uc010jjc.2_Nonsense_Mutation_p.G86*|GABRG2_uc003lyy.3_Nonsense_Mutation_p.G86*|GABRG2_uc011dej.1_Translation_Start_Site	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	86	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	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;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)		GCCTGATATAGGAGGTTTGTT	0.388													26	192	---	---	---	---	PASS
SH3PXD2B	285590	broad.mit.edu	37	5	171789871	171789871	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171789871C>T	uc003mbr.2	-	7	601	c.430G>A	c.(430-432)GGT>AGT	p.G144S		NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	144					adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GTTTGGTCACCCCCTGTGGAT	0.547													18	90	---	---	---	---	PASS
JARID2	3720	broad.mit.edu	37	6	15496611	15496611	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15496611A>T	uc003nbj.2	+	7	1399	c.1155A>T	c.(1153-1155)AAA>AAT	p.K385N	JARID2_uc011diu.1_Missense_Mutation_p.K249N|JARID2_uc011div.1_Missense_Mutation_p.K213N|JARID2_uc011diw.1_Missense_Mutation_p.K347N	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	385					central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				GCAATGCAAAAACCCGCAAAC	0.547													51	85	---	---	---	---	PASS
AARS2	57505	broad.mit.edu	37	6	44270802	44270802	+	Splice_Site	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44270802C>A	uc010jza.1	-	16	2258	c.2255_splice	c.e16+1	p.T752_splice	SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron	NM_020745	NP_065796	Q5JTZ9	SYAM_HUMAN	alanyl-tRNA synthetase 2, mitochondrial						alanyl-tRNA aminoacylation	mitochondrion	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			ovary(1)	1	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		L-Alanine(DB00160)	GAGTGACTCACGTCCCACAGC	0.632													5	60	---	---	---	---	PASS
SEC63	11231	broad.mit.edu	37	6	108279240	108279240	+	5'UTR	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108279240C>A	uc003psc.3	-	1						NM_007214	NP_009145	Q9UGP8	SEC63_HUMAN	SEC63-like protein						protein folding|protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|receptor activity|unfolded protein binding			ovary(1)|skin(1)	2		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		CCTCGCTCTTCTCACCGCCGC	0.687													11	28	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117681074	117681074	+	Silent	SNP	T	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117681074T>C	uc003pxp.1	-	23	3745	c.3546A>G	c.(3544-3546)AGA>AGG	p.R1182R	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	1182	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CACTGATAACTCTTTCTGCTG	0.403			T	GOPC|ROS1	glioblastoma|NSCLC								36	110	---	---	---	---	PASS
THBS2	7058	broad.mit.edu	37	6	169648851	169648851	+	Silent	SNP	G	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169648851G>C	uc003qwt.2	-	4	518	c.270C>G	c.(268-270)CTC>CTG	p.L90L		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	90	TSP N-terminal.|Heparin-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGTCCTGCTTGAGCTGGGCCG	0.627													26	56	---	---	---	---	PASS
GNAI1	2770	broad.mit.edu	37	7	79764504	79764504	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79764504A>T	uc003uhb.1	+	1	365	c.28A>T	c.(28-30)AAG>TAG	p.K10*	GNAI1_uc011kgt.1_5'Flank	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	10					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CGCCGAGGACAAGGCGGCGGT	0.657													8	14	---	---	---	---	PASS
RBM28	55131	broad.mit.edu	37	7	127975595	127975595	+	Splice_Site	SNP	A	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127975595A>C	uc003vmp.2	-	8	1061	c.946_splice	c.e8+1	p.A316_splice	RBM28_uc003vmo.2_Intron|RBM28_uc011koj.1_Splice_Site_p.A175_splice|RBM28_uc011kok.1_Splice_Site_p.A263_splice	NM_018077	NP_060547	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28						mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2						ATCCAAACAAACCTTTATCCT	0.388													17	76	---	---	---	---	PASS
CLN8	2055	broad.mit.edu	37	8	1728427	1728427	+	Silent	SNP	C	G	G	rs145929862		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1728427C>G	uc003wpo.3	+	3	860	c.555C>G	c.(553-555)TCC>TCG	p.S185S		NM_018941	NP_061764	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8	185	TLC.				cell death|ceramide biosynthetic process|cholesterol metabolic process|lipid transport|negative regulation of proteolysis|phospholipid metabolic process	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		CGGGCTGGTCCGAGTCTCTGT	0.463													14	62	---	---	---	---	PASS
TACC1	6867	broad.mit.edu	37	8	38677391	38677391	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38677391A>C	uc010lwp.2	+	3	1008	c.629A>C	c.(628-630)GAA>GCA	p.E210A	TACC1_uc011lby.1_Missense_Mutation_p.E15A|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Missense_Mutation_p.E15A|TACC1_uc003xmc.3_Missense_Mutation_p.E15A|TACC1_uc011lbz.1_Missense_Mutation_p.E226A|TACC1_uc003xmb.3_Missense_Mutation_p.E165A|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Missense_Mutation_p.E210A|TACC1_uc011lcb.1_Missense_Mutation_p.E15A|TACC1_uc011lcc.1_Missense_Mutation_p.E15A|TACC1_uc011lcd.1_RNA|TACC1_uc003xmh.3_Missense_Mutation_p.E15A|TACC1_uc010lwq.2_Missense_Mutation_p.E15A	NM_006283	NP_006274	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing	210	Interaction with YEATS4.|Interaction with TDRD7.				cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			GCCTCCGCAGAAGCTGATCTA	0.597													14	71	---	---	---	---	PASS
MYST3	7994	broad.mit.edu	37	8	41800216	41800216	+	Intron	SNP	T	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41800216T>G	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_3'UTR	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)			AATTTACTTTTCTGTGAAAGA	0.294													4	11	---	---	---	---	PASS
HNF4G	3174	broad.mit.edu	37	8	76456146	76456146	+	Silent	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76456146A>G	uc003yaq.2	+	3	348	c.78A>G	c.(76-78)GCA>GCG	p.A26A	HNF4G_uc003yap.1_Silent_p.A26A|HNF4G_uc003yar.2_Silent_p.A63A	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	26	Nuclear receptor.|NR C4-type.				endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			ACTATGGGGCATCCAGCTGTG	0.463													53	119	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77617698	77617698	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77617698G>A	uc003yav.2	+	2	1762	c.1375G>A	c.(1375-1377)GAG>AAG	p.E459K	ZFHX4_uc003yat.1_Missense_Mutation_p.E459K|ZFHX4_uc003yau.1_Missense_Mutation_p.E459K|ZFHX4_uc003yaw.1_Missense_Mutation_p.E459K	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	459						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CCCAAACGGGGAGTGCCCTGT	0.473										HNSCC(33;0.089)			17	23	---	---	---	---	PASS
GRINA	2907	broad.mit.edu	37	8	145066243	145066243	+	Silent	SNP	A	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145066243A>T	uc003zan.1	+	4	856	c.690A>T	c.(688-690)GCA>GCT	p.A230A	GRINA_uc003zao.1_Silent_p.A230A|GRINA_uc003zap.1_Silent_p.A230A	NM_001009184	NP_001009184	Q7Z429	GRINA_HUMAN	glutamate receptor, ionotropic, N-methyl	230	Helical; (Potential).					integral to membrane				central_nervous_system(1)	1	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACCTTGTTGCACTGGTAACCC	0.582													39	87	---	---	---	---	PASS
