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
CYP4A22	284541	broad.mit.edu	37	1	47612030	47612030	+	Intron	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47612030C>T	uc001cqv.1	+						CYP4A22_uc009vyo.2_3'UTR|CYP4A22_uc009vyp.2_3'UTR	NM_001010969	NP_001010969	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A,							endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding			skin(2)|ovary(1)|breast(1)	4						GGAGACTTTGCTCCCTCTGCT	0.443													2	4	---	---	---	---	PASS
ATP1B1	481	broad.mit.edu	37	1	169076145	169076145	+	RNA	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169076145C>T	uc001gfs.1	+	1		c.199C>T						P05026	AT1B1_HUMAN	Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)					AGTTTCTGGGCAGGACCGGTG	0.662													3	21	---	---	---	---	PASS
PPM1G	5496	broad.mit.edu	37	2	27615535	27615535	+	Intron	SNP	C	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27615535C>G	uc002rkl.2	-						PPM1G_uc002rkm.2_Intron|FTHL3_uc002rkn.1_RNA	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G						cell cycle arrest|protein dephosphorylation	cytoplasm|nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					AATCAAAGAACTTAAGTGGGT	0.383													2	3	---	---	---	---	PASS
ANKRD36	375248	broad.mit.edu	37	2	97869931	97869931	+	Missense_Mutation	SNP	A	T	T	rs76309140		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97869931A>T	uc010yva.1	+	50	3236	c.2992A>T	c.(2992-2994)ACA>TCA	p.T998S	ANKRD36_uc002sxp.3_RNA	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	998											0						CATTCAGGCTACAAGTGATGA	0.289													3	15	---	---	---	---	PASS
KIF5C	3800	broad.mit.edu	37	2	149853959	149853959	+	Intron	SNP	A	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149853959A>C	uc010zbu.1	+						KIF5C_uc002tws.1_Intron|KIF5C_uc002twt.2_3'UTR|KIF5C_uc002twu.1_5'Flank	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)		CGTATATGGCAAGGGACAGGG	0.483													4	3	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168101917	168101917	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168101917A>T	uc002udx.2	+	8	4033	c.4015A>T	c.(4015-4017)AAA>TAA	p.K1339*	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Nonsense_Mutation_p.K1164*|XIRP2_uc010fpq.2_Nonsense_Mutation_p.K1117*|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1164					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CACAGTTAAAAAAGAAGAGGT	0.383													27	131	---	---	---	---	PASS
MYO3B	140469	broad.mit.edu	37	2	171243748	171243748	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171243748A>G	uc002ufy.2	+	14	1650	c.1507A>G	c.(1507-1509)ACT>GCT	p.T503A	MYO3B_uc002ufv.2_Missense_Mutation_p.T490A|MYO3B_uc010fqb.1_Missense_Mutation_p.T490A|MYO3B_uc002ufz.2_Missense_Mutation_p.T503A|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	503	Myosin head-like.				response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						GTTTACACCAACTGGAGTTGT	0.433													29	124	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179484439	179484439	+	Silent	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179484439T>C	uc010zfg.1	-	199	39125	c.38901A>G	c.(38899-38901)CGA>CGG	p.R12967R	TTN_uc010zfh.1_Silent_p.R6662R|TTN_uc010zfi.1_Silent_p.R6595R|TTN_uc010zfj.1_Silent_p.R6470R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13894							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)			AAATCTGTAGTCGATGTATCT	0.423													58	266	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179504809	179504809	+	Silent	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179504809G>A	uc010zfg.1	-	171	33272	c.33048C>T	c.(33046-33048)CTC>CTT	p.L11016L	TTN_uc010zfh.1_Silent_p.L4711L|TTN_uc010zfi.1_Silent_p.L4644L|TTN_uc010zfj.1_Silent_p.L4519L|TTN_uc010fre.1_Silent_p.L894L|TTN_uc002umw.1_RNA|TTN_uc002umx.1_Silent_p.L231L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	11943							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)			CAGGTGCAGGGAGAGGTATTG	0.388													29	175	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216262451	216262451	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216262451T>C	uc002vfa.2	-	22	3735	c.3469A>G	c.