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
MMEL1	79258	broad.mit.edu	37	1	2530196	2530196	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2530196G>C	uc001ajy.2	-	12	1289	c.1075C>G	c.(1075-1077)CTA>GTA	p.L359V	MMEL1_uc009vlg.1_RNA	NM_033467	NP_258428	Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	359	Lumenal (Potential).				proteolysis	extracellular region|integral to membrane|intracellular membrane-bounded organelle	metal ion binding|metalloendopeptidase activity				0	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		ACAGAGGATAGCACAGTTTGT	0.408													26	74	---	---	---	---	PASS
C1orf158	93190	broad.mit.edu	37	1	12820749	12820749	+	Silent	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12820749G>A	uc001auh.2	+	4	666	c.450G>A	c.(448-450)CAG>CAA	p.Q150Q		NM_152290	NP_689503	Q8N1D5	CA158_HUMAN	hypothetical protein LOC93190	150										ovary(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		AGCAGAGACAGCTCACACCCA	0.557													62	135	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974955	16974955	+	RNA	SNP	A	G	G	rs149751487	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974955A>G	uc010och.1	+	7		c.1415A>G			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						GCATGCTTTGATGTCTGGGAC	0.657													3	69	---	---	---	---	PASS
PDE4B	5142	broad.mit.edu	37	1	66798124	66798124	+	Intron	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66798124G>A	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron|PDE4B_uc001dcq.2_Missense_Mutation_p.G18S	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)	CGGTGGTAGCGGTGACTCTGC	0.517													28	49	---	---	---	---	PASS
FCRL4	83417	broad.mit.edu	37	1	157556209	157556209	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157556209G>A	uc001fqw.2	-	6	1020	c.884C>T	c.(883-885)CCC>CTC	p.P295L	FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	295	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				GCCCCCTGAGGGCTGGGTCTC	0.617													34	120	---	---	---	---	PASS
HSPA7	3311	broad.mit.edu	37	1	161577393	161577393	+	3'UTR	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161577393C>T	uc010pkp.1	+	1						NR_024151				RecName: Full=Putative heat shock 70 kDa protein 7; AltName: Full=Heat shock 70 kDa protein B;												0						GGACAACCAGCCTGGGGTCTT	0.577													13	52	---	---	---	---	PASS
CDC73	79577	broad.mit.edu	37	1	193119512	193119512	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193119512G>C	uc001gtb.2	+	9	1150	c.907G>C	c.(907-909)GAA>CAA	p.E303Q		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	303					cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						AGGAAAAGAAGGCAAGTTGCT	0.373									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				5	95	---	---	---	---	PASS
KIF21B	23046	broad.mit.edu	37	1	200954092	200954092	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200954092T>A	uc001gvs.1	-	27	4015	c.3698A>T	c.(3697-3699)GAT>GTT	p.D1233V	KIF21B_uc001gvr.1_Missense_Mutation_p.D1233V|KIF21B_uc009wzl.1_Missense_Mutation_p.D1233V|KIF21B_uc010ppn.1_Missense_Mutation_p.D1233V	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1233					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						GAATCCCACATCTGTGGACCT	0.612													30	73	---	---	---	---	PASS
CYB5R1	51706	broad.mit.edu	37	1	202932260	202932260	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202932260C>T	uc001gyt.2	-	8	750	c.679G>A	c.(679-681)GAG>AAG	p.E227K	CYB5R1_uc010pqe.1_RNA	NM_016243	NP_057327	Q9UHQ9	NB5R1_HUMAN	cytochrome b5 reductase 1	227					sterol biosynthetic process	integral to membrane	cytochrome-b5 reductase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.141)			TGCAGTTCCTCTAAGTCCTCC	0.473													41	96	---	---	---	---	PASS
OPTC	26254	broad.mit.edu	37	1	203465362	203465362	+	Missense_Mutation	SNP	G	A	A	rs140125203		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203465362G>A	uc001gzu.1	+	2	345	c.229G>A	c.(229-231)GAG>AAG	p.E77K		NM_014359	NP_055174	Q9UBM4	OPT_HUMAN	opticin precursor	77						proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.109)			CCAACTCCCCGAGGTGAGGGA	0.562													13	30	---	---	---	---	PASS
PROX1	5629	broad.mit.edu	37	1	214170133	214170133	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214170133G>A	uc001hkh.2	+	2	527	c.255G>A	c.(253-255)ATG>ATA	p.M85I	PROX1_uc001hkg.1_Missense_Mutation_p.M85I	NM_002763	NP_002754	Q92786	PROX1_HUMAN	prospero homeobox 1	85					aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		ATGCCATGATGCCTTTTCCAG	0.473													31	118	---	---	---	---	PASS
CDC42BPA	8476	broad.mit.edu	37	1	227213828	227213828	+	Silent	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227213828C>T	uc001hqr.2	-	30	5296	c.4353G>A	c.(4351-4353)GTG>GTA	p.V1451V	CDC42BPA_uc001hqq.2_Silent_p.V750V|CDC42BPA_uc001hqs.2_Silent_p.V1370V|CDC42BPA_uc009xes.2_Silent_p.V1423V|CDC42BPA_uc010pvs.1_Silent_p.V1431V|CDC42BPA_uc001hqp.2_Silent_p.V607V|CDC42BPA_uc001hqt.2_Silent_p.V329V|CDC42BPA_uc001hqu.1_Silent_p.V658V	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	1464	CNH.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				TTTCACTGTACACCGAGAGAT	0.398													20	62	---	---	---	---	PASS
WNT9A	7483	broad.mit.edu	37	1	228112054	228112054	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228112054T>C	uc001hri.2	-	3	488	c.400A>G	c.(400-402)ACG>GCG	p.T134A		NM_003395	NP_003386	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family,	134					anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|cornea development in camera-type eye|embryonic arm morphogenesis|embryonic skeletal joint morphogenesis|endoderm development|iris morphogenesis|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|neuron differentiation|positive regulation of smoothened signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding|signal transducer activity			central_nervous_system(1)|pancreas(1)	2		Prostate(94;0.0405)				AGTGCGTGCGTCAGGCCAGCC	0.672													4	76	---	---	---	---	PASS
TTC15	51112	broad.mit.edu	37	2	3391616	3391616	+	Silent	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3391616C>T	uc002qxm.1	+	2	428	c.222C>T	c.(220-222)GAC>GAT	p.D74D	TTC15_uc002qxn.1_Silent_p.D74D|TTC15_uc010ewm.1_Silent_p.D74D|TTC15_uc002qxl.1_Silent_p.D74D	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	tetratricopeptide repeat domain 15	74							binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)		TCATCTCTGACTCCCCCAACA	0.662													15	27	---	---	---	---	PASS
CNNM3	26505	broad.mit.edu	37	2	97483238	97483238	+	Silent	SNP	A	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97483238A>C	uc002swy.2	+	1	1248	c.1224A>C	c.(1222-1224)CGA>CGC	p.R408R	CNNM3_uc002swz.2_Silent_p.R408R	NM_017623	NP_060093	Q8NE01	CNNM3_HUMAN	cyclin M3 isoform 1	408	CBS 2.				ion transport	integral to membrane|plasma membrane	protein binding			ovary(1)	1						AATTCAAGCGAGGTAACGGCC	0.602													16	177	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179399168	179399168	+	Silent	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179399168C>T	uc010zfg.1	-	307	94694	c.94470G>A	c.(94468-94470)AGG>AGA	p.R31490R	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.R25185R|TTN_uc010zfi.1_Silent_p.R25118R|TTN_uc010zfj.1_Silent_p.R24993R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32417							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)			TGCGAGATTTCCTCTCTTTCA	0.413													58	152	---	---	---	---	PASS
ACCN4	55515	broad.mit.edu	37	2	220396729	220396729	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220396729C>G	uc002vma.2	+	3	1129	c.1115C>G	c.(1114-1116)ACG>AGG	p.T372R	ACCN4_uc010fwi.1_Missense_Mutation_p.T372R|ACCN4_uc010fwj.1_Missense_Mutation_p.T372R|ACCN4_uc002vly.1_Missense_Mutation_p.T372R|ACCN4_uc002vlz.2_Missense_Mutation_p.T372R|ACCN4_uc002vmb.2_Missense_Mutation_p.T26R	NM_182847	NP_878267	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 2	372	Extracellular (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)		GCAGATGAGACGTCGTTTGAG	0.632													80	160	---	---	---	---	PASS
KCNJ13	3769	broad.mit.edu	37	2	233632892	233632892	+	3'UTR	SNP	G	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233632892G>T	uc002vto.2	-	2					GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vti.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtn.2_3'UTR|KCNJ13_uc002vtp.2_3'UTR	NM_002242	NP_002233	O60928	IRK13_HUMAN	potassium inwardly-rectifying channel J13							voltage-gated potassium channel complex	inward rectifier potassium channel activity				0		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		ATTAAAAAATGGATAAGTCTT	0.348													4	138	---	---	---	---	PASS