AQP3	360	broad.mit.edu	37	9	33443673	33443673	+	Intron	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33443673G>A	uc003zsx.2	-						SUGT1P1_uc010mjq.1_Intron|AQP3_uc003zsv.1_3'UTR|AQP3_uc003zsw.2_5'Flank|AQP3_uc010mju.2_Intron	NM_004925	NP_004916	Q92482	AQP3_HUMAN	aquaporin 3						excretion|odontogenesis|positive regulation of immune system process|regulation of keratinocyte differentiation|response to calcium ion|response to retinoic acid|response to vitamin D	basolateral plasma membrane|cell-cell junction|cytoplasm	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		CAAAGCAGAGGCCACAGCTGT	0.532													6	20	---	---	---	---	PASS
GRHPR	9380	broad.mit.edu	37	9	37424868	37424868	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37424868A>G	uc003zzu.1	+	2	151	c.110A>G	c.(109-111)GAT>GGT	p.D37G	GRHPR_uc010mlu.2_5'UTR|GRHPR_uc010mlv.1_5'UTR|GRHPR_uc003zzt.1_5'UTR	NM_012203	NP_036335	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	37					cellular nitrogen compound metabolic process|excretion|glyoxylate metabolic process	peroxisomal matrix	glycerate dehydrogenase activity|glyoxylate reductase (NADP) activity|hydroxypyruvate reductase activity|NAD binding|protein binding				0				GBM - Glioblastoma multiforme(29;0.00687)		TGGGACTCGGATGAGCCCATC	0.667													9	26	---	---	---	---	PASS
SMC5	23137	broad.mit.edu	37	9	72965029	72965029	+	Splice_Site	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72965029G>T	uc004ahr.2	+	23	3007	c.2890_splice	c.e23-1	p.E964_splice	SMC5_uc011lry.1_Splice_Site_p.E109_splice	NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						ATGTTTTATAGGAAGATTATG	0.299													3	46	---	---	---	---	PASS
PRKG1	5592	broad.mit.edu	37	10	53667290	53667290	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53667290C>T	uc001jjm.2	+	5	871	c.677C>T	c.(676-678)CCT>CTT	p.P226L	PRKG1_uc001jjn.2_Missense_Mutation_p.P241L|PRKG1_uc001jjo.2_Missense_Mutation_p.P241L	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform	226	cGMP 2.				actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CAGAGCCTTCCTGAAGAGATC	0.408													37	199	---	---	---	---	PASS
RUFY2	55680	broad.mit.edu	37	10	70141061	70141061	+	Silent	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70141061A>G	uc001job.2	-	11	1467	c.1140T>C	c.(1138-1140)GAT>GAC	p.D380D	RUFY2_uc001jnz.1_RNA|RUFY2_uc001joc.2_Silent_p.D311D|RUFY2_uc010qiw.1_Silent_p.D287D|RUFY2_uc001jod.1_Silent_p.D345D	NM_017987	NP_060457	Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain-containing 2 isoform a	394	Potential.					nucleus	metal ion binding			ovary(1)	1						CTATCAGAGTATCTTGTTTCT	0.363													79	172	---	---	---	---	PASS
PSTK	118672	broad.mit.edu	37	10	124742525	124742525	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124742525C>T	uc001lgy.1	+	2	933	c.493C>T	c.(493-495)CAG>TAG	p.Q165*		NM_153336	NP_699167	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	165							ATP binding|kinase activity			liver(1)	1		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		TGAAGTCTACCAGCTGGCTCG	0.323													51	142	---	---	---	---	PASS
OR52J3	119679	broad.mit.edu	37	11	5068545	5068545	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5068545C>T	uc010qyv.1	+	1	790	c.790C>T	c.(790-792)CGA>TGA	p.R264*		NM_001001916	NP_001001916	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J,	264	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|lung(1)|skin(1)	3		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCTTACTCATCGATTTGGACA	0.438													51	230	---	---	---	---	PASS
RPS13	6207	broad.mit.edu	37	11	17098784	17098784	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17098784A>C	uc001mmp.2	-	3	114	c.82T>G	c.(82-84)TTG>GTG	p.L28V		NM_001017	NP_001008	P62277	RS13_HUMAN	ribosomal protein S13	28					endocrine pancreas development|negative regulation of RNA splicing|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	mRNA binding|protein binding|structural constituent of ribosome				0						TCAGATGTCAACTTCAACCAC	0.498													46	89	---	---	---	---	PASS
KCNC1	3746	broad.mit.edu	37	11	17793895	17793895	+	Silent	SNP	T	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17793895T>C	uc001mnk.3	+	2	1309	c.1254T>C	c.(1252-1254)GCT>GCC	p.A418A	KCNC1_uc009yhc.1_Silent_p.A418A	NM_004976	NP_004967	P48547	KCNC1_HUMAN	Shaw-related voltage-gated potassium channel	418	Helical; Name=Segment S6; (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)	1						TGGTGGGGGCTCTGTGTGCGC	0.602													39	65	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57089477	57089477	+	5'UTR	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57089477G>T	uc001njr.2	-	1					TNKS1BP1_uc001njs.2_Intron|TNKS1BP1_uc009ymd.1_Intron	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1						nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				TTGCCAGTAGGTTTAGCAGAG	0.547													5	15	---	---	---	---	PASS
VSIG2	23584	broad.mit.edu	37	11	124619711	124619711	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124619711C>T	uc001qas.2	-	4	555	c.479G>A	c.(478-480)GGC>GAC	p.G160D	VSIG2_uc001qat.2_Missense_Mutation_p.G160D	NM_014312	NP_055127	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	160	Extracellular (Potential).|Ig-like C2-type.					integral to plasma membrane|membrane fraction				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		TGCAGTAGAGCCTCCCACAGA	0.433													36	80	---	---	---	---	PASS
LRRC23	10233	broad.mit.edu	37	12	7023184	7023184	+	3'UTR	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7023184C>A	uc001qrt.3	+	8					LRRC23_uc001qrp.2_3'UTR|LRRC23_uc001qrq.2_Silent_p.I296I|LRRC23_uc001qrr.2_3'UTR|LRRC23_uc001qrs.2_Silent_p.I245I|LRRC23_uc009zfh.2_3'UTR|ENO2_uc001qru.1_5'Flank|ENO2_uc009zfi.1_5'Flank|ENO2_uc010sfq.1_5'Flank|ENO2_uc001qrv.1_5'Flank	NM_001135217	NP_001128689	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23 isoform a											ovary(1)	1						GGCCCAGGATCTGCTCTGTGC	0.622													57	131	---	---	---	---	PASS
CLEC2D	29121	broad.mit.edu	37	12	9822375	9822375	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9822375A>C	uc001qwg.1	+	1	67	c.45A>C	c.(43-45)GAA>GAC	p.E15D	CLEC2D_uc001qwf.1_Missense_Mutation_p.E15D|CLEC2D_uc009zgs.1_RNA|CLEC2D_uc001qwh.1_RNA|CLEC2D_uc009zgt.1_RNA	NM_013269	NP_037401	Q9UHP7	CLC2D_HUMAN	osteoclast inhibitory lectin isoform 1	15	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway	cell surface|endoplasmic reticulum|integral to plasma membrane|membrane fraction	sugar binding|transmembrane receptor activity				0						CACCATCTGAATTGCCTGCAA	0.463													20	52	---	---	---	---	PASS
PRPF40B	25766	broad.mit.edu	37	12	50037528	50037528	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50037528A>G	uc001rur.1	+	23	2436	c.2372A>G	c.(2371-2373)CAC>CGC	p.H791R	FMNL3_uc001ruv.1_3'UTR|FMNL3_uc001ruw.1_3'UTR|PRPF40B_uc001rup.1_Missense_Mutation_p.H812R|PRPF40B_uc001ruq.1_Missense_Mutation_p.H778R|PRPF40B_uc001rus.1_Missense_Mutation_p.H733R|FMNL3_uc001rut.1_3'UTR|FMNL3_uc001ruu.1_3'UTR	NM_001031698	NP_001026868	Q6NWY9	PR40B_HUMAN	Huntingtin interacting protein C isoform 1	791					mRNA processing|RNA splicing	nuclear speck				skin(2)|ovary(1)|pancreas(1)|kidney(1)	5						AAGAGAAGACACAAGTCGGTG	0.463													5	43	---	---	---	---	PASS