(3469-3471)AGA>GGA	p.R1157G	FN1_uc002vfb.2_Missense_Mutation_p.R1157G|FN1_uc002vfc.2_Missense_Mutation_p.R1157G|FN1_uc002vfd.2_Missense_Mutation_p.R1157G|FN1_uc002vfe.2_Missense_Mutation_p.R1157G|FN1_uc002vff.2_Missense_Mutation_p.R1157G|FN1_uc002vfg.2_Missense_Mutation_p.R1157G|FN1_uc002vfh.2_Missense_Mutation_p.R1157G|FN1_uc002vfi.2_Missense_Mutation_p.R1157G|FN1_uc002vfj.2_Missense_Mutation_p.R1157G	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	1157	|Fibronectin type-III 6.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TGTCCATCTCTCAGGACTTGG	0.438													73	137	---	---	---	---	PASS
LRRC3B	116135	broad.mit.edu	37	3	26751684	26751684	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26751684C>A	uc003cdp.2	+	2	1110	c.521C>A	c.(520-522)ACG>AAG	p.T174K	LRRC3B_uc003cdq.2_Missense_Mutation_p.T174K	NM_052953	NP_443185	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B precursor	174	LRRCT.					integral to membrane				pancreas(2)|ovary(1)|skin(1)	4						ATCTGTAAAACGTCCGTGTTG	0.498													5	15	---	---	---	---	PASS
PLXNB1	5364	broad.mit.edu	37	3	48461035	48461035	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48461035A>G	uc003csw.2	-	11	2930	c.2660T>C	c.(2659-2661)CTC>CCC	p.L887P	PLXNB1_uc003csu.2_Missense_Mutation_p.L704P|PLXNB1_uc003csx.2_Missense_Mutation_p.L887P|PLXNB1_uc010hjx.1_RNA	NM_002673	NP_002664	O43157	PLXB1_HUMAN	plexin B1 precursor	887	Extracellular (Potential).				axon guidance|cell migration|intracellular signal transduction|regulation of cell shape|regulation of cytoskeleton organization|regulation of small GTPase mediated signal transduction|semaphorin-plexin signaling pathway	extracellular region|integral to plasma membrane|intracellular|semaphorin receptor complex	GTPase activator activity|semaphorin receptor activity|semaphorin receptor binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GCTGGACGGGAGGATGAGGGG	0.667													5	16	---	---	---	---	PASS
CNTN3	5067	broad.mit.edu	37	3	74350836	74350836	+	Missense_Mutation	SNP	C	T	T	rs139142211		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74350836C>T	uc003dpm.1	-	14	1987	c.1907G>A	c.(1906-1908)CGG>CAG	p.R636Q		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	636	Fibronectin type-III 1.				cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		GAAAGGTGTCCGAGCCTGGAT	0.433													6	73	---	---	---	---	PASS
ROBO1	6091	broad.mit.edu	37	3	78706388	78706388	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78706388T>C	uc003dqe.2	-	18	2682	c.2474A>G	c.(2473-2475)CAC>CGC	p.H825R	ROBO1_uc003dqb.2_Missense_Mutation_p.H786R|ROBO1_uc003dqc.2_Missense_Mutation_p.H789R|ROBO1_uc003dqd.2_Missense_Mutation_p.H789R|ROBO1_uc010hoh.2_Missense_Mutation_p.H17R|ROBO1_uc011bgl.1_Missense_Mutation_p.H397R	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	825	Extracellular (Potential).|Fibronectin type-III 3.				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TTTGTTGATGTGGTATCGAGT	0.453													6	12	---	---	---	---	PASS
ROBO1	6091	broad.mit.edu	37	3	78706390	78706390	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78706390G>T	uc003dqe.2	-	18	2680	c.2472C>A	c.(2470-2472)TAC>TAA	p.Y824*	ROBO1_uc003dqb.2_Nonsense_Mutation_p.Y785*|ROBO1_uc003dqc.2_Nonsense_Mutation_p.Y788*|ROBO1_uc003dqd.2_Nonsense_Mutation_p.Y788*|ROBO1_uc010hoh.2_Nonsense_Mutation_p.Y16*|ROBO1_uc011bgl.1_Nonsense_Mutation_p.Y396*	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	824	Extracellular (Potential).|Fibronectin type-III 3.				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TGTTGATGTGGTATCGAGTTT	0.453													5	11	---	---	---	---	PASS