SETMAR	6419	broad.mit.edu	37	3	4355062	4355062	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4355062A>G	uc011asp.1	+	2	704	c.637A>G	c.(637-639)ACT>GCT	p.T213A	SUMF1_uc003bps.1_Intron|SETMAR_uc003bpw.3_Missense_Mutation_p.T200A|SETMAR_uc003bpy.3_Intron|SETMAR_uc011asq.1_Intron|SETMAR_uc011asr.1_Intron|SETMAR_uc010hbx.2_Missense_Mutation_p.T8A	NM_006515	NP_006506	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion	200	SET.|Histone-lysine N-methyltransferase.				DNA integration|DNA repair|transposition, DNA-mediated	chromosome|nucleus	DNA binding|endonuclease activity|histone-lysine N-methyltransferase activity|transposase activity|zinc ion binding			ovary(1)	1		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		TGTTGACCCTACTTATATAGG	0.368								Chromatin_Structure|Direct_reversal_of_damage					35	120	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47059132	47059132	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47059132C>T	uc003cqs.2	-	20	7582	c.7529G>A	c.(7528-7530)CGC>CAC	p.R2510H	SETD2_uc003cqv.2_Missense_Mutation_p.R2577H|SETD2_uc003cqr.2_Missense_Mutation_p.R109H	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2510	Interaction with POLR2A.			R->A: Impairs interaction with hyperphosphorylated POLR2A.	regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GAGTACCTTGCGAGCCAGATG	0.453			N|F|S|Mis		clear cell renal carcinoma								16	31	---	---	---	---	PASS
NICN1	84276	broad.mit.edu	37	3	49466658	49466658	+	Silent	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49466658C>T	uc003cwz.1	-	1	100	c.15G>A	c.(13-15)TTG>TTA	p.L5L	NICN1_uc003cxa.2_RNA|NICN1_uc011bcr.1_Silent_p.L5L	NM_032316	NP_115692	Q9BSH3	NICN1_HUMAN	nicolin 1	5						microtubule|nucleus					0				BRCA - Breast invasive adenocarcinoma(193;4.52e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGCAAGGCACCAAAACGCGGG	0.652													13	23	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52598242	52598242	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52598242A>C	uc003des.2	-	23	3711	c.3699T>G	c.(3697-3699)TGT>TGG	p.C1233W	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.C1233W|PBRM1_uc003der.2_Missense_Mutation_p.C1201W|PBRM1_uc003det.2_Missense_Mutation_p.C1248W|PBRM1_uc003deu.2_Missense_Mutation_p.C1248W|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.C1233W|PBRM1_uc010hmk.1_Missense_Mutation_p.C1208W|PBRM1_uc003dey.2_Missense_Mutation_p.C1208W|PBRM1_uc003dez.1_Missense_Mutation_p.C1232W	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1233	BAH 2.				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)		ACAACACAGCACACTTTCCTG	0.368			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								36	60	---	---	---	---	PASS
SEC22A	26984	broad.mit.edu	37	3	122927986	122927986	+	Intron	SNP	A	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122927986A>C	uc003ege.2	+						SEC22A_uc003egf.2_5'UTR	NM_012430	NP_036562	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)		ACATTTTTACATATGCTTATC	0.189													12	36	---	---	---	---	PASS
ECT2	1894	broad.mit.edu	37	3	172480526	172480526	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172480526T>C	uc003fii.2	+	9	980	c.842T>C	c.(841-843)GTA>GCA	p.V281A	ECT2_uc010hwv.1_Missense_Mutation_p.V312A|ECT2_uc003fih.2_Missense_Mutation_p.V280A|ECT2_uc003fij.1_Missense_Mutation_p.V281A|ECT2_uc003fik.1_Missense_Mutation_p.V281A|ECT2_uc003fil.1_Missense_Mutation_p.V312A	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene	281	BRCT 2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			ACTCACCTTGTAGTTGAAGAG	0.348													31	92	---	---	---	---	PASS
FAM193A	8603	broad.mit.edu	37	4	2733610	2733610	+	3'UTR	SNP	G	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2733610G>C	uc010icl.2	+	20					FAM193A_uc010ick.2_3'UTR|FAM193A_uc003gfd.2_3'UTR|FAM193A_uc011bvm.1_3'UTR|FAM193A_uc011bvn.1_3'UTR|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603											ovary(3)	3						GGACTCCCTGGAGAGGGACAC	0.597													50	139	---	---	---	---	PASS
THAP9	79725	broad.mit.edu	37	4	83839153	83839153	+	Silent	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83839153C>T	uc003hnt.2	+	5	1907	c.1788C>T	c.(1786-1788)GTC>GTT	p.V596V	THAP9_uc003hns.1_Silent_p.V452V|THAP9_uc003hnu.1_RNA|THAP9_uc003hnv.2_Silent_p.V313V	NM_024672	NP_078948	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	596							DNA binding|metal ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	5		Hepatocellular(203;0.114)				TCCCAAAGGTCATGCCTTTTC	0.348													42	80	---	---	---	---	PASS
C4orf51	646603	broad.mit.edu	37	4	146650343	146650343	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146650343G>C	uc003ikk.2	+	4	389	c.389G>C	c.(388-390)GGT>GCT	p.G130A		NM_001080531	NP_001074000	C9J302	CD051_HUMAN	chromosome 4 open reading frame 51	130											0						TGGGATTTTGGTGATTGTTTT	0.323													18	26	---	---	---	---	PASS
GOLPH3	64083	broad.mit.edu	37	5	32126354	32126354	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32126354C>A	uc003jhp.1	-	4	1146	c.861G>T	c.(859-861)GAG>GAT	p.E287D		NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3	287					cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						CCCACAGAACCTCATTGGTGT	0.507													51	146	---	---	---	---	PASS
LIFR	3977	broad.mit.edu	37	5	38484964	38484964	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38484964C>A	uc010ive.1	-	18	2836	c.2504G>T	c.(2503-2505)GGA>GTA	p.G835V	LIFR_uc003jli.2_Missense_Mutation_p.G835V	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor	835	Helical; (Potential).				positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)					AATAATTAATCCCACAGCTGA	0.378			T	PLAG1	salivary adenoma								8	17	---	---	---	---	PASS
WDR36	134430	broad.mit.edu	37	5	110428228	110428228	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110428228A>T	uc003kpd.2	+	1	359	c.242A>T	c.(241-243)AAC>ATC	p.N81I	WDR36_uc010jbu.2_RNA	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	81					response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)|skin(1)	2		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		CTTTTCAGCAACGACATTCCA	0.602													10	81	---	---	---	---	PASS
RREB1	6239	broad.mit.edu	37	6	7181959	7181959	+	Intron	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7181959C>T	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_5'UTR	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				TCACTCTGGGCGTGAATGTGG	0.473													13	41	---	---	---	---	PASS
RXRB	6257	broad.mit.edu	37	6	33163494	33163494	+	Intron	SNP	A	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33163494A>T	uc003odb.2	-						RXRB_uc003odc.2_Intron|RXRB_uc003odd.2_Intron|RXRB_uc011dqr.1_Intron|RXRB_uc011dqs.1_3'UTR	NM_021976	NP_068811	P28702	RXRB_HUMAN	retinoid X receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			ovary(3)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)	GTGGGGCAGCAAGGGTCAGGA	0.542													22	32	---	---	---	---	PASS
CPNE5	57699	broad.mit.edu	37	6	36730739	36730739	+	Silent	SNP	A	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36730739A>G	uc003omr.1	-	12	877	c.810T>C	c.(808-810)AGT>AGC	p.S270S	CPNE5_uc003oms.1_Silent_p.S249S	NM_020939	NP_065990	Q9HCH3	CPNE5_HUMAN	copine V	270										skin(1)	1						GCTCCCGGTAACTGGTGGTGA	0.597													28	98	---	---	---	---	PASS
MAP3K7	6885	broad.mit.edu	37	6	91228282	91228282	+	Splice_Site	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91228282C>A	uc003pnz.1	-	16	1687	c.1525_splice	c.e16-1	p.P509_splice	MAP3K7_uc003pny.1_Splice_Site_p.P46_splice|MAP3K7_uc003poa.1_Intron|MAP3K7_uc003pob.1_Splice_Site_p.P482_splice|MAP3K7_uc003poc.1_Intron	NM_145331	NP_663304	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)	6		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		GTGCTAGAGGCTGAAAATAAT	0.328													18	58	---	---	---	---	PASS
ARMC2	84071	broad.mit.edu	37	6	109294785	109294785	+	3'UTR	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109294785G>A	uc003pss.3	+	18					ARMC2_uc011eao.1_3'UTR	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2								binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		GGTAACAAACGTGAACATTTT	0.358													5	114	---	---	---	---	PASS
AKD1	221264	broad.mit.edu	37	6	109871300	109871300	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109871300G>A	uc003ptn.2	-	25	3034	c.2957C>T	c.(2956-2958)CCA>CTA	p.P986L	AKD1_uc011eat.1_Missense_Mutation_p.P65L	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1	986					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						CACCTTCAATGGTTCTTCATG	0.398													5	179	---	---	---	---	PASS
GPR126	57211	broad.mit.edu	37	6	142737063	142737063	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142737063G>T	uc010khc.2	+	20	3211	c.2800G>T	c.(2800-2802)GCA>TCA	p.A934S	GPR126_uc010khd.2_Missense_Mutation_p.A906S|GPR126_uc010khe.2_Missense_Mutation_p.A934S|GPR126_uc010khf.2_Missense_Mutation_p.A906S	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1	934	Helical; Name=3; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		CATTGCTGTTGCAGTCCTGTT	0.453													64	226	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1539240	1539240	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1539240C>T	uc003skn.2	-	6	814	c.713G>A	c.(712-714)CGG>CAG	p.R238Q	INTS1_uc003skq.2_Missense_Mutation_p.R238Q	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	238					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CACCCAGATCCGCTCCCCCAG	0.652													7	53	---	---	---	---	PASS
KDELR2	11014	broad.mit.edu	37	7	6502730	6502730	+	3'UTR	SNP	C	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6502730C>G	uc003sqe.3	-	5					DAGLB_uc003sqd.3_Intron|KDELR2_uc003sqf.3_Missense_Mutation_p.R143P	NM_006854	NP_006845	P33947	ERD22_HUMAN	KDEL receptor 2 isoform 1						intracellular protein transport|protein retention in ER lumen|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	KDEL sequence binding|protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		GAATTCTGTCCGAGCACCCTG	0.418													76	188	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	39873259	39873259	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39873259C>A	uc010kxp.2	+	1	447	c.90C>A	c.(88-90)CAC>CAA	p.H30Q						SubName: Full=Similar to sequence-specific single-stranded-DNA-binding protein;																		ATTTACTGCACGTAAGAGTAC	0.507													7	21	---	---	---	---	PASS