PITPNM2	57605	broad.mit.edu	37	12	123488978	123488978	+	Silent	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123488978C>T	uc001uej.1	-	7	1150	c.1011G>A	c.(1009-1011)TCG>TCA	p.S337S	PITPNM2_uc001uek.1_Silent_p.S337S|PITPNM2_uc009zxu.1_Silent_p.S337S	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,	337					metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		AGCTCTCATCCGAGTCCCTGG	0.592													28	59	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111102707	111102707	+	Silent	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111102707C>A	uc001vqx.2	+	20	1534	c.1245C>A	c.(1243-1245)CCC>CCA	p.P415P		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	415	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			TCGGAGACCCCGGCATCCCTG	0.637													24	57	---	---	---	---	PASS
MKRN3	7681	broad.mit.edu	37	15	23811752	23811752	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23811752C>A	uc001ywh.3	+	1	1299	c.823C>A	c.(823-825)CAC>AAC	p.H275N	MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Missense_Mutation_p.H275N	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	275	Makorin-type Cys-His.					ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			lung(6)|large_intestine(2)|ovary(2)	10		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		GCAGACCTTGCACCCCATGGA	0.522													20	49	---	---	---	---	PASS
SPRED1	161742	broad.mit.edu	37	15	38616982	38616982	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38616982A>G	uc001zka.3	+	4	730	c.395A>G	c.(394-396)AAT>AGT	p.N132S		NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain	132					inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		GAATCAAAAAATGAAGCTGAA	0.313									Legius_syndrome				8	20	---	---	---	---	PASS
PML	5371	broad.mit.edu	37	15	74326934	74326934	+	Intron	SNP	A	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74326934A>C	uc002awv.2	+						PML_uc002awm.2_Silent_p.A591A|PML_uc002awl.2_3'UTR|PML_uc002awj.1_3'UTR|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002awx.2_Intron|PML_uc002awy.2_5'UTR	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5						CCCAGGGGGCACAGCCACAGC	0.577			T	RARA|PAX5	APL|ALL								8	23	---	---	---	---	PASS
ZNF174	7727	broad.mit.edu	37	16	3451937	3451937	+	5'UTR	SNP	T	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3451937T>C	uc002cvc.2	+	1					ZNF434_uc002cux.3_5'Flank|ZNF434_uc010uwx.1_5'Flank|ZNF434_uc002cuy.3_5'Flank|ZNF434_uc002cuz.2_5'Flank|ZNF434_uc010uwy.1_5'Flank|ZNF434_uc010uxa.1_5'Flank|ZNF174_uc002cva.2_5'UTR|ZNF174_uc002cvb.2_5'UTR	NM_003450	NP_003441	Q15697	ZN174_HUMAN	zinc finger protein 174 isoform a						negative regulation of transcription from RNA polymerase II promoter|viral reproduction	actin cytoskeleton|cytoplasm|nucleus	protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding				0						ATTCAGAGACTTCTCCAGGGT	0.463													36	65	---	---	---	---	PASS
PAPD5	64282	broad.mit.edu	37	16	50257298	50257298	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50257298G>A	uc010vgo.1	+	8	1371	c.1336G>A	c.(1336-1338)GGT>AGT	p.G446S	PAPD5_uc010cbi.2_RNA|PAPD5_uc002efz.2_Missense_Mutation_p.G237S|PAPD5_uc002ega.2_Missense_Mutation_p.G237S	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a	367	PAP-associated.				cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		TTTACAACCAGGTATTGAAAT	0.363													7	20	---	---	---	---	PASS
VAC14	55697	broad.mit.edu	37	16	70816984	70816984	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70816984T>C	uc002ezm.2	-	7	1021	c.763A>G	c.(763-765)AAG>GAG	p.K255E	VAC14_uc010cfw.2_Missense_Mutation_p.K21E|VAC14_uc002ezn.2_Intron	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog	255					interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				TCAGCAAACTTCACACTGGAG	0.517													37	221	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18049342	18049342	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18049342G>A	uc010vxh.1	+	29	6768	c.6430G>A	c.(6430-6432)GCT>ACT	p.A2144T		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2144	Tail.|MyTH4 1.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					TGCCCACAATGCTGAGCGGGG	0.602													6	31	---	---	---	---	PASS
BTBD17	388419	broad.mit.edu	37	17	72353257	72353257	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72353257C>T	uc002jkn.2	-	3	976	c.976G>A	c.(976-978)GTC>ATC	p.V326I		NM_001080466	NP_001073935	A6NE02	BTBDH_HUMAN	BTB (POZ) domain containing 17 precursor	326						extracellular region					0						TTGTTGATGACCCACGGGGCG	0.721													3	1	---	---	---	---	PASS
CDK3	1018	broad.mit.edu	37	17	73998146	73998146	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73998146T>A	uc010dgt.2	+	4	314	c.238T>A	c.(238-240)TTT>ATT	p.F80I	CDK3_uc002jqg.3_Missense_Mutation_p.F108I	NM_001258	NP_001249	Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	80	Protein kinase.				cell division|cell proliferation|mitosis		ATP binding|cyclin-dependent protein kinase activity			central_nervous_system(1)	1						CTATCTGGTGTTTGAGTTCCT	0.577													31	67	---	---	---	---	PASS
STARD6	147323	broad.mit.edu	37	18	51863590	51863590	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51863590G>T	uc010xdt.1	-	3	172	c.172C>A	c.(172-174)CCA>ACA	p.P58T		NM_139171	NP_631910	P59095	STAR6_HUMAN	START domain containing protein 6	58	START.				lipid transport		lipid binding			ovary(1)	1				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)		AGTTTAGCTGGTGATTCTGGA	0.313													50	95	---	---	---	---	PASS
TMPRSS9	360200	broad.mit.edu	37	19	2422196	2422196	+	Silent	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2422196G>A	uc010xgx.1	+	13	2397	c.2397G>A	c.(2395-2397)CAG>CAA	p.Q799Q		NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	799	Extracellular (Potential).				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTAGGGGACAGACGCCATTTC	0.647													49	119	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9084963	9084963	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9084963C>A	uc002mkp.2	-	1	7056	c.6852G>T	c.(6850-6852)TTG>TTT	p.L2284F		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2284	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CTCTTGAAGTCAACTCATGAG	0.458													3	39	---	---	---	---	PASS
CRTC1	23373	broad.mit.edu	37	19	18886547	18886547	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18886547C>A	uc002nkb.3	+	13	1697	c.1609C>A	c.(1609-1611)CTC>ATC	p.L537I	CRTC1_uc010ebv.2_Missense_Mutation_p.L553I|CRTC1_uc010ebw.2_Missense_Mutation_p.L373I|CRTC1_uc002nkc.3_Missense_Mutation_p.L235I	NM_015321	NP_056136	Q6UUV9	CRTC1_HUMAN	mucoepidermoid carcinoma translocated 1 isoform	537					interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding		CRTC1/MAML2(516)	salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1)	519						CATGATGGGCCTCACGGGCAG	0.642													13	29	---	---	---	---	PASS
DLL3	10683	broad.mit.edu	37	19	39991266	39991266	+	Silent	SNP	T	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39991266T>A	uc002olx.2	+	3	421	c.363T>A	c.(361-363)TCT>TCA	p.S121S	DLL3_uc010egq.2_Silent_p.S121S|DLL3_uc002olw.2_Silent_p.S121S	NM_016941	NP_058637	Q9NYJ7	DLL3_HUMAN	delta-like 3 protein isoform 1 precursor	121	Extracellular (Potential).				Notch signaling pathway|skeletal system development	integral to membrane	Notch binding			central_nervous_system(2)|breast(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCACCTTCTCTTTCATCATCG	0.532													9	122	---	---	---	---	PASS