WDR5B	54554	broad.mit.edu	37	3	122134164	122134164	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122134164T>C	uc003efa.1	-	1	719	c.212A>G	c.(211-213)TAT>TGT	p.Y71C		NM_019069	NP_061942	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	71	WD 1.									ovary(3)	3				GBM - Glioblastoma multiforme(114;0.0704)		TTTTCCATCATATGCTCCCCA	0.413													68	192	---	---	---	---	PASS
DGKG	1608	broad.mit.edu	37	3	185882703	185882703	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185882703C>T	uc003fqa.2	-	23	2737	c.2200G>A	c.(2200-2202)GCC>ACC	p.A734T	DGKG_uc003fqb.2_Missense_Mutation_p.A695T|DGKG_uc003fqc.2_Missense_Mutation_p.A709T|DGKG_uc011brx.1_Missense_Mutation_p.A675T	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1	734					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	GTGACAGAGGCGCACTGGGCC	0.577													12	56	---	---	---	---	PASS
FAM193A	8603	broad.mit.edu	37	4	2674032	2674032	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2674032T>C	uc010icl.2	+	11	1742	c.1391T>C	c.(1390-1392)GTT>GCT	p.V464A	FAM193A_uc010ick.2_Missense_Mutation_p.V664A|FAM193A_uc003gfd.2_Missense_Mutation_p.V464A|FAM193A_uc011bvm.1_Missense_Mutation_p.V486A|FAM193A_uc011bvn.1_Missense_Mutation_p.V464A|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Missense_Mutation_p.V318A	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	464										ovary(3)	3						TTGCACACTGTTCCACACCTG	0.562													15	37	---	---	---	---	PASS
GPR78	27201	broad.mit.edu	37	4	8584304	8584304	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8584304G>A	uc003glk.2	+	2	1134	c.715G>A	c.(715-717)GCC>ACC	p.A239T	CPZ_uc003gll.2_RNA	NM_080819	NP_543009	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	239	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(4)|ovary(2)	6						CCGCCACCGCGCCACCAGGAA	0.622													29	112	---	---	---	---	PASS
SEC24B	10427	broad.mit.edu	37	4	110402835	110402835	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110402835G>A	uc003hzk.2	+	4	1118	c.1063G>A	c.(1063-1065)GTG>ATG	p.V355M	SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Missense_Mutation_p.V386M|SEC24B_uc011cfq.1_Missense_Mutation_p.V355M|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314	O95487	SC24B_HUMAN	SEC24 (S. cerevisiae) homolog B isoform a	355					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CTTTACAGGCGTGCAGTATGG	0.338													38	226	---	---	---	---	PASS
PCDH10	57575	broad.mit.edu	37	4	134072133	134072133	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134072133G>A	uc003iha.2	+	1	1664	c.838G>A	c.(838-840)GGC>AGC	p.G280S	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.G280S	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	280	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		CCCGGACGAGGGCCAGAACGG	0.632													19	52	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183714119	183714119	+	Silent	SNP	C	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183714119C>G	uc003ivd.1	+	25	6331	c.6294C>G	c.(6292-6294)CTC>CTG	p.L2098L		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	2098	YD 16.|Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TCAGGTCGCTCATGTACTGGA	0.393													24	37	---	---	---	---	PASS
C5orf38	153571	broad.mit.edu	37	5	2755174	2755174	+	3'UTR	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2755174C>T	uc003jdc.2	+	4					C5orf38_uc011cmg.1_3'UTR|C5orf38_uc011cmh.1_RNA|C5orf38_uc011cmi.1_RNA|C5orf38_uc011cmj.1_RNA	NM_178569	NP_848664	Q86SI9	CEI_HUMAN	hypothetical protein LOC153571 precursor							extracellular region					0				GBM - Glioblastoma multiforme(108;0.205)		TACGTGGACACGCAAGTTTCA	0.577													47	155	---	---	---	---	PASS
EDIL3	10085	broad.mit.edu	37	5	83356228	83356228	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83356228G>A	uc003kio.1	-	9	1447	c.1028C>T	c.(1027-1029)ACG>ATG	p.T343M	EDIL3_uc003kip.1_Missense_Mutation_p.T333M|EDIL3_uc011ctt.1_Missense_Mutation_p.T120M	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like	343	F5/8 type C 2.				cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		CATGTTGAGCGTTCTGAAGAT	0.483													41	82	---	---	---	---	PASS