CDK13	8621	broad.mit.edu	37	7	40085608	40085608	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40085608A>T	uc003thh.3	+	6	2809	c.2527A>T	c.(2527-2529)ATC>TTC	p.I843F	CDK13_uc003thi.3_Missense_Mutation_p.I843F|CDK13_uc011kbf.1_Missense_Mutation_p.I229F	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1	843	Protein kinase.				alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5						ATGTTCCAATATCCTTCTAAA	0.219													58	216	---	---	---	---	PASS
ZMIZ2	83637	broad.mit.edu	37	7	44805139	44805139	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44805139C>A	uc003tlr.2	+	16	2326	c.2203C>A	c.(2203-2205)CCC>ACC	p.P735T	ZMIZ2_uc003tlq.2_Missense_Mutation_p.P677T|ZMIZ2_uc003tls.2_Missense_Mutation_p.P709T|ZMIZ2_uc003tlt.2_Missense_Mutation_p.P358T|ZMIZ2_uc010kyj.2_Missense_Mutation_p.P257T|ZMIZ2_uc003tlu.2_5'Flank	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	735	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding			ovary(2)|large_intestine(2)|breast(1)	5						CCCCCTGCAGCCCCCCTCAGT	0.692													8	21	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100349530	100349530	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100349530C>A	uc003uwj.2	+	14	1967	c.1802C>A	c.(1801-1803)TCC>TAC	p.S601Y	ZAN_uc003uwk.2_Missense_Mutation_p.S601Y|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	601	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CCCACCATCTCCACAGAAAAA	0.468													4	61	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100677787	100677787	+	Silent	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100677787C>A	uc003uxp.1	+	3	3143	c.3090C>A	c.(3088-3090)ACC>ACA	p.T1030T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1030	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|15.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					CTGAAGGTACCAGCATGCCAA	0.498													8	657	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121653811	121653811	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121653811G>A	uc003vjy.2	+	12	5106	c.4711G>A	c.(4711-4713)GCA>ACA	p.A1571T	PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1571	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						TTTCAGTTTTGCAGACACTAA	0.448													63	168	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142206550	142206550	+	Intron	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142206550C>T	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc011krx.1_Intron|uc011ksa.1_Intron|uc011ksc.1_RNA|uc003vyj.2_Missense_Mutation_p.R102H					SubName: Full=V_segment translation product; Flags: Fragment;																		TGTCTGGGAGCGGGTAGCTGA	0.522													45	118	---	---	---	---	PASS
TRPV5	56302	broad.mit.edu	37	7	142626641	142626641	+	Silent	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142626641G>A	uc003wby.1	-	4	633	c.369C>T	c.(367-369)ATC>ATT	p.I123I	TRPV5_uc003wbz.2_Silent_p.I123I	NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,	123	ANK 3.|Cytoplasmic (Potential).				protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)|skin(1)	6	Melanoma(164;0.059)					TCACAACAGCGATGTGCAGTG	0.622													46	137	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151846037	151846037	+	Silent	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151846037C>A	uc003wla.2	-	52	13194	c.12975G>T	c.(12973-12975)CTG>CTT	p.L4325L	MLL3_uc003wkz.2_Silent_p.L3443L|MLL3_uc003wkx.2_Silent_p.L483L|MLL3_uc003wky.2_Silent_p.L1889L	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	4325					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		CTGTCACCTTCAGCTCATCTG	0.542			N		medulloblastoma								4	71	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	4495044	4495044	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4495044C>A	uc011kwk.1	-	2	512	c.122G>T	c.(121-123)GGC>GTC	p.G41V		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	41	Extracellular (Potential).|CUB 1.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTCAATAGTGCCATTGGGACC	0.468													38	66	---	---	---	---	PASS
LZTS1	11178	broad.mit.edu	37	8	20112763	20112763	+	5'UTR	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20112763C>T	uc003wzr.2	-	1					LZTS1_uc010ltg.1_5'UTR	NM_021020	NP_066300	Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1						cell cycle|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	cell junction|dendritic spine|Golgi apparatus|nucleolus|nucleoplasm|postsynaptic density|postsynaptic membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		AAGGGGCAGTCGTGGCTCCGT	0.632													4	15	---	---	---	---	PASS
ELP3	55140	broad.mit.edu	37	8	27970578	27970578	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27970578G>A	uc003xgo.3	+	7	653	c.505G>A	c.(505-507)GTG>ATG	p.V169M	ELP3_uc003xgn.3_Missense_Mutation_p.V154M|ELP3_uc011laq.1_Missense_Mutation_p.V97M|ELP3_uc011lar.1_Missense_Mutation_p.V77M|ELP3_uc011las.1_Missense_Mutation_p.V50M|ELP3_uc011lat.1_Missense_Mutation_p.V50M	NM_018091	NP_060561	Q9H9T3	ELP3_HUMAN	elongation protein 3 homolog	169					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	histone acetyltransferase activity|iron-sulfur cluster binding|metal ion binding|phosphorylase kinase regulator activity|protein binding				0		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		GGAGTTTATTGTGATGGGTGG	0.333													16	154	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52359592	52359592	+	Silent	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52359592C>A	uc003xqu.3	-	12	1598	c.1497G>T	c.(1495-1497)GTG>GTT	p.V499V		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	499	Ig-like C2-type 3.				hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCTGCACAGACACCTTTTTCA	0.453													71	225	---	---	---	---	PASS
ZCCHC6	79670	broad.mit.edu	37	9	88938317	88938317	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88938317G>A	uc004aoq.2	-	13	2563	c.2348C>T	c.(2347-2349)TCA>TTA	p.S783L	ZCCHC6_uc011ltf.1_RNA|ZCCHC6_uc004aor.2_RNA|ZCCHC6_uc004aos.2_RNA|ZCCHC6_uc004aot.2_Missense_Mutation_p.S660L|ZCCHC6_uc004aou.2_Missense_Mutation_p.S783L	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	783					RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						AGTGCTCTCTGACTCATTATT	0.443													34	218	---	---	---	---	PASS
CERCAM	51148	broad.mit.edu	37	9	131196482	131196482	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131196482G>T	uc004buz.3	+	10	1703	c.1305G>T	c.(1303-1305)GAG>GAT	p.E435D	CERCAM_uc004buy.1_Missense_Mutation_p.E357D|CERCAM_uc010mxz.2_Missense_Mutation_p.E357D|CERCAM_uc010mya.1_Missense_Mutation_p.E276D	NM_016174	NP_057258	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule 1	435					cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1						AGGATGTGGAGGCAGAGAAAC	0.637													12	37	---	---	---	---	PASS
CERCAM	51148	broad.mit.edu	37	9	131196483	131196483	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131196483G>T	uc004buz.3	+	10	1704	c.1306G>T	c.(1306-1308)GCA>TCA	p.A436S	CERCAM_uc004buy.1_Missense_Mutation_p.A358S|CERCAM_uc010mxz.2_Missense_Mutation_p.A358S|CERCAM_uc010mya.1_Missense_Mutation_p.A277S	NM_016174	NP_057258	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule 1	436					cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1						GGATGTGGAGGCAGAGAAACT	0.637													12	38	---	---	---	---	PASS
CARD9	64170	broad.mit.edu	37	9	139266450	139266450	+	Silent	SNP	G	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139266450G>C	uc004chg.3	-	2	247	c.81C>G	c.(79-81)CCC>CCG	p.P27P	CARD9_uc011mdw.1_Silent_p.P27P|CARD9_uc011mdx.1_Intron|CARD9_uc010nbj.2_Silent_p.P27P	NM_052813	NP_434700	Q9H257	CARD9_HUMAN	caspase recruitment domain protein 9 isoform 1	27	CARD.				positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of stress-activated MAPK cascade|regulation of apoptosis	cytoplasm	CARD domain binding|protein homodimerization activity			pancreas(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		TGATGCGTGAGGGGTCGATGA	0.622													81	124	---	---	---	---	PASS
CAMK1D	57118	broad.mit.edu	37	10	12833177	12833177	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12833177A>C	uc001ilo.2	+	6	821	c.586A>C	c.(586-588)AAA>CAA	p.K196Q	CAMK1D_uc001iln.2_Missense_Mutation_p.K196Q	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	196	Protein kinase.					calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		CCTCGCCCAGAAACCTTACAG	0.493													21	117	---	---	---	---	PASS
C10orf68	79741	broad.mit.edu	37	10	33134530	33134530	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33134530A>C	uc001iwn.3	+	15	1698	c.1225A>C	c.(1225-1227)ACG>CCG	p.T409P	C10orf68_uc001iwl.1_Missense_Mutation_p.T368P|C10orf68_uc001iwm.1_Missense_Mutation_p.T413P|C10orf68_uc010qei.1_Missense_Mutation_p.T385P|C10orf68_uc001iwo.3_RNA	NM_024688	NP_078964	Q9H943	CJ068_HUMAN	chromosome 10 open reading frame 68	409										skin(2)|ovary(1)	3						GGAGTCAACCACGACACAATT	0.308													16	171	---	---	---	---	PASS