GLTSCR2	29997	broad.mit.edu	37	19	48248796	48248796	+	5'UTR	SNP	C	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48248796C>G	uc002phm.2	+	1					GLTSCR2_uc002phk.2_5'UTR|GLTSCR2_uc002phl.2_5'UTR|GLTSCR2_uc010elj.2_5'UTR	NM_015710	NP_056525	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2							nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		ACGCCAGTGGCTGAGTTCTTC	0.577													10	136	---	---	---	---	PASS
SPHK2	56848	broad.mit.edu	37	19	49129225	49129225	+	Silent	SNP	G	A	A	rs71335810		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49129225G>A	uc002pjr.2	+	3	483	c.117G>A	c.(115-117)CCG>CCA	p.P39P	SPHK2_uc010xzt.1_Intron|SPHK2_uc002pjs.2_Silent_p.P39P|SPHK2_uc002pjt.2_Intron|SPHK2_uc002pju.2_Silent_p.P3P|SPHK2_uc002pjv.2_Silent_p.P3P|SPHK2_uc002pjw.2_Silent_p.P101P|SPHK2_uc010xzu.1_Silent_p.P3P	NM_020126	NP_064511	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	39	Required for binding to sulfatide and phosphoinositides and for membrane localization.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cell proliferation|sphinganine-1-phosphate biosynthetic process	cytosol|lysosomal membrane|membrane fraction	ATP binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|Ras GTPase binding|sphinganine kinase activity			lung(1)	1		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CCATGGCCCCGCCCCCACCGC	0.692													10	9	---	---	---	---	PASS
KLK4	9622	broad.mit.edu	37	19	51410162	51410162	+	3'UTR	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51410162C>T	uc002pua.1	-	5					KLK4_uc002pty.1_3'UTR|KLK4_uc002ptz.1_RNA|KLK4_uc002pub.1_3'UTR|KLK4_uc002puc.1_RNA	NM_004917	NP_004908	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4 preproprotein						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)		ATTTGGGGGTCAATTTCATGG	0.353													25	224	---	---	---	---	PASS
LILRP2	79166	broad.mit.edu	37	19	55221840	55221840	+	RNA	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55221840A>G	uc002qgs.1	+	1		c.2240A>G			LILRP2_uc002qgt.1_Intron	NR_003061				Homo sapiens leukocyte immunoglobulin-like receptor pseudogene 2 (LILRP2), non-coding RNA.												0						GGGAGGTGTCAGCTCAGAACG	0.637													9	16	---	---	---	---	PASS
TGM3	7053	broad.mit.edu	37	20	2312884	2312884	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2312884A>G	uc002wfx.3	+	10	1667	c.1570A>G	c.(1570-1572)ATC>GTC	p.I524V		NM_003245	NP_003236	Q08188	TGM3_HUMAN	transglutaminase 3 precursor	524					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)	AGCCTGGACCATCATCTACAA	0.527													7	31	---	---	---	---	PASS
OSM	5008	broad.mit.edu	37	22	30659850	30659850	+	3'UTR	SNP	C	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30659850C>G	uc003ahb.2	-	3						NM_020530	NP_065391	P13725	ONCM_HUMAN	oncostatin M precursor						cell proliferation|immune response|negative regulation of cell proliferation|negative regulation of hormone secretion|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of MAPKKK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of growth	extracellular space|oncostatin-M receptor complex	cytokine activity|growth factor activity|oncostatin-M receptor binding			skin(1)	1			Epithelial(10;0.206)			GCATCCTTCACCGGCAAGGGG	0.622													31	94	---	---	---	---	PASS
GRAP2	9402	broad.mit.edu	37	22	40343157	40343157	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40343157A>T	uc003ayh.1	+	2	310	c.47A>T	c.(46-48)GAA>GTA	p.E16V	GRAP2_uc003ayi.2_RNA|GRAP2_uc011aom.1_Intron|GRAP2_uc011aon.1_Intron|GRAP2_uc010gya.1_Missense_Mutation_p.E16V|GRAP2_uc011aoo.1_5'UTR|GRAP2_uc011aop.1_Missense_Mutation_p.E16V|GRAP2_uc011aoq.1_Intron|GRAP2_uc003ayj.1_Missense_Mutation_p.E16V	NM_004810	NP_004801	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	16	SH3 1.				cell-cell signaling|Ras protein signal transduction|T cell costimulation|T cell receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			upper_aerodigestive_tract(1)|central_nervous_system(1)	2						GGTGAGGATGAACTGAGCTTT	0.498													44	92	---	---	---	---	PASS
TTLL1	25809	broad.mit.edu	37	22	43464519	43464519	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43464519T>G	uc003bdi.2	-	5	641	c.400A>C	c.(400-402)ACC>CCC	p.T134P	TTLL1_uc010gzh.2_Missense_Mutation_p.T134P|TTLL1_uc003bdj.2_Missense_Mutation_p.T20P|TTLL1_uc003bdh.2_Missense_Mutation_p.T96P	NM_012263	NP_036395	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	134	TTL.				protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity			skin(1)	1		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		ATGATCCAGGTGCTGGACGGG	0.527													89	218	---	---	---	---	PASS
SCML1	6322	broad.mit.edu	37	X	17762279	17762279	+	5'UTR	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17762279G>A	uc004cyb.2	+	2					SCML1_uc004cyc.2_5'UTR|SCML1_uc004cyd.2_Intron|SCML1_uc004cye.2_Intron	NM_001037540	NP_001032629	Q9UN30	SCML1_HUMAN	sex comb on midleg-like 1 isoform a						anatomical structure morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)	3	Hepatocellular(33;0.183)					CAACTCAGAGGAAGTGGAGTT	0.373													55	112	---	---	---	---	PASS
DDX53	168400	broad.mit.edu	37	X	23018221	23018221	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23018221G>A	uc004daj.2	+	1	135	c.47G>A	c.(46-48)AGA>AAA	p.R16K		NM_182699	NP_874358	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	16						nucleus	ATP binding|ATP-dependent helicase activity|RNA binding			large_intestine(1)|ovary(1)|kidney(1)	3						GCTAATCCAAGAGACCTTGGG	0.627													7	20	---	---	---	---	PASS
DCAF8L2	347442	broad.mit.edu	37	X	27766433	27766433	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27766433G>T	uc011mjy.1	+	1	1508	c.1421G>T	c.(1420-1422)GGT>GTT	p.G474V		NM_001136533	NP_001130005			DDB1 and CUL4 associated factor 8-like 2											central_nervous_system(1)|pancreas(1)	2						ACAGTCAAAGGTGTTAATTTC	0.428													17	30	---	---	---	---	PASS
DDX3X	1654	broad.mit.edu	37	X	41203496	41203496	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41203496C>T	uc004dfe.2	+	10	1724	c.869C>T	c.(868-870)TCA>TTA	p.S290L	DDX3X_uc010nhf.1_Missense_Mutation_p.S274L|DDX3X_uc004dff.2_Missense_Mutation_p.S290L|DDX3X_uc011mkq.1_Missense_Mutation_p.S274L|DDX3X_uc011mkr.1_Missense_Mutation_p.S290L|DDX3X_uc011mks.1_Intron|DDX3X_uc004dfg.2_RNA|DDX3X_uc011mkt.1_RNA	NM_001356	NP_001347	O00571	DDX3X_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3	290	Necessary for interaction with XPO1.|Helicase ATP-binding.				interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6						TTATAGTTTTCATACCGATCT	0.353										HNSCC(61;0.18)			77	166	---	---	---	---	PASS
PHF16	9767	broad.mit.edu	37	X	46917973	46917973	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46917973A>C	uc004dgx.2	+	11	2017	c.1966A>C	c.(1966-1968)AAA>CAA	p.K656Q	PHF16_uc004dgy.2_Missense_Mutation_p.K656Q	NM_001077445	NP_001070913	Q92613	JADE3_HUMAN	PHD finger protein 16	656					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0						TGGGAATGGGAAAAGTCAGCC	0.537													19	33	---	---	---	---	PASS
HUWE1	10075	broad.mit.edu	37	X	53674403	53674403	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53674403C>G	uc004dsp.2	-	6	661	c.259G>C	c.(259-261)GAG>CAG	p.E87Q		NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	87					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						TTCAGTTGCTCTCTTTCTGGC	0.493													30	162	---	---	---	---	PASS