PCDHA3	56145	broad.mit.edu	37	5	140182765	140182765	+	Silent	SNP	C	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182765C>A	uc003lhf.2	+	1	1983	c.1983C>A	c.(1981-1983)GCC>GCA	p.A661A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.A661A	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	661	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATTGACCGCCACGGCCACTG	0.697													21	69	---	---	---	---	PASS
PCDHA7	56141	broad.mit.edu	37	5	140216218	140216218	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140216218C>A	uc003lhq.2	+	1	2250	c.2250C>A	c.(2248-2250)TTC>TTA	p.F750L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.F750L	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	750	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGTCATTCTCCCAGCAGA	0.632													27	73	---	---	---	---	PASS
MFAP3	4238	broad.mit.edu	37	5	153432673	153432673	+	Silent	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153432673C>T	uc003lvf.2	+	3	1005	c.489C>T	c.(487-489)CTC>CTT	p.L163L	MFAP3_uc010jib.2_Silent_p.L163L|MFAP3_uc011ddb.1_Silent_p.L17L	NM_001135037	NP_001128509	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3 isoform 2	163	Helical; (Potential).					integral to membrane|plasma membrane					0	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		CAATCACACTCATCTTGAATG	0.458													66	107	---	---	---	---	PASS
SLIT3	6586	broad.mit.edu	37	5	168114104	168114104	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168114104C>T	uc003mab.2	-	30	3614	c.3194G>A	c.(3193-3195)GGC>GAC	p.G1065D	SLIT3_uc010jjg.2_Missense_Mutation_p.G1072D	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	1065	EGF-like 4.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCCGCTGTAGCCAGGGACACA	0.602													9	71	---	---	---	---	PASS
FOXI1	2299	broad.mit.edu	37	5	169535223	169535223	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169535223C>G	uc003mai.3	+	2	790	c.745C>G	c.(745-747)CAG>GAG	p.Q249E	FOXI1_uc003maj.3_Intron	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	249					epidermal cell fate specification|otic placode formation|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CACGGAGCCTCAGGACATCTT	0.597									Pendred_syndrome				11	171	---	---	---	---	PASS
FLT4	2324	broad.mit.edu	37	5	180056415	180056415	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180056415T>G	uc003mma.3	-	7	908	c.829A>C	c.(829-831)AAG>CAG	p.K277Q	FLT4_uc003mlz.3_Missense_Mutation_p.K277Q|FLT4_uc003mmb.1_5'UTR|FLT4_uc011dgy.1_Missense_Mutation_p.K277Q|FLT4_uc011dgz.1_Intron	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2	277	Ig-like C2-type 3.|Extracellular (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)	GGCACCCACTTACCCCGCTCT	0.677									Congenital_Hereditary_Lymphedema				29	49	---	---	---	---	PASS
KIF13A	63971	broad.mit.edu	37	6	17898399	17898399	+	Silent	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17898399C>T	uc003ncg.3	-	3	264	c.159G>A	c.(157-159)AAG>AAA	p.K53K	KIF13A_uc003ncf.2_Silent_p.K53K|KIF13A_uc003nch.3_Silent_p.K53K|KIF13A_uc003nci.3_Silent_p.K53K	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	53	Kinesin-motor.				cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TAGTGCTTACCTTGGGAGGTT	0.403													8	34	---	---	---	---	PASS
HIST1H1D	3007	broad.mit.edu	37	6	26234451	26234451	+	3'UTR	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26234451G>A	uc003nhd.2	-	1						NM_005320	NP_005311	P16402	H13_HUMAN	histone cluster 1, H1d						nucleosome assembly	nucleosome|nucleus	DNA binding			skin(1)	1		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GGGTGGCTCTGAAAAGAGCCG	0.552													9	51	---	---	---	---	PASS
FAM135A	57579	broad.mit.edu	37	6	71186969	71186969	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71186969T>G	uc003pfj.2	+	6	609	c.476T>G	c.(475-477)TTC>TGC	p.F159C	FAM135A_uc003pfi.2_Missense_Mutation_p.F159C|FAM135A_uc003pfh.2_Missense_Mutation_p.F116C|FAM135A_uc003pfk.2_Missense_Mutation_p.F159C|FAM135A_uc003pfl.2_Intron	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c	159										central_nervous_system(1)	1						TTTGATTACTTCCACCTTTCT	0.358													24	87	---	---	---	---	PASS