GSTO2	119391	broad.mit.edu	37	10	106059125	106059125	+	3'UTR	SNP	G	A	A	rs139792812	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106059125G>A	uc001kyb.2	+	7					GSTO2_uc010qqx.1_3'UTR|GSTO2_uc001kyc.2_3'UTR|GSTO2_uc010qqy.1_3'UTR|uc001kyd.1_5'Flank	NM_183239	NP_899062	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2						water-soluble vitamin metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)	GAACCAATCCGTCTCTCTTTC	0.463													28	71	---	---	---	---	PASS
HMX2	3167	broad.mit.edu	37	10	124909310	124909310	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124909310G>T	uc001lhc.1	+	2	750	c.493G>T	c.(493-495)GAG>TAG	p.E165*		NM_005519	NP_005510	A2RU54	HMX2_HUMAN	H6 family homeobox 2	165	Homeobox.				cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_neural(114;0.169)|Colorectal(57;0.207)|Glioma(114;0.222)		Colorectal(40;0.123)|COAD - Colon adenocarcinoma(40;0.141)		GTACCAGCTCGAGTCCACCTT	0.682													3	45	---	---	---	---	PASS
RCOR2	283248	broad.mit.edu	37	11	63683945	63683945	+	5'UTR	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63683945C>A	uc001nyc.2	-	1						NM_173587	NP_775858	Q8IZ40	RCOR2_HUMAN	REST corepressor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)|skin(1)	2						GCCCAGCTGCCCCGGGGGGCG	0.706											OREG0021039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	10	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65266030	65266030	+	RNA	SNP	C	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65266030C>G	uc010roh.1	+	1		c.798C>G				NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						CGCAGGACTGCAAGCAGTTGG	0.517													15	47	---	---	---	---	PASS
AMICA1	120425	broad.mit.edu	37	11	118068750	118068750	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118068750T>G	uc001psk.2	-	8	1142	c.968A>C	c.(967-969)AAA>ACA	p.K323T	AMICA1_uc001psg.2_Missense_Mutation_p.K133T|AMICA1_uc001psh.2_Missense_Mutation_p.K284T|AMICA1_uc009yzw.1_RNA|AMICA1_uc001psi.2_Missense_Mutation_p.K313T|AMICA1_uc001psj.2_Missense_Mutation_p.K312T|AMICA1_uc010rxw.1_Missense_Mutation_p.K284T|AMICA1_uc010rxx.1_Missense_Mutation_p.K323T|AMICA1_uc001psl.1_Missense_Mutation_p.K279T	NM_001098526	NP_001091996	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen	323	Cytoplasmic (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		GGGTTTTTCTTTTATCTCTGG	0.458											OREG0021382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	61	138	---	---	---	---	PASS
KLRC1	3821	broad.mit.edu	37	12	10599220	10599220	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10599220A>C	uc001qyl.2	-	7	796	c.632T>G	c.(631-633)CTA>CGA	p.L211R	KLRC1_uc009zhm.1_Missense_Mutation_p.L211R|KLRC1_uc001qym.2_Missense_Mutation_p.L193R|KLRC1_uc001qyn.2_Missense_Mutation_p.L211R|KLRC1_uc001qyo.2_Missense_Mutation_p.L193R	NM_002259	NP_002250	P26715	NKG2A_HUMAN	killer cell lectin-like receptor subfamily C,	211	C-type lectin.|Extracellular (Potential).				cell surface receptor linked signaling pathway|regulation of immune response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0						ATTTACTTGTAGCACTGCACA	0.348													101	207	---	---	---	---	PASS
SENP1	29843	broad.mit.edu	37	12	48495290	48495290	+	5'UTR	SNP	A	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48495290A>T	uc001rqx.2	-	2					SENP1_uc001rqw.2_5'UTR|SENP1_uc001rqy.2_5'UTR|SENP1_uc001rqz.2_5'UTR|SENP1_uc009zkx.2_5'UTR	NM_014554	NP_055369	Q9P0U3	SENP1_HUMAN	sentrin/SUMO-specific protease 1						activation of caspase activity|induction of apoptosis by extracellular signals|protein desumoylation|proteolysis	cytoplasm|nucleus	endopeptidase activity|SUMO-specific protease activity			pancreas(2)|lung(1)	3		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TTTAGCAAAGATACAAAGTCC	0.343													15	34	---	---	---	---	PASS
PRKAG1	5571	broad.mit.edu	37	12	49398646	49398646	+	Intron	SNP	C	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49398646C>G	uc001rsy.2	-						uc001rsw.2_Intron|PRKAG1_uc010smd.1_Intron|PRKAG1_uc001rsx.2_Intron|PRKAG1_uc001rsz.2_Intron|PRKAG1_uc009zlb.2_Intron|PRKAG1_uc010sme.1_3'UTR	NM_002733	NP_002724	P54619	AAKG1_HUMAN	AMP-activated protein kinase, noncatalytic						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|positive regulation of protein kinase activity|regulation of fatty acid oxidation|regulation of glycolysis|spermatogenesis	cytosol	cAMP-dependent protein kinase activity|cAMP-dependent protein kinase regulator activity|protein kinase binding			kidney(1)	1						gtgtgtgtgtCTTTTCTCTCT	0.244													5	74	---	---	---	---	PASS
XRCC6BP1	91419	broad.mit.edu	37	12	58340855	58340855	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58340855C>A	uc001sqp.2	+	3	351	c.311C>A	c.(310-312)TCT>TAT	p.S104Y		NM_033276	NP_150592	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	104					double-strand break repair via nonhomologous end joining	DNA-dependent protein kinase-DNA ligase 4 complex	DNA-dependent protein kinase activity|metal ion binding|metalloendopeptidase activity			ovary(1)	1						GCTTCAACATCTCAGGTAGGC	0.388													51	237	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20039633	20039633	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20039633C>G	uc001umd.2	-	9	795	c.584G>C	c.(583-585)AGA>ACA	p.R195T	TPTE2_uc009zzk.2_RNA|TPTE2_uc009zzl.2_Missense_Mutation_p.R84T|TPTE2_uc001ume.2_Missense_Mutation_p.R118T|TPTE2_uc009zzm.2_5'UTR|TPTE2_uc010tcm.1_RNA	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	195						endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TTCAAGTTGTCTTTTTTGATG	0.328													15	58	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32915021	32915021	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32915021A>G	uc001uub.1	+	11	6756	c.6529A>G	c.(6529-6531)ATT>GTT	p.I2177V		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	2177					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TGTTGAGAACATTCATGTTTT	0.318			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			20	71	---	---	---	---	PASS
MAB21L1	4081	broad.mit.edu	37	13	36049121	36049121	+	3'UTR	SNP	G	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36049121G>T	uc001uvc.2	-	1					NBEA_uc001uvb.2_Intron|NBEA_uc010abi.2_Intron|NBEA_uc010tee.1_Intron|NBEA_uc010tef.1_5'Flank|NBEA_uc010teg.1_5'Flank	NM_005584	NP_005575	Q13394	MB211_HUMAN	mab-21-like protein 1						anatomical structure morphogenesis	nucleus				ovary(2)	2		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		TGGAATATTAGGAATTGAACA	0.348													4	116	---	---	---	---	PASS
HEATR5A	25938	broad.mit.edu	37	14	31926626	31926626	+	5'UTR	SNP	A	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31926626A>G	uc010tpk.1	-	1					C14orf126_uc001wrj.2_5'UTR	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		GCGGCCGGACAGTTACTAGGC	0.706													2	1	---	---	---	---	PASS
CTDSPL2	51496	broad.mit.edu	37	15	44751276	44751276	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44751276A>T	uc001ztr.2	+	2	480	c.64A>T	c.(64-66)AGA>TGA	p.R22*	CTDSPL2_uc001zts.2_Nonsense_Mutation_p.R22*|CTDSPL2_uc001ztt.2_Nonsense_Mutation_p.R22*|CTDSPL2_uc010bdv.2_Nonsense_Mutation_p.R22*	NM_016396	NP_057480	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	22							phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		ACGCACTGCCAGAGCAAAGAG	0.403													47	138	---	---	---	---	PASS
FANCI	55215	broad.mit.edu	37	15	89837084	89837084	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89837084T>C	uc010bnp.1	+	23	2402	c.2312T>C	c.(2311-2313)ATT>ACT	p.I771T	FANCI_uc002bnm.1_Missense_Mutation_p.I771T|FANCI_uc002bnn.1_RNA|FANCI_uc002bnp.1_Missense_Mutation_p.I592T|FANCI_uc002bnq.1_Missense_Mutation_p.I184T	NM_001113378	NP_001106849	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I isoform	771					cell cycle|DNA repair	nucleoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					TTTGAGGACATTCTGAGCTTA	0.318								Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				84	212	---	---	---	---	PASS
FBXL16	146330	broad.mit.edu	37	16	745593	745593	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:745593G>C	uc002cjc.2	-	4	1167	c.964C>G	c.(964-966)CTC>GTC	p.L322V	FBXL16_uc002cja.2_5'Flank|FBXL16_uc002cjb.2_Missense_Mutation_p.L110V	NM_153350	NP_699181	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	322	LRR 3.										0		Hepatocellular(780;0.0218)				AGCGCGGTGAGGTTGGGCAGG	0.687													13	25	---	---	---	---	PASS
WSCD1	23302	broad.mit.edu	37	17	6021491	6021491	+	Missense_Mutation	SNP	G	A	A	rs112285134		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6021491G>A	uc010cli.2	+	8	1737	c.1358G>A	c.(1357-1359)CGC>CAC	p.R453H	WSCD1_uc002gcn.2_Missense_Mutation_p.R453H|WSCD1_uc002gco.2_Missense_Mutation_p.R453H|WSCD1_uc010clj.2_Missense_Mutation_p.R144H	NM_015253	NP_056068	Q658N2	WSCD1_HUMAN	WSC domain containing 1	453						integral to membrane	sulfotransferase activity				0						GCAGCTGACCGCAACTGGAAG	0.517													18	63	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14513764C>T	uc010dln.2	-	10	1884	c.1430G>A	c.(1429-1431)CGG>CAG	p.R477Q	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	477										skin(3)	3						AAGTTGTTTCCGGGTATCATT	0.358													4	96	---	---	---	---	PASS