OGT	8473	broad.mit.edu	37	X	70784541	70784541	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70784541G>A	uc004eaa.1	+	19	2744	c.2527G>A	c.(2527-2529)GTA>ATA	p.V843I	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_Missense_Mutation_p.V833I|OGT_uc004eac.2_Missense_Mutation_p.V704I|OGT_uc004ead.2_Missense_Mutation_p.V462I	NM_181672	NP_858058	O15294	OGT1_HUMAN	O-linked GlcNAc transferase isoform 1	843					cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)					AGATGCCATCGTATACTGTAA	0.403													55	102	---	---	---	---	PASS
PHKA1	5255	broad.mit.edu	37	X	71831023	71831023	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71831023C>A	uc004eax.3	-	22	2682	c.2381G>T	c.(2380-2382)TGG>TTG	p.W794L	PHKA1_uc004eay.3_Missense_Mutation_p.W794L|PHKA1_uc011mqi.1_Missense_Mutation_p.W735L	NM_002637	NP_002628	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle) isoform	794					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(3)|skin(1)	4	Renal(35;0.156)					TTCAGTGTTCCAGTCAGGTCC	0.423													32	68	---	---	---	---	PASS
NAP1L2	4674	broad.mit.edu	37	X	72433729	72433729	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72433729G>C	uc004ebi.2	-	1	956	c.600C>G	c.(598-600)GAC>GAG	p.D200E	NAP1L2_uc011mqj.1_Missense_Mutation_p.D58E	NM_021963	NP_068798	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2	200	Glu-rich (acidic).				nucleosome assembly	chromatin assembly complex				lung(1)	1	Renal(35;0.156)					CATAACCATCGTCCTCATCCA	0.328													9	143	---	---	---	---	PASS
LPAR4	2846	broad.mit.edu	37	X	78011131	78011131	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78011131G>T	uc010nme.2	+	2	1170	c.765G>T	c.(763-765)ATG>ATT	p.M255I		NM_005296	NP_005287	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	255	Helical; Name=6; (Potential).					integral to plasma membrane	lipid binding|purinergic nucleotide receptor activity, G-protein coupled			ovary(3)	3						CAGTACATATGGCAGTCTTTG	0.428													32	69	---	---	---	---	PASS
IGSF1	3547	broad.mit.edu	37	X	130416649	130416649	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130416649C>A	uc004ewd.2	-	7	1253	c.1015G>T	c.(1015-1017)GTG>TTG	p.V339L	IGSF1_uc004ewe.3_Missense_Mutation_p.V328L|IGSF1_uc004ewf.2_Missense_Mutation_p.V319L	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	339	Ig-like C2-type 4.|Extracellular (Potential).				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5						CGTAGGCTCACATTCTGACCC	0.493													22	105	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	7898	7898	+	RNA	SNP	T	C	C			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:7898T>C	uc004cou.3	+	1		c.313T>C			uc011mfi.1_5'Flank|uc004cov.3_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP42.																		GCCACCAATGGTACTGAACCT	0.507													3	1	---	---	---	---	PASS
CROCC	9696	broad.mit.edu	37	1	17124938	17124940	+	Intron	DEL	TTC	-	-	rs71661410		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17124938_17124940delTTC	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		ttcttttcttttcttttcttttc	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20200621	20200635	+	IGR	DEL	CACCACCACCACCAC	-	-	rs144954291		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20200621_20200635delCACCACCACCACCAC								RNF186 (58850 upstream) : OTUD3 (8253 downstream)																							ccaccaccatcaccaccaccaccaccaccaccacc	0.214													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48209051	48209052	+	IGR	INS	-	TGGTGA	TGGTGA	rs142247408	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48209051_48209052insTGGTGA								FOXD2 (302689 upstream) : SKINTL (358335 downstream)																							ggtagtggtggtggtggtggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98913996	98914003	+	IGR	DEL	TCTTTGTC	-	-	rs149834095		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98913996_98914003delTCTTTGTC								MIR137 (402269 upstream) : SNX7 (213233 downstream)																							tttctttctttctttgtctgtctttctt	0.058													3	4	---	---	---	---	
GATAD2B	57459	broad.mit.edu	37	1	153790789	153790790	+	Intron	DEL	TC	-	-	rs147391372	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153790789_153790790delTC	uc001fdb.3	-							NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GTCAAGGttttctttttttttt	0.193													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49118352	49118363	+	IGR	DEL	CCTCCCTCCCTC	-	-	rs4952927	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49118352_49118363delCCTCCCTCCCTC								LHCGR (135472 upstream) : FSHR (71290 downstream)																							ttccttccttcctccctccctccctccctccc	0.175													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65975365	65975372	+	Intron	DEL	CTTCCTTC	-	-	rs11695184		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65975365_65975372delCTTCCTTC	uc010fcy.1	+						uc010fcz.1_Intron					Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		ttctttctttcttccttccttccttcct	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105387604	105387605	+	IGR	INS	-	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105387604_105387605insA								LOC150568 (258390 upstream) : POU3F3 (84364 downstream)																							tcaacaacaacaaaaaaaaaaa	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106105740	106105741	+	IGR	INS	-	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106105740_106105741insA								FHL2 (50510 upstream) : NCK2 (255613 downstream)																							aggaaggaaggaaggaaggaag	0.000													4	2	---	---	---	---	
PAX8	7849	broad.mit.edu	37	2	114004578	114004579	+	Intron	DEL	GT	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114004578_114004579delGT	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron|PAX8_uc010fku.1_Intron|LOC654433_uc002tjq.3_Intron|LOC654433_uc010fks.2_Intron|LOC654433_uc010fkt.2_Intron|LOC654433_uc002tjr.3_Intron	NM_003466	NP_003457	Q06710	PAX8_HUMAN	paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2						ACAGGTGCTGGTGTGTGTGTGT	0.569			T	PPARG	follicular thyroid		Thyroid dysgenesis 						4	2	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121712728	121712730	+	Intron	DEL	CCT	-	-	rs77066773		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121712728_121712730delCCT	uc010flp.2	+						GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				TTTCTCTCTGCCttttttttttt	0.537													9	4	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160634565	160634566	+	Intron	DEL	CC	-	-	rs35013477		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160634565_160634566delCC	uc002ubb.3	-						LY75_uc010fos.2_Intron|CD302_uc002uba.2_Intron|CD302_uc010zco.1_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		TAAAAATAAACCCTTTTATTAG	0.233													4	3	---	---	---	---	
RQCD1	9125	broad.mit.edu	37	2	219447953	219447978	+	Intron	DEL	TGTGTCTCTCTCTCTCTCTCTCTCTC	-	-	rs36210927	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219447953_219447978delTGTGTCTCTCTCTCTCTCTCTCTCTC	uc010zkh.1	+						RQCD1_uc002vih.1_Intron|RQCD1_uc010zki.1_Intron	NM_005444	NP_005435	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|sex differentiation|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(1)|skin(1)	2		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		tgtgtgtgtgtgtgtctctctctctctctctctctctctctctctc	0.226													5	3	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10183745	10183746	+	Frame_Shift_Ins	INS	-	CC	CC			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183745_10183746insCC	uc003bvc.2	+	1	427_428	c.214_215insCC	c.(214-216)TCCfs	p.S72fs	VHL_uc003bvd.2_Frame_Shift_Ins_p.S72fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	72			Missing (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.S72fs*87(7)|p.E70fs*85(1)|p.S72_V87>L(1)|p.P71fs*84(1)|p.Q73fs*86(1)|p.R60fs*35(1)|p.N67_V74del(1)|p.E70_S72>A(1)|p.V74fs*51(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GCGCGAGCCCTCCCAGGTCATC	0.723		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				13	8	---	---	---	---	