FBXL4	26235	broad.mit.edu	37	6	99365256	99365256	+	Silent	SNP	A	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99365256A>C	uc003ppf.1	-	4	1210	c.852T>G	c.(850-852)CCT>CCG	p.P284P	FBXL4_uc003ppg.1_Silent_p.P284P|FBXL4_uc003pph.1_Intron	NM_012160	NP_036292	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	284	F-box.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex				skin(2)	2		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		TTACCTCATAAGGTAGTTTAT	0.353													30	105	---	---	---	---	PASS
MED23	9439	broad.mit.edu	37	6	131931276	131931276	+	Silent	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131931276G>T	uc003qcs.1	-	11	1161	c.987C>A	c.(985-987)CTC>CTA	p.L329L	MED23_uc003qcq.2_Silent_p.L335L|MED23_uc011eca.1_Silent_p.L18L|MED23_uc003qct.1_Silent_p.L335L|MED23_uc011ecb.1_RNA	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	329					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		GCTGCCACAGGAGTTGGCTTG	0.483													9	101	---	---	---	---	PASS
LATS1	9113	broad.mit.edu	37	6	150004564	150004564	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150004564C>T	uc003qmu.1	-	4	2209	c.1661G>A	c.(1660-1662)GGA>GAA	p.G554E	LATS1_uc010kif.1_Missense_Mutation_p.G449E|LATS1_uc003qmv.1_Missense_Mutation_p.G554E|LATS1_uc003qmw.2_Missense_Mutation_p.G554E|LATS1_uc010kig.1_Missense_Mutation_p.G449E	NM_004690	NP_004681	O95835	LATS1_HUMAN	LATS homolog 1	554	Interaction with YAP1.				cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation	microtubule organizing center|spindle pole	ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TGGTGGTGGTCCTTGATAGTT	0.493													43	146	---	---	---	---	PASS
MLL5	55904	broad.mit.edu	37	7	104719411	104719411	+	Splice_Site	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104719411G>A	uc003vcm.2	+	12	1782	c.1248_splice	c.e12+1	p.E416_splice	MLL5_uc010lja.1_Splice_Site_p.E270_splice|MLL5_uc010ljb.1_Splice_Site_p.E416_splice|MLL5_uc003vcl.2_Splice_Site_p.E416_splice|MLL5_uc010ljc.2_Splice_Site_p.E416_splice|MLL5_uc003vco.1_Intron|MLL5_uc010ljd.1_Splice_Site_p.E54_splice	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5						cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						CAATGCAGAGGTAAGCTTATA	0.443													28	145	---	---	---	---	PASS
OR2A1	346528	broad.mit.edu	37	7	143929685	143929685	+	Silent	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143929685G>T	uc011kub.1	-	1	252	c.252C>A	c.(250-252)CTC>CTA	p.L84L		NM_001005287	NP_001005287	Q8NGT9	OR2A1_HUMAN	olfactory receptor, family 2, subfamily A,	84	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Melanoma(164;0.14)					CTGGATGCAGGAGGTTCGCCA	0.562													15	105	---	---	---	---	PASS
PRKACG	5568	broad.mit.edu	37	9	71628614	71628614	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71628614C>T	uc004agy.2	-	1	426	c.395G>A	c.(394-396)CGC>CAC	p.R132H		NM_002732	NP_002723	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic,	132	Protein kinase.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|gluconeogenesis|intracellular protein kinase cascade|male gonad development|nerve growth factor receptor signaling pathway|regulation of insulin secretion|spermatogenesis|transmembrane transport|triglyceride catabolic process|water transport	cytosol|nucleoplasm	ATP binding|cAMP-dependent protein kinase activity			ovary(1)|pancreas(1)|skin(1)	3						GCGCTGTAGGCGGGAGAACAT	0.582													12	38	---	---	---	---	PASS
BICD2	23299	broad.mit.edu	37	9	95475710	95475710	+	3'UTR	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95475710G>A	uc004aso.1	-	8					BICD2_uc004asp.1_3'UTR	NM_015250	NP_056065	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 isoform 2						microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule	cytoplasmic vesicle|cytoskeleton|Golgi apparatus|plasma membrane	Rab GTPase binding			skin(1)	1						TGACAGGGCCGGGTGGCCAAG	0.532													3	6	---	---	---	---	PASS