ATP5A1	498	broad.mit.edu	37	18	43666148	43666148	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43666148C>T	uc002lbr.1	-	10	1450	c.1360G>A	c.(1360-1362)GAT>AAT	p.D454N	ATP5A1_uc010dnl.1_Missense_Mutation_p.D404N|ATP5A1_uc002lbs.1_Missense_Mutation_p.D404N|ATP5A1_uc002lbt.1_Missense_Mutation_p.D454N	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	454					ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0						GTGGCAGCATCGAGGTCAGAA	0.463													29	69	---	---	---	---	PASS
MKNK2	2872	broad.mit.edu	37	19	2041152	2041152	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2041152C>T	uc002lus.2	-	12	1242	c.997G>A	c.(997-999)GAC>AAC	p.D333N	MKNK2_uc002luq.1_Missense_Mutation_p.D77N|MKNK2_uc010xgu.1_Missense_Mutation_p.D172N|MKNK2_uc010xgv.1_Missense_Mutation_p.D202N|MKNK2_uc002lur.2_Missense_Mutation_p.D333N|MKNK2_uc002lut.1_Missense_Mutation_p.D77N	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2	333	Protein kinase.				cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGCCCAGTCCTTGTCGGGG	0.602													8	184	---	---	---	---	PASS
ZNF846	162993	broad.mit.edu	37	19	9869141	9869141	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9869141C>A	uc002mmb.1	-	6	1143	c.612G>T	c.(610-612)TGG>TGT	p.W204C	ZNF846_uc010xky.1_RNA|ZNF846_uc010xkz.1_RNA|ZNF846_uc010dww.2_Missense_Mutation_p.W75C|ZNF846_uc002mmc.1_Missense_Mutation_p.W75C	NM_001077624	NP_001071092	Q147U1	ZN846_HUMAN	zinc finger protein 846	204	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GAAAAGTTCTCCAACAGTCTT	0.353													5	189	---	---	---	---	PASS
PGLYRP2	114770	broad.mit.edu	37	19	15587107	15587107	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15587107A>T	uc002nbf.3	-	2	507	c.374T>A	c.(373-375)CTG>CAG	p.L125Q	PGLYRP2_uc002nbg.3_Missense_Mutation_p.L125Q	NM_052890	NP_443122	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2 precursor	125					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptide amidation|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)	3						CAGCCCCGCCAGCAGAGGCTC	0.612													50	127	---	---	---	---	PASS
ZNF493	284443	broad.mit.edu	37	19	21607620	21607620	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21607620A>G	uc002npx.2	+	2	2055	c.1775A>G	c.(1774-1776)AAA>AGA	p.K592R	ZNF493_uc002npw.2_Missense_Mutation_p.K720R|ZNF493_uc002npy.2_Missense_Mutation_p.K592R	NM_175910	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 1	592	C2H2-type 21.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GAATGTGGCAAAGCTTTTAAC	0.368													16	52	---	---	---	---	PASS
GYS1	2997	broad.mit.edu	37	19	49481407	49481407	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49481407C>T	uc002plp.2	-	9	1418	c.1177G>A	c.(1177-1179)GCC>ACC	p.A393T	GYS1_uc010xzy.1_Missense_Mutation_p.A26T|GYS1_uc010emm.2_Missense_Mutation_p.A329T|GYS1_uc010xzz.1_Missense_Mutation_p.A313T|GYS1_uc010yaa.1_RNA	NM_002103	NP_002094	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle) isoform 1	393					glucose metabolic process|glycogen biosynthetic process	cytosol	glycogen (starch) synthase activity|protein binding			ovary(2)	2		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		ACCGTGTTGGCCGTGTCCCTG	0.473													5	179	---	---	---	---	PASS
C21orf99	149992	broad.mit.edu	37	21	14439357	14439357	+	RNA	SNP	C	G	G			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14439357C>G	uc002yja.3	+	10		c.2875C>G				NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						TGAATCAGCTCAATCAATCGC	0.274													2	7	---	---	---	---	PASS
DOPEY2	9980	broad.mit.edu	37	21	37653892	37653892	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37653892A>C	uc002yvg.2	+	32	6222	c.6143A>C	c.(6142-6144)TAC>TCC	p.Y2048S	DOPEY2_uc011aeb.1_Missense_Mutation_p.Y1997S	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	2048					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						TACCACCTTTACCTTCCACTG	0.264													11	31	---	---	---	---	PASS
TLR7	51284	broad.mit.edu	37	X	12906241	12906241	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12906241C>T	uc004cvc.2	+	3	2753	c.2614C>T	c.(2614-2616)CAT>TAT	p.H872Y		NM_016562	NP_057646	Q9NYK1	TLR7_HUMAN	toll-like receptor 7 precursor	872	Cytoplasmic (Potential).				cellular response to mechanical stimulus|defense response to virus|I-kappaB phosphorylation|inflammatory response|innate immune response|positive regulation of chemokine production|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus	early phagosome|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosome|plasma membrane	double-stranded RNA binding|single-stranded RNA binding|siRNA binding|transmembrane receptor activity			ovary(2)|lung(2)|breast(1)	5					Imiquimod(DB00724)	GTATATTTACCATTTCTGTAA	0.403													122	126	---	---	---	---	PASS
IKBKG	8517	broad.mit.edu	37	X	153770607	153770607	+	Silent	SNP	G	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153770607G>T	uc011mzr.1	+	1	149	c.129G>T	c.(127-129)GGG>GGT	p.G43G	G6PD_uc004flx.1_Intron|G6PD_uc004fly.1_Intron	NM_001099856	NP_001093326	Q9Y6K9	NEMO_HUMAN	inhibitor of kappa light polypeptide gene	Error:Variant_position_missing_in_Q9Y6K9_after_alignment					activation of MAPK activity|induction of apoptosis|innate immune response|interspecies interaction between organisms|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|response to DNA damage stimulus|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription, DNA-dependent	cytosol|nucleus	metal ion binding|protein domain specific binding|signal transducer activity				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CATCAGGTGGGGAAAGATGCT	0.517									Incontinentia_Pigmenti_type_2				4	26	---	---	---	---	PASS
MMEL1	79258	broad.mit.edu	37	1	2528294	2528295	+	Intron	INS	-	GCG	GCG			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2528294_2528295insGCG	uc001ajy.2	-						MMEL1_uc009vlg.1_Intron	NM_033467	NP_258428	Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1						proteolysis	extracellular region|integral to membrane|intracellular membrane-bounded organelle	metal ion binding|metalloendopeptidase activity				0	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		TGGGTGCTGCTGCGGCGGGGGG	0.658													2	6	---	---	---	---	
ACOT7	11332	broad.mit.edu	37	1	6390127	6390128	+	Intron	DEL	GT	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6390127_6390128delGT	uc001ams.2	-						ACOT7_uc010nzq.1_Intron|ACOT7_uc001amt.2_Intron|ACOT7_uc001amu.2_Intron|ACOT7_uc001amv.2_Intron|ACOT7_uc001amq.2_Intron|ACOT7_uc001amr.2_Intron	NM_181864	NP_863654	O00154	BACH_HUMAN	acyl-CoA thioesterase 7 isoform hBACHb							mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		tgtgtgtgtggtgtgtgtgtgt	0.262													4	2	---	---	---	---	
CTRC	11330	broad.mit.edu	37	1	15772454	15772455	+	Intron	INS	-	ATTT	ATTT	rs150994793	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15772454_15772455insATTT	uc001awi.1	+						CTRC_uc001awj.1_Intron	NM_007272	NP_009203	Q99895	CTRC_HUMAN	chymotrypsin C preproprotein						proteolysis		serine-type endopeptidase activity				0		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ttcactcatgcattcattcatt	0.000													4	8	---	---	---	---	
KIF17	57576	broad.mit.edu	37	1	21039808	21039808	+	Intron	DEL	A	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21039808delA	uc001bdr.3	-						KIF17_uc001bds.3_Intron	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a						microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		ttttttaattaaaaaaaaaaa	0.259													4	2	---	---	---	---	
TCEB3	6924	broad.mit.edu	37	1	24082687	24082687	+	Intron	DEL	A	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24082687delA	uc001bho.2	+							NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A						positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		CAGGGCACTCAAAAAGCCCGT	0.493													4	2	---	---	---	---	
SGIP1	84251	broad.mit.edu	37	1	67160938	67160939	+	Intron	INS	-	A	A	rs5774833		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67160938_67160939insA	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|SGIP1_uc009wat.2_Intron|SGIP1_uc001dcu.2_5'UTR	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						TTTCCTGAACTAAAAAAAAAAA	0.441													4	3	---	---	---	---	
ABCD3	5825	broad.mit.edu	37	1	94883978	94883980	+	5'UTR	DEL	GCC	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94883978_94883980delGCC	uc001dqn.3	+	1					ABCD3_uc001dqm.3_5'UTR|ABCD3_uc010oto.1_5'UTR|ABCD3_uc010otp.1_5'UTR|ABCD3_uc009wdr.2_5'UTR	NM_002858	NP_002849	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D, member 3						peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		CAGTAAGGTAgccgccgccgccg	0.404													5	3	---	---	---	---	
AHCYL1	10768	broad.mit.edu	37	1	110558746	110558746	+	Intron	DEL	T	-	-	rs145081118		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110558746delT	uc001dyx.2	+						AHCYL1_uc010ovw.1_Intron|AHCYL1_uc001dyy.2_Intron|AHCYL1_uc010ovx.1_Intron	NM_006621	NP_006612	O43865	SAHH2_HUMAN	S-adenosylhomocysteine hydrolase-like 1						one-carbon metabolic process	endoplasmic reticulum	adenosylhomocysteinase activity			ovary(1)	1		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		ATTGAAAGGCTTTTTTTTTTC	0.343													7	4	---	---	---	---	
NBPF7	343505	broad.mit.edu	37	1	120379737	120379737	+	Intron	DEL	G	-	-	rs67014534		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120379737delG	uc010oxk.1	-							NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505							cytoplasm				ovary(1)|skin(1)	2	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)		tctcaaaaaagaaaaaaaaag	0.139													5	3	---	---	---	---	