ROBO2	6092	broad.mit.edu	37	3	77459701	77459706	+	Intron	DEL	TCTTCT	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77459701_77459706delTCTTCT	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		ttcttcctcctcttcttcctcctctt	0.019													7	4	---	---	---	---	
ROBO2	6092	broad.mit.edu	37	3	77459766	77459771	+	Intron	DEL	CTTCTT	-	-	rs10530677		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77459766_77459771delCTTCTT	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		cctcttcctccttcttctcctcctct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	121673418	121673419	+	IGR	INS	-	CTTCCTTT	CTTCCTTT	rs137874716	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121673418_121673419insCTTCCTTT								SLC15A2 (10384 upstream) : ILDR1 (32752 downstream)																							ttccttccttcctttctttctC	0.005													3	3	---	---	---	---	
NPHP3	27031	broad.mit.edu	37	3	132438748	132438749	+	Intron	DEL	AT	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132438748_132438749delAT	uc003epe.1	-						NCRNA00119_uc003epg.1_5'Flank|NPHP3_uc003epf.1_Intron|NCRNA00119_uc010htu.1_5'Flank	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						atatatatacatatatatatat	0.248													4	4	---	---	---	---	
CP	1356	broad.mit.edu	37	3	148901169	148901169	+	Intron	DEL	A	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148901169delA	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003ewx.3_Intron|CP_uc003ewz.2_Intron	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CAAGAAAATGAAACCCATAGA	0.294													47	28	---	---	---	---	
GOLIM4	27333	broad.mit.edu	37	3	167727938	167727938	+	3'UTR	DEL	A	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167727938delA	uc003ffe.2	-	16					GOLIM4_uc011bpe.1_3'UTR|GOLIM4_uc011bpf.1_3'UTR|GOLIM4_uc011bpg.1_3'UTR	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4						transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5						CAAAAGTTTTAAAAAAGTCTA	0.299													19	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12947367	12947368	+	IGR	INS	-	GAAG	GAAG	rs35599383		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12947367_12947368insGAAG								None (None upstream) : HSP90AB2P (387669 downstream)																							acaaatgctcagaaggaaggaa	0.025													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	83132494	83132494	+	IGR	DEL	T	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83132494delT								RASGEF1B (739433 upstream) : HNRNPD (141973 downstream)																							GCCTCAGCACTTGCCCTGTCC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165331908	165331909	+	IGR	INS	-	CCTTCCTTCCTTCCTTCCTTCCTT	CCTTCCTTCCTTCCTTCCTTCCTT			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165331908_165331909insCCTTCCTTCCTTCCTTCCTTCCTT								MARCH1 (26706 upstream) : TRIM61 (543691 downstream)																							cttccttccttccttccttcct	0.109													7	4	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21344713	21344713	+	Intron	DEL	T	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21344713delT	uc011cnn.1	+											Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						ccttccttcctttccttcctt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	68309947	68309952	+	Intron	DEL	TCTTCC	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68309947_68309952delTCTTCC	uc003jvf.1	-											Homo sapiens cDNA FLJ46633 fis, clone TRACH2025705.																		ttcttcctcttcttcctcttcctctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	149816504	149816507	+	IGR	DEL	GGAA	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149816504_149816507delGGAA								CD74 (24172 upstream) : RPS14 (7287 downstream)																							aaagaaagatggaaggaaggaagg	0.000													4	4	---	---	---	---	
UNC5A	90249	broad.mit.edu	37	5	176285702	176285705	+	Intron	DEL	GAAA	-	-	rs72388387		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176285702_176285705delGAAA	uc003mey.2	+						UNC5A_uc003mex.1_Intron	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATGGAAAGCGAaagaaagaaaga	0.172													6	4	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69810839	69810839	+	Intron	DEL	A	-	-	rs138343850	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69810839delA	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				ggaaggaaggaaaggagggag	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	158195269	158195270	+	IGR	INS	-	G	G	rs150472202	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158195269_158195270insG								ZDHHC14 (100293 upstream) : SNX9 (49024 downstream)																							gaggtggaggagtggaggaggt	0.322													8	4	---	---	---	---	
TCP10	6953	broad.mit.edu	37	6	167789428	167789431	+	Intron	DEL	AGTT	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167789428_167789431delAGTT	uc003qvv.1	-						TCP10_uc003qvu.2_Intron|TCP10_uc003qvw.2_3'UTR	NM_004610	NP_004601	Q12799	TCP10_HUMAN	t-complex 10							cytosol				breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		GCATGGAAACAGTTAGGAGCCCTC	0.569													7	4	---	---	---	---	
TBRG4	9238	broad.mit.edu	37	7	45139801	45139802	+	3'UTR	INS	-	G	G			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45139801_45139802insG	uc003tmv.2	-	11					TBRG4_uc003tmu.2_3'UTR|TBRG4_uc003tmw.2_3'UTR|TBRG4_uc003tmx.2_3'UTR|TBRG4_uc011kcd.1_3'UTR	NM_004749	NP_004740	Q969Z0	TBRG4_HUMAN	cell cycle progression 2 protein isoform 1						apoptosis|cell cycle arrest|cellular respiration|G1 phase of mitotic cell cycle|positive regulation of cell proliferation	mitochondrion	ATP binding|protein binding|protein kinase activity				0						TCAGAGTGGCTGGCCACCCTCC	0.589													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68223774	68223775	+	IGR	INS	-	GGGA	GGGA			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68223774_68223775insGGGA								None (None upstream) : AUTS2 (840130 downstream)																							ggagggagggaggggaaaaaga	0.015													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70786853	70786853	+	Intron	DEL	T	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70786853delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ccttccttcctttccttcctt	0.000													7	4	---	---	---	---	
MYOM2	9172	broad.mit.edu	37	8	2039908	2039908	+	Intron	DEL	T	-	-	rs11309012		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2039908delT	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CTCTGATGGGTAGACAGGAGG	0.483													4	4	---	---	---	---	
C8orf41	80185	broad.mit.edu	37	8	33373131	33373140	+	5'Flank	DEL	TCCTTCTTCC	-	-	rs35708537		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33373131_33373140delTCCTTCTTCC	uc003xjl.3	-						C8orf41_uc003xjk.3_5'Flank|C8orf41_uc010lvv.2_5'Flank|C8orf41_uc003xjm.3_5'Flank|C8orf41_uc003xjn.1_5'Flank	NM_025115	NP_079391	Q6NXR4	CH041_HUMAN	hypothetical protein LOC80185								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)		ccttccttcttccttcttccttcttccttc	0.024													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61945613	61945620	+	IGR	DEL	AGAAAGAT	-	-	rs60907426		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61945613_61945620delAGAAAGAT								CHD7 (166150 upstream) : CLVS1 (254905 downstream)																							agaaaaagaaagaaagatagaaagaaag	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	67328399	67328402	+	IGR	DEL	GAAG	-	-	rs150500788		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67328399_67328402delGAAG								CRH (237701 upstream) : RRS1 (12861 downstream)																							aggaaggaaagaaggaaggaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144474218	144474225	+	IGR	DEL	ACCCATCA	-	-	rs7461499	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144474218_144474225delACCCATCA								RHPN1 (7829 upstream) : MAFA (37290 downstream)																							ccatccatccacccatcaatccatccat	0.000													4	3	---	---	---	---	
GLDC	2731	broad.mit.edu	37	9	6594803	6594804	+	Intron	INS	-	AAAG	AAAG			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6594803_6594804insAAAG	uc003zkc.2	-							NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	aaaaggaaataaaagaaagaaa	0.069													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	65577179	65577179	+	IGR	DEL	T	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:65577179delT								FAM74A4 (82793 upstream) : LOC442421 (919291 downstream)																							GAAAACTTTGttttttttttt	0.383													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90812188	90812189	+	IGR	INS	-	TTCCTTCCTTCC	TTCCTTCCTTCC	rs74278576		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90812188_90812189insTTCCTTCCTTCC								CDK20 (222521 upstream) : SPIN1 (190651 downstream)																							TCTTCTTTTTTttccttccttc	0.287													4	2	---	---	---	---	
PNPLA7	375775	broad.mit.edu	37	9	140379177	140379178	+	Frame_Shift_Ins	INS	-	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140379177_140379178insA	uc004cnf.2	-	20	2470_2471	c.2133_2134insT	c.(2131-2136)CTTGGGfs	p.L711fs	C9orf167_uc011mew.1_Intron|PNPLA7_uc004cnd.1_5'UTR|PNPLA7_uc004cne.1_5'UTR|PNPLA7_uc011mfa.1_Frame_Shift_Ins_p.L119fs|PNPLA7_uc010ncj.1_Frame_Shift_Ins_p.L736fs	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	711_712					lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GTGGGGAGCCCAAGCTGGTGGC	0.668													20	9	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99072082	99072083	+	Intron	INS	-	TCC	TCC	rs151051937	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99072082_99072083insTCC	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		cttcctttcctttccttccttc	0.000													7	4	---	---	---	---	
C1S	716	broad.mit.edu	37	12	7169412	7169412	+	Intron	DEL	A	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7169412delA	uc001qsj.2	+						C1S_uc001qsk.2_Intron|C1S_uc001qsl.2_Intron|C1S_uc009zfr.2_Intron|C1S_uc009zfs.2_Intron	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	tgtctctattaaaaaaaaaaa	0.000													4	2	---	---	---	---	
LRP6	4040	broad.mit.edu	37	12	12291105	12291106	+	Intron	INS	-	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12291105_12291106insA	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				actccgtctccaaaaaaaaaaa	0.139													7	4	---	---	---	---	
KRT1	3848	broad.mit.edu	37	12	53069236	53069256	+	In_Frame_Del	DEL	TAGCTGCTACCTCCGGAGCCA	-	-	rs66529359		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53069236_53069256delTAGCTGCTACCTCCGGAGCCA	uc001sau.1	-	9	1715_1735	c.1656_1676delTGGCTCCGGAGGTAGCAGCTA	c.(1654-1677)TATGGCTCCGGAGGTAGCAGCTAC>TAC	p.552_559YGSGGSSY>Y	KRT1_uc001sav.1_Splice_Site_p.G556_splice	NM_006121	NP_006112	P04264	K2C1_HUMAN	keratin 1	552_559	Gly/Ser-rich.|Tail.				complement activation, lectin pathway|epidermis development|fibrinolysis|regulation of angiogenesis|response to oxidative stress	plasma membrane	protein binding|receptor activity|structural constituent of cytoskeleton|sugar binding			ovary(1)|skin(1)	2						tccggagccgtagctgctacctccggagccatagctgccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	61263464	61263487	+	IGR	DEL	TTCCTTCCTTCCTTCCTTCCTTCC	-	-	rs72204013	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61263464_61263487delTTCCTTCCTTCCTTCCTTCCTTCC								None (None upstream) : FAM19A2 (838556 downstream)																							TTGATtttctttccttccttccttccttccttccttccttcctt	0.138													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110072327	110072328	+	IGR	INS	-	ACC	ACC	rs147833484	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110072327_110072328insACC								MVK (37257 upstream) : C12orf34 (79862 downstream)																							ccaccaccactaccaccaccac	0.020													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129821986	129821987	+	Intron	INS	-	CA	CA	rs141343914	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129821986_129821987insCA	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		ATacacacacgcacacacacac	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83420922	83420933	+	IGR	DEL	AGGGAGGGAGGG	-	-	rs146231255	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83420922_83420933delAGGGAGGGAGGG								None (None upstream) : None (None downstream)																							gcaggaaggaagggagggagggaggaaggaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21302181	21302182	+	IGR	INS	-	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21302181_21302182insA								RNASE1 (31145 upstream) : RNASE3 (57380 downstream)																							ccggtattaataaaaaaaaaaa	0.000													5	3	---	---	---	---	
HECTD1	25831	broad.mit.edu	37	14	31647112	31647112	+	Intron	DEL	T	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31647112delT	uc001wrc.1	-							NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		tttttagaaattttttttttt	0.318													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34669613	34669616	+	IGR	DEL	GAAG	-	-	rs71451998		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34669613_34669616delGAAG								EGLN3 (249326 upstream) : C14orf147 (232529 downstream)																							agaagaaagagaaggaaggaagga	0.181													7	4	---	---	---	---	
DACT1	51339	broad.mit.edu	37	14	59108597	59108598	+	Intron	INS	-	T	T	rs35083114		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59108597_59108598insT	uc001xdw.2	+						DACT1_uc010trv.1_Intron|DACT1_uc001xdx.2_Intron|DACT1_uc010trw.1_Intron	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1						multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5						TAGTGCCATACTTACATCTAGA	0.406													9	5	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107190987	107190990	+	Intron	DEL	TCTG	-	-	rs148926978	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107190987_107190990delTCTG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						tatccctccttctgtccttccatc	0.029													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6464640	6464641	+	IGR	INS	-	CTC	CTC	rs143155894	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6464640_6464641insCTC								PITPNM3 (4763 upstream) : KIAA0753 (17005 downstream)																							tcttcctccttctcttctttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20648273	20648273	+	IGR	DEL	T	-	-	rs36007188		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20648273delT								LGALS9B (277425 upstream) : CCDC144NL (118437 downstream)																							AACACTAGACTTTTTTTTTTT	0.313													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32560352	32560353	+	IGR	INS	-	AGAA	AGAA	rs140694482	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32560352_32560353insAGAA								ACCN1 (76527 upstream) : CCL2 (21943 downstream)																							gaaagagagagagaaagaaaga	0.000													5	3	---	---	---	---	