CELF3	11189	broad.mit.edu	37	1	151677284	151677285	+	Intron	INS	-	GT	GT	rs138717096	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151677284_151677285insGT	uc001eys.1	-						CELF3_uc010pdh.1_Intron|CELF3_uc001eyr.2_Intron|CELF3_uc009wmy.2_Intron|CELF3_uc009wmx.1_Intron	NM_007185	NP_009116	Q5SZQ8	CELF3_HUMAN	trinucleotide repeat containing 4						nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	mRNA binding|nucleotide binding			ovary(1)|central_nervous_system(1)	2						GGTCACGGAGGGTGTGTGTGTG	0.460													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158165971	158165974	+	IGR	DEL	CCTT	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158165971_158165974delCCTT								CD1D (9757 upstream) : CD1A (57953 downstream)																							GCCCTCCGTCccttccttccttcc	0.265													6	5	---	---	---	---	
GCKR	2646	broad.mit.edu	37	2	27729202	27729202	+	Intron	DEL	G	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27729202delG	uc002rky.2	+						GCKR_uc010ezd.2_Intron|GCKR_uc010ylu.1_Intron	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein						carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)					TCGGAACGCAGTCTGGGCCTA	0.562													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38710019	38710019	+	3'UTR	DEL	T	-	-	rs57303101		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38710019delT	uc002rqu.1	+	2										SubName: Full=RPLP0 protein;																		CTTtaaaaaataaataaataa	0.239													9	6	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39075474	39075474	+	Frame_Shift_Del	DEL	C	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39075474delC	uc002rrf.2	-	10	2200	c.2101delG	c.(2101-2103)GCAfs	p.A701fs	DHX57_uc002rrd.3_Frame_Shift_Del_p.A85fs|DHX57_uc002rre.2_Frame_Shift_Del_p.A134fs	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	701	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				TTTAGAGTTGCACTCATTAAA	0.353													130	59	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85930718	85930725	+	IGR	DEL	TCCCTCCC	-	-	rs113231454		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85930718_85930725delTCCCTCCC								GNLY (4844 upstream) : ATOH8 (50184 downstream)																							tttccttccttccctccctccctccctc	0.034													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106984902	106984903	+	IGR	DEL	AA	-	-	rs7570576		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106984902_106984903delAA								UXS1 (174107 upstream) : PLGLA (17866 downstream)																							ATGATGAATTAAtttctttttt	0.238													4	2	---	---	---	---	
PLEKHB2	55041	broad.mit.edu	37	2	132109442	132109446	+	Intron	DEL	TTTTG	-	-	rs70994755		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132109442_132109446delTTTTG	uc002tsh.2	+									Q96CS7	PKHB2_HUMAN	SubName: Full=Putative uncharacterized protein PLEKHB2;							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)		attttcttTCTTTTGTTTTGTTTTA	0.234													7	4	---	---	---	---	
NOSTRIN	115677	broad.mit.edu	37	2	169691000	169691001	+	Intron	INS	-	GC	GC	rs145224351	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169691000_169691001insGC	uc002ueg.2	+						NOSTRIN_uc002uef.2_Intron|NOSTRIN_uc002uei.2_Intron|NOSTRIN_uc010fpu.2_Intron|NOSTRIN_uc002ueh.2_Intron|NOSTRIN_uc002uej.2_Intron	NM_001039724	NP_001034813	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0						ATTACTGGCGTGCGCGCGCGCG	0.322													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221501609	221501610	+	IGR	INS	-	GT	GT	rs140576371	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221501609_221501610insGT								SLC4A3 (994908 upstream) : EPHA4 (781139 downstream)																							taaGAACCtgcgtgtgtgtgtg	0.020													1	5	---	---	---	---	
TRIP12	9320	broad.mit.edu	37	2	230634173	230634174	+	Intron	INS	-	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230634173_230634174insA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		GACCTCTTTCCaaaaaaaaaaa	0.337													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75264910	75264911	+	IGR	DEL	AA	-	-	rs35563675		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75264910_75264911delAA								CNTN3 (694567 upstream) : FAM86D (205794 downstream)																							TGATGACCCCaaaaaaaaaaaa	0.297													4	2	---	---	---	---	
RNF168	165918	broad.mit.edu	37	3	196215352	196215353	+	Intron	INS	-	A	A	rs66889619		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196215352_196215353insA	uc003fwq.2	-						RNF168_uc010iah.2_Intron	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168						double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		gactccatctcaaaaaaaaaaa	0.104													3	8	---	---	---	---	
NFXL1	152518	broad.mit.edu	37	4	47916233	47916234	+	Intron	INS	-	A	A	rs77518238		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47916233_47916234insA	uc010igh.2	-						uc003gxr.1_5'Flank|NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						CTGCAAAGGAGAAAAAAAAAAA	0.629													4	2	---	---	---	---	
C5orf33	133686	broad.mit.edu	37	5	36197929	36197930	+	Intron	INS	-	A	A	rs138853300	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36197929_36197930insA	uc003jkf.3	-						C5orf33_uc003jke.3_Intron|C5orf33_uc010iux.2_Intron|C5orf33_uc003jkg.3_Intron|C5orf33_uc011cov.1_Intron	NM_001085411	NP_001078880	Q4G0N4	NAKD1_HUMAN	hypothetical protein LOC133686 isoform 1								NAD+ kinase activity				0	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			aacacagtaacaaaaaacctta	0.005													3	3	---	---	---	---	
HMGCS1	3157	broad.mit.edu	37	5	43297956	43297956	+	Intron	DEL	G	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43297956delG	uc003jnr.3	-						HMGCS1_uc003jnp.3_5'Flank|HMGCS1_uc003jnq.3_Intron	NM_001098272	NP_001091742	Q01581	HMCS1_HUMAN	hydroxymethylglutaryl-CoA synthase 1						cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	hydroxymethylglutaryl-CoA synthase activity				0						aaaaaaaaaagaaaaaaaaac	0.020													3	3	---	---	---	---	
ISL1	3670	broad.mit.edu	37	5	50687458	50687458	+	Intron	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50687458delT	uc003jor.2	+							NM_002202	NP_002193	P61371	ISL1_HUMAN	islet-1						generation of precursor metabolites and energy|multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3		Lung NSC(810;0.000845)|Breast(144;0.0411)				TCTTGGCATCTTTTTTTTTTT	0.428													4	2	---	---	---	---	
IK	3550	broad.mit.edu	37	5	140036984	140036985	+	Intron	INS	-	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140036984_140036985insT	uc003lgq.2	+						IK_uc011czk.1_Intron	NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein						cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tttgtgcaggctgttttatctc	0.104													6	6	---	---	---	---	
RNF144B	255488	broad.mit.edu	37	6	18459626	18459627	+	Intron	INS	-	TAAT	TAAT	rs141870285	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18459626_18459627insTAAT	uc003ncs.2	+							NM_182757	NP_877434	Q7Z419	R144B_HUMAN	IBR domain containing 2						apoptosis|positive regulation of anti-apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			GGTGGAAACTGTAATTATATAA	0.327													5	4	---	---	---	---	
GLO1	2739	broad.mit.edu	37	6	38670700	38670702	+	Intron	DEL	CGG	-	-	rs112098082		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38670700_38670702delCGG	uc003ooc.2	-							NM_006708	NP_006699	Q04760	LGUL_HUMAN	glyoxalase I						anti-apoptosis|carbohydrate metabolic process	cytoplasm	lactoylglutathione lyase activity|metal ion binding			ovary(1)	1					Glutathione(DB00143)	GGCCCGGTCCCGGCCCAGCGGAG	0.695													25	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	71730648	71730649	+	IGR	DEL	CA	-	-	rs9455294		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71730648_71730649delCA								B3GAT2 (63860 upstream) : OGFRL1 (267828 downstream)																							gataaacgcgcacgcacgcaca	0.000													3	3	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163273057	163273058	+	Intron	INS	-	AGGA	AGGA	rs73019521		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163273057_163273058insAGGA	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		ggaaggaaggaaggaaggaagg	0.149													6	3	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76796901	76796901	+	Intron	DEL	A	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76796901delA	uc003uga.2	+						CCDC146_uc003ufz.1_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GTTTATTTTTATTATTTTCCA	0.264													8	6	---	---	---	---	
PEX1	5189	broad.mit.edu	37	7	92135419	92135420	+	Intron	INS	-	AAGACTTAAAATTTCT	AAGACTTAAAATTTCT	rs145764168	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92135419_92135420insAAGACTTAAAATTTCT	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_Intron	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTAGAAAGCCAAAGAAATTTTA	0.272													8	5	---	---	---	---	
FAM3C	10447	broad.mit.edu	37	7	121023197	121023197	+	Intron	DEL	A	-	-	rs35702337		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121023197delA	uc003vjx.2	-						FAM3C_uc010lkm.2_Intron	NM_014888	NP_055703	Q92520	FAM3C_HUMAN	family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)					CATTGGCATTAAAAAAAAAAA	0.209													5	5	---	---	---	---	