AATK	9625	broad.mit.edu	37	17	79098839	79098847	+	Intron	DEL	GCAGGGTGA	-	-	rs141491493		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79098839_79098847delGCAGGGTGA	uc010dia.2	-						AATK_uc010dhz.2_5'Flank|hsa-mir-3065|MI0014228_5'Flank	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase							integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			aggggcaggggcagggtgagcagggtgag	0.330													2	4	---	---	---	---	
SMCHD1	23347	broad.mit.edu	37	18	2751166	2751167	+	Intron	INS	-	AT	AT	rs148373283	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2751166_2751167insAT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						ATTTAAATAACGTGTGCTTTAA	0.267													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	77393921	77393923	+	IGR	DEL	TGA	-	-	rs112228378	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77393921_77393923delTGA								NFATC1 (104599 upstream) : CTDP1 (45878 downstream)																							gtggtgatggtgatgatggtggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27733392	27733392	+	IGR	DEL	T	-	-	rs143429325		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27733392delT								None (None upstream) : LOC148189 (548010 downstream)																							tggaaacgggttttttttcat	0.000													4	3	---	---	---	---	
SARS2	54938	broad.mit.edu	37	19	39422788	39422788	+	5'Flank	DEL	G	-	-	rs57541708		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39422788delG	uc002oka.2	-						SARS2_uc002ojz.2_5'Flank|SARS2_uc010xup.1_5'Flank|SARS2_uc002okb.2_5'Flank|SARS2_uc010xuq.1_Intron|SARS2_uc010xur.1_5'Flank|SARS2_uc010xus.1_5'Flank|MRPS12_uc002okc.2_Intron|MRPS12_uc002okd.2_Intron|MRPS12_uc002oke.2_Intron	NM_017827	NP_060297	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2 isoform b precursor						seryl-tRNA aminoacylation	mitochondrial matrix	ATP binding|protein binding|serine-tRNA ligase activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			aaaaaaaaaagaaaaaaaaaa	0.134													4	3	---	---	---	---	
ERCC2	2068	broad.mit.edu	37	19	45859073	45859073	+	Intron	DEL	T	-	-	rs35665496		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45859073delT	uc002pbj.2	-						ERCC2_uc002pbh.2_Intron|ERCC2_uc002pbi.2_Intron|ERCC2_uc010ejz.2_Intron|ERCC2_uc002pbk.2_Intron	NM_000400	NP_000391	P18074	ERCC2_HUMAN	excision repair cross-complementing rodent						cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction	cytoplasm|holo TFIIH complex|MMXD complex	5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding			lung(2)|pancreas(1)	3		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		tgttctaagcttttttttttt	0.209			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				10	5	---	---	---	---	
KLK5	25818	broad.mit.edu	37	19	51453034	51453053	+	Intron	DEL	CACCCCCACCCCCACTTCCC	-	-	rs59705989	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51453034_51453053delCACCCCCACCCCCACTTCCC	uc002pue.2	-						KLK5_uc002puf.2_Intron|KLK5_uc002pug.2_Intron	NM_001077491	NP_001070959	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5 preproprotein						epidermis development|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		acctccaTGAcacccccacccccacttccccacccccacc	0.245													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16755431	16755434	+	IGR	DEL	AAAG	-	-	rs74177310		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16755431_16755434delAAAG								OTOR (22623 upstream) : PCSK2 (451318 downstream)																							ggaagatagaaaagaaagaaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31635325	31635325	+	IGR	DEL	A	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31635325delA								BPIL3 (3473 upstream) : C20orf185 (7905 downstream)																							ACTCCCTCTCACTCGTAGTGG	0.557													6	3	---	---	---	---	
NFATC2	4773	broad.mit.edu	37	20	50092197	50092197	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50092197delG	uc002xwd.2	-	4	1553	c.1333delC	c.(1333-1335)CTCfs	p.L445fs	NFATC2_uc002xwc.2_Frame_Shift_Del_p.L445fs|NFATC2_uc010zyv.1_Frame_Shift_Del_p.L226fs|NFATC2_uc010zyw.1_Frame_Shift_Del_p.L226fs|NFATC2_uc010zyx.1_Frame_Shift_Del_p.L425fs|NFATC2_uc010zyy.1_Frame_Shift_Del_p.L226fs|NFATC2_uc010zyz.1_Frame_Shift_Del_p.L226fs|NFATC2_uc002xwe.2_Frame_Shift_Del_p.L425fs	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,	445	RHD.				B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)					TAGCCATGGAGCTGGTGGGGG	0.502													34	19	---	---	---	---	
LAMA5	3911	broad.mit.edu	37	20	60904422	60904426	+	Intron	DEL	CAGCC	-	-	rs3065756		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60904422_60904426delCAGCC	uc002ycq.2	-							NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTGGCAGCAGcagcccagcccagcc	0.600													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18383004	18383011	+	IGR	DEL	GAAGGAAG	-	-			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18383004_18383011delGAAGGAAG								C21orf34 (400910 upstream) : CXADR (502319 downstream)																							CAAaagggaagaaggaaggaaggaagga	0.188													4	2	---	---	---	---	
PCNT	5116	broad.mit.edu	37	21	47858287	47858288	+	Intron	INS	-	A	A			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47858287_47858288insA	uc002zji.3	+						PCNT_uc002zjj.2_Intron	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					TGCCTCAGCCTAACCCACCATG	0.594													39	17	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26344513	26344514	+	Intron	INS	-	CTTC	CTTC			TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26344513_26344514insCTTC	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						ttccttccttcctttctctttc	0.020													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27415593	27415594	+	IGR	INS	-	TCTT	TCTT	rs5761907	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27415593_27415594insTCTT								MIAT (300644 upstream) : MN1 (728672 downstream)																							ctttctttctctctttccttcc	0.000													4	2	---	---	---	---	
MN1	4330	broad.mit.edu	37	22	28146768	28146769	+	3'UTR	INS	-	G	G	rs139246561	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28146768_28146769insG	uc003adj.2	-	2					MN1_uc010gvg.2_RNA	NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1								binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10						ACCAACCTAGAGAAAAAAAAAA	0.292			T	ETV6	AML|meningioma								4	6	---	---	---	---	
RFPL2	10739	broad.mit.edu	37	22	32595898	32595899	+	Intron	INS	-	C	C	rs150809092	by1000genomes	TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32595898_32595899insC	uc003amg.3	-						RFPL2_uc003amf.3_Intron|RFPL2_uc003amh.3_Intron	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2								zinc ion binding			skin(1)	1						CCGCTCGCCCACTCACAGGCCA	0.634													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	5197160	5197161	+	IGR	INS	-	AGGA	AGGA	rs10701505		TCGA-B0-5085-01A-01D-1462-08	TCGA-B0-5085-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5197160_5197161insAGGA								None (None upstream) : NLGN4X (610923 downstream)																							aaggaagagagaggaaggaagg	0.124													3	3	---	---	---	---	