STC1	6781	broad.mit.edu	37	8	23709570	23709571	+	Intron	DEL	TG	-	-	rs113294965		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23709570_23709571delTG	uc003xdw.1	-							NM_003155	NP_003146	P52823	STC1_HUMAN	stanniocalcin 1 precursor						cell surface receptor linked signaling pathway|cell-cell signaling|cellular calcium ion homeostasis		hormone activity			skin(3)|upper_aerodigestive_tract(1)	4		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		TGAGTGCCTCtgtgtgtgtgtg	0.431													4	5	---	---	---	---	
MTBP	27085	broad.mit.edu	37	8	121530792	121530792	+	Intron	DEL	T	-	-	rs34427476		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121530792delT	uc003ypc.1	+							NM_022045	NP_071328	Q96DY7	MTBP_HUMAN	Mdm2, transformed 3T3 cell double minute 2, p53						cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			ATGTTAGATCTTTTTTTTCTC	0.323													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68413567	68413567	+	RNA	DEL	G	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413567delG	uc004aex.2	+	1		c.122delG								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CTCCCCCAGTGGCGCCGGATC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69786404	69786404	+	IGR	DEL	G	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69786404delG								LOC100133920 (121455 upstream) : FOXD4L5 (389305 downstream)																							CCGCGGCGGTGGGGGGGGCAA	0.622													3	5	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126220283	126220284	+	Intron	INS	-	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126220283_126220284insT	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						ttttcttttccttttttttttt	0.213													4	2	---	---	---	---	
BAT2L1	84726	broad.mit.edu	37	9	134348819	134348819	+	Intron	DEL	G	-	-	rs5900941		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134348819delG	uc004can.3	+						BAT2L1_uc010mzj.1_Intron|BAT2L1_uc004cao.3_Intron	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like								protein binding				0						TAACTTCTTTGGGCCTTTGGT	0.478													3	4	---	---	---	---	
NRP1	8829	broad.mit.edu	37	10	33595283	33595284	+	Intron	INS	-	GTGTGTGT	GTGTGTGT	rs150221222	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33595283_33595284insGTGTGTGT	uc001iwx.3	-						NRP1_uc001iwv.3_Intron|NRP1_uc009xlz.2_Intron|NRP1_uc001iww.3_Intron|NRP1_uc001iwy.3_Intron|NRP1_uc001iwz.2_Intron|NRP1_uc001ixa.2_Intron|NRP1_uc001ixb.1_Intron|NRP1_uc001ixc.1_Intron	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)	GGGTCAGAAGGgtgtgtgtgtg	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42530673	42530674	+	IGR	INS	-	A	A	rs58302682		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42530673_42530674insA								None (None upstream) : LOC441666 (296641 downstream)																							tctctctaaagaacgttcaact	0.000													5	7	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95066945	95066945	+	Intron	DEL	A	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95066945delA	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						tgccagtagcacccccccgcc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	99823423	99823430	+	IGR	DEL	TCTTTCTT	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99823423_99823430delTCTTTCTT								CRTAC1 (32838 upstream) : C10orf28 (70951 downstream)																							cctccctccctctttctttctttctttc	0.000													4	2	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108432894	108432895	+	Intron	INS	-	T	T	rs72369490		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108432894_108432895insT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		gaagagggtacttttttttttt	0.005													4	5	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112363876	112363877	+	Intron	DEL	CT	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112363876_112363877delCT	uc001kze.2	+							NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		aaaaaaaaaactaaaaaTTAAA	0.109													9	5	---	---	---	---	
VWA2	340706	broad.mit.edu	37	10	116014989	116014989	+	Intron	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116014989delT	uc001lbl.1	+						VWA2_uc001lbk.1_Intron|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)		catctttttcttttttttttt	0.000													11	5	---	---	---	---	
VEGFB	7423	broad.mit.edu	37	11	64003992	64003992	+	Intron	DEL	C	-	-	rs67594350		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64003992delC	uc001nyw.2	+						VEGFB_uc001nyx.2_Intron	NM_003377	NP_003368	P49765	VEGFB_HUMAN	vascular endothelial growth factor B precursor						anti-apoptosis|induction of positive chemotaxis|negative regulation of gene expression|negative regulation of neuron apoptosis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of endothelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of mast cell chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of vascular endothelial growth factor receptor signaling pathway|positive regulation of vascular wound healing|vascular endothelial growth factor receptor signaling pathway	extracellular region|extracellular space|membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity|heparin binding|vascular endothelial growth factor receptor 1 binding				0						tcgagaccatcctggctaaca	0.035													3	6	---	---	---	---	
XRRA1	143570	broad.mit.edu	37	11	74645032	74645033	+	Intron	INS	-	TTCA	TTCA	rs140602440	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74645032_74645033insTTCA	uc009yub.2	-						XRRA1_uc001ovm.2_Intron|XRRA1_uc001ovo.2_Intron|XRRA1_uc001ovq.3_Intron|XRRA1_uc001ovp.3_Intron|XRRA1_uc001ovr.2_Intron	NM_182969	NP_892014	Q6P2D8	XRRA1_HUMAN	X-ray radiation resistance associated 1						response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1						TTGTTTGCTTGttcattcattc	0.193													5	3	---	---	---	---	
GAB2	9846	broad.mit.edu	37	11	77960895	77960895	+	Intron	DEL	T	-	-	rs67790560		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77960895delT	uc001ozh.2	-						GAB2_uc001ozg.2_Intron	NM_080491	NP_536739	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			AAATTGACTGTTTTTTTTTGC	0.308													5	4	---	---	---	---	
CORO1C	23603	broad.mit.edu	37	12	109071794	109071795	+	Intron	INS	-	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109071794_109071795insA	uc001tnj.2	-						CORO1C_uc009zva.2_Intron|CORO1C_uc010sxf.1_Intron	NM_014325	NP_055140	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C isoform 1						actin cytoskeleton organization|phagocytosis|signal transduction	actin cytoskeleton	actin filament binding			skin(3)	3						gactccatctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
ACACB	32	broad.mit.edu	37	12	109697644	109697652	+	Intron	DEL	TTGGATCAC	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109697644_109697652delTTGGATCAC	uc001tob.2	+						ACACB_uc001toc.2_Intron|ACACB_uc010sxl.1_Intron|ACACB_uc001tod.2_Intron|ACACB_uc010sxm.1_Intron	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	AGAGTGGCTGTTGGATcactggggtgttg	0.254													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965106	117965107	+	Intron	DEL	AG	-	-	rs68177299		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965106_117965107delAG	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acacacacacagacacacacac	0.223													2	4	---	---	---	---	
UNC119B	84747	broad.mit.edu	37	12	121147574	121147576	+	5'Flank	DEL	TTC	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121147574_121147576delTTC	uc001tyz.2	+							NM_001080533	NP_001074002	A6NIH7	U119B_HUMAN	unc-119 homolog B											haematopoietic_and_lymphoid_tissue(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					acactggccattcttCTTCTTGG	0.227													16	13	---	---	---	---	
FZD10	11211	broad.mit.edu	37	12	130649316	130649317	+	3'UTR	INS	-	T	T	rs112714527		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130649316_130649317insT	uc001uii.2	+	1					uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor						brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|gonad development|negative regulation of Rho GTPase activity|neuron differentiation|non-canonical Wnt receptor signaling pathway|positive regulation of JUN kinase activity|positive regulation of Rac GTPase activity|regulation of actin cytoskeleton organization|vasculature development	cell projection|cell surface|cytoplasm|integral to plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(3)|breast(1)|central_nervous_system(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		tcttcttcttcttttttttttt	0.386													4	2	---	---	---	---	
INTS6	26512	broad.mit.edu	37	13	51936274	51936274	+	3'UTR	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51936274delT	uc001vfk.2	-	18					SERPINE3_uc010tgp.1_Intron|INTS6_uc001vfi.2_3'UTR|INTS6_uc001vfj.2_3'UTR|INTS6_uc001vfl.2_3'UTR	NM_012141	NP_036273	Q9UL03	INT6_HUMAN	integrator complex subunit 6 isoform a						snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity			ovary(1)|lung(1)	2		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		TTAATGTAGATTTTTTTTTTT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22111425	22111425	+	Intron	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22111425delT	uc001wbk.3	+											SubName: Full=Putative uncharacterized protein ENSP00000374930;																		GAATCTCTCCTTAATGGCAAT	0.353													10	8	---	---	---	---	
MARK3	4140	broad.mit.edu	37	14	103934350	103934350	+	Intron	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103934350delT	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron|MARK3_uc010tyb.1_Intron	NM_001128918	NP_001122390	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)			GTTTGCTCTGTTTTTCTCATT	0.408													71	34	---	---	---	---	
TRPM7	54822	broad.mit.edu	37	15	50882045	50882046	+	Intron	INS	-	TTTTTTG	TTTTTTG	rs148695282	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50882045_50882046insTTTTTTG	uc001zyt.3	-						TRPM7_uc010bew.1_Intron	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,						cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AGGTTACAGttttttttgtttt	0.178													4	3	---	---	---	---	
GOLGA6L10	647042	broad.mit.edu	37	15	83014189	83014190	+	Intron	DEL	AA	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83014189_83014190delAA	uc010unt.1	-						uc002bhl.2_Intron|uc002bhm.2_Intron|GOLGA6L10_uc010uny.1_Intron|GOLGA6L10_uc002bia.1_5'Flank			A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						CTGGATTCTCAAAAAAAAAAAA	0.515													6	3	---	---	---	---	
LRRK1	79705	broad.mit.edu	37	15	101481669	101481670	+	Intron	INS	-	TG	TG	rs72076312		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101481669_101481670insTG	uc002bwr.2	+						LRRK1_uc010usb.1_Intron|LRRK1_uc010usc.1_Intron|LRRK1_uc002bwq.1_Intron	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1						small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			gtctatgtctctgtgtgtgtgt	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102293062	102293064	+	Intron	DEL	CTC	-	-	rs62026972		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102293062_102293064delCTC	uc010usj.1	+						uc002bxo.2_5'Flank|uc002bxp.3_RNA|uc002bxq.2_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank|uc002bys.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		AGTTCATCTTCTCAGAGCTGCTG	0.576													4	4	---	---	---	---	
BAIAP3	8938	broad.mit.edu	37	16	1396789	1396806	+	Intron	DEL	GCAGGTGGGGCCAGCGGG	-	-	rs3215518		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1396789_1396806delGCAGGTGGGGCCAGCGGG	uc002clk.1	+						BAIAP3_uc002clj.2_Intron|BAIAP3_uc010uuz.1_Intron|BAIAP3_uc010uva.1_Intron|BAIAP3_uc010uvc.1_Intron	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3						G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)				AGGCCATTCTGCAGGTGGGGCCAGCGGGGCAGGTGGGG	0.716													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	3010024	3010035	+	IGR	DEL	ACCTACCTACCT	-	-	rs111260640		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3010024_3010035delACCTACCTACCT								FLYWCH1 (8816 upstream) : KREMEN2 (4182 downstream)																							caaccaaccaacctacctacctacctacctac	0.009													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9250235	9250236	+	IGR	INS	-	T	T			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9250235_9250236insT								C16orf72 (36690 upstream) : GRIN2A (597031 downstream)																							GAGGTCCTTTATTTTTTTTTTT	0.376													5	4	---	---	---	---	
TNFRSF17	608	broad.mit.edu	37	16	12061912	12061913	+	3'UTR	INS	-	T	T	rs149410582	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12061912_12061913insT	uc002dbv.2	+	3					TNFRSF17_uc010buy.2_3'UTR|TNFRSF17_uc010buz.2_3'UTR	NM_001192	NP_001183	Q02223	TNR17_HUMAN	tumor necrosis factor receptor superfamily,						cell proliferation|multicellular organismal development	endomembrane system|integral to membrane|plasma membrane					0						TGATTAAACTCTTTTTTTTCCT	0.386			T	IL2	intestinal T-cell lymphoma								4	4	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22145815	22145816	+	Intron	INS	-	C	C			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22145815_22145816insC	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc010bxc.2_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		atttcctggggctaccataact	0.208													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26855911	26855912	+	IGR	INS	-	A	A			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26855911_26855912insA								HS3ST4 (706903 upstream) : C16orf82 (222307 downstream)																							aagactctgtcaaaaaaaaaaa	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74419892	74419892	+	Intron	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74419892delT	uc010vmt.1	+											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		cctttctctcttttttttttt	0.169													6	5	---	---	---	---	
MYBBP1A	10514	broad.mit.edu	37	17	4443460	4443470	+	Intron	DEL	GAGGGTCCTGT	-	-	rs3833100	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4443460_4443470delGAGGGTCCTGT	uc002fyb.3	-						MYBBP1A_uc002fxz.3_Intron|MYBBP1A_uc002fya.3_Intron|MYBBP1A_uc010vsa.1_Intron	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2						nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2						AGGCTCCTGCGAGGGTCCTGTGAGGGTCCTA	0.455													9	4	---	---	---	---	
MED1	5469	broad.mit.edu	37	17	37604389	37604389	+	Intron	DEL	T	-	-	rs149247547		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37604389delT	uc002hrv.3	-						MED1_uc010wee.1_Intron|MED1_uc002hru.2_Intron	NM_004774	NP_004765	Q15648	MED1_HUMAN	mediator complex subunit 1						androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		TCTATCCACCttttttttttt	0.189										HNSCC(31;0.082)			4	3	---	---	---	---	
KANK3	256949	broad.mit.edu	37	19	8398950	8398961	+	In_Frame_Del	DEL	TCGCTGTCGCCA	-	-	rs111751275		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8398950_8398961delTCGCTGTCGCCA	uc010dwa.2	-	5	1533_1544	c.1467_1478delTGGCGACAGCGA	c.(1465-1479)GATGGCGACAGCGAG>GAG	p.DGDS489del	KANK3_uc002mjp.1_In_Frame_Del_p.MATA1del	NM_198471	NP_940873	Q6NY19	KANK3_HUMAN	ankyrin repeat domain 47	489_492											0						GCCACCGTTCTCGCTGTCGCCATCGCTGTCGC	0.693													2	5	---	---	---	---	
HNRNPM	4670	broad.mit.edu	37	19	8520629	8520630	+	Intron	INS	-	T	T	rs151081584	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8520629_8520630insT	uc010dwe.2	+						HNRNPM_uc010dwc.1_Intron|HNRNPM_uc010xke.1_Intron|HNRNPM_uc010dwd.2_Intron	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0						tttgttttgtgttttttttttg	0.366													9	4	---	---	---	---	
MEGF8	1954	broad.mit.edu	37	19	42858271	42858271	+	Intron	DEL	T	-	-	rs36065839		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42858271delT	uc002otl.3	+						MEGF8_uc002otm.3_Intron	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8							integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)				AGTATTGCTGTTTTTTTTTTT	0.517													4	2	---	---	---	---	
SYT3	84258	broad.mit.edu	37	19	51132916	51132917	+	Intron	DEL	CC	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51132916_51132917delCC	uc002pst.2	-						SYT3_uc002psv.2_Intron|SYT3_uc010ycd.1_Intron	NM_032298	NP_115674	Q9BQG1	SYT3_HUMAN	synaptotagmin III							cell junction|endosome|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|breast(1)	3		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		ggagtccaggcccccagcccct	0.000													9	4	---	---	---	---	
PPP1R12C	54776	broad.mit.edu	37	19	55605558	55605559	+	Intron	INS	-	TTA	TTA			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55605558_55605559insTTA	uc002qix.2	-						PPP1R12C_uc010yfs.1_Intron|PPP1R12C_uc002qiy.2_Intron	NM_017607	NP_060077	Q9BZL4	PP12C_HUMAN	protein phosphatase 1, regulatory subunit 12C							cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		acctccagcccctcctccctca	0.000													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	18842473	18842473	+	Intron	DEL	G	-	-	rs66618606		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18842473delG	uc010grj.1	+						uc002zoe.2_RNA					Homo sapiens mRNA; cDNA DKFZp434K191 (from clone DKFZp434K191).																		AGCTGCTGGTGGGGAGGTCTT	0.647													4	4	---	---	---	---	
FAM109B	150368	broad.mit.edu	37	22	42472306	42472306	+	Intron	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42472306delT	uc003bbz.2	+							NM_001002034	NP_001002034	Q6ICB4	SESQ2_HUMAN	hypothetical protein LOC150368						endosome organization|receptor recycling|retrograde transport, endosome to Golgi	clathrin-coated vesicle|early endosome|recycling endosome|trans-Golgi network	protein homodimerization activity				0						atgttatttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	20702094	20702094	+	IGR	DEL	T	-	-			TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20702094delT								RPS6KA3 (416571 upstream) : CNKSR2 (690886 downstream)																							cctccctccctttttccttcc	0.199													4	2	---	---	---	---	
SHROOM4	57477	broad.mit.edu	37	X	50378792	50378792	+	Intron	DEL	G	-	-	rs5915290	by1000genomes	TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50378792delG	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron|SHROOM4_uc004dpf.1_Intron	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)					AAAAAAAAAAGGGGGAAGAAA	0.483													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28582961	28582962	+	IGR	INS	-	AT	AT	rs4008413		TCGA-A3-3311-01A-01D-0966-08	TCGA-A3-3311-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28582961_28582962insAT								None (None upstream) : None (None downstream)																							AAGTATAAAACAAAAACCTAAA	0.322													4	4	---	---	---	---	