NR4A3	8013	broad.mit.edu	37	9	102591255	102591255	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102591255G>A	uc004baf.1	+	3	1660	c.931G>A	c.(931-933)GGC>AGC	p.G311S	NR4A3_uc004bae.2_Missense_Mutation_p.G311S|NR4A3_uc004bag.1_Missense_Mutation_p.G311S|NR4A3_uc004bai.2_Missense_Mutation_p.G322S	NM_006981	NP_008912	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	311	Nuclear receptor.|NR C4-type.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding		EWSR1/NR4A3(140)|TAF15/NR4A3(33)	bone(173)	173		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				AACCTGCGAGGGCTGCAAGGG	0.677			T	EWSR1	extraskeletal myxoid chondrosarcoma								2	6	---	---	---	---	PASS
RGS3	5998	broad.mit.edu	37	9	116299108	116299108	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116299108C>G	uc004bhq.2	+	20	2156	c.1947C>G	c.(1945-1947)CAC>CAG	p.H649Q	RGS3_uc004bhr.2_Missense_Mutation_p.H537Q|RGS3_uc004bhs.2_Missense_Mutation_p.H539Q|RGS3_uc004bht.2_Missense_Mutation_p.H368Q|RGS3_uc010muy.2_Missense_Mutation_p.H368Q|RGS3_uc004bhu.2_Missense_Mutation_p.H275Q|RGS3_uc004bhv.2_5'UTR	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	649					inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						TGGAAGCGCACTCGCAGGAGC	0.592													52	149	---	---	---	---	PASS
KIAA1217	56243	broad.mit.edu	37	10	24834980	24834980	+	Silent	SNP	C	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24834980C>A	uc001iru.3	+	21	5962	c.5559C>A	c.(5557-5559)CTC>CTA	p.L1853L	KIAA1217_uc001irs.2_Silent_p.L1174L|KIAA1217_uc001irt.3_Silent_p.L1219L|KIAA1217_uc010qcy.1_Silent_p.L1284L|KIAA1217_uc010qcz.1_Silent_p.L1259L|KIAA1217_uc001irw.2_3'UTR|KIAA1217_uc001irz.2_3'UTR|KIAA1217_uc001irx.2_3'UTR|KIAA1217_uc001iry.2_3'UTR	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	1853	Ser-rich.				embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						CTGCCTCCCTCATCCCTTCTG	0.502													33	154	---	---	---	---	PASS
ZNF438	220929	broad.mit.edu	37	10	31138528	31138528	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31138528A>G	uc010qdz.1	-	7	1241	c.806T>C	c.(805-807)ATG>ACG	p.M269T	ZNF438_uc001ivn.2_Missense_Mutation_p.M220T|ZNF438_uc010qdy.1_Missense_Mutation_p.M259T|ZNF438_uc001ivo.3_Intron|ZNF438_uc009xlg.2_Missense_Mutation_p.M269T|ZNF438_uc001ivp.3_Missense_Mutation_p.M259T|ZNF438_uc010qea.1_Missense_Mutation_p.M269T|ZNF438_uc010qeb.1_Missense_Mutation_p.M269T|ZNF438_uc010qec.1_Intron	NM_182755	NP_877432	Q7Z4V0	ZN438_HUMAN	zinc finger protein 438 isoform a	269					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		Prostate(175;0.0587)				TAAATTGGTCATGGTTTTTGC	0.403													77	277	---	---	---	---	PASS
PLAU	5328	broad.mit.edu	37	10	75673067	75673067	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75673067C>T	uc001jwa.2	+	6	534	c.388C>T	c.(388-390)CGA>TGA	p.R130*	C10orf55_uc001jvz.1_Intron|PLAU_uc010qkw.1_Nonsense_Mutation_p.R113*|PLAU_uc010qkx.1_Nonsense_Mutation_p.R44*|PLAU_uc001jwb.2_RNA|PLAU_uc001jwc.2_Nonsense_Mutation_p.R130*|PLAU_uc009xrq.1_Nonsense_Mutation_p.R94*	NM_002658	NP_002649	P00749	UROK_HUMAN	plasminogen activator, urokinase isoform 1	130	Kringle.				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(2)|kidney(1)	3	Prostate(51;0.0112)				Amiloride(DB00594)|Urokinase(DB00013)	CAACCGGAGGCGACCCTGGTG	0.572													17	121	---	---	---	---	PASS
ZFYVE27	118813	broad.mit.edu	37	10	99512825	99512825	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99512825G>A	uc001koo.2	+	10	1128	c.928G>A	c.(928-930)GAG>AAG	p.E310K	ZFYVE27_uc001kon.2_Missense_Mutation_p.E315K|ZFYVE27_uc001koq.2_Missense_Mutation_p.E217K|ZFYVE27_uc010qpa.1_Missense_Mutation_p.E185K|ZFYVE27_uc001kop.2_Missense_Mutation_p.E303K|ZFYVE27_uc010qpb.1_Missense_Mutation_p.E210K|ZFYVE27_uc010qpc.1_RNA|ZFYVE27_uc010qpd.1_Missense_Mutation_p.E271K|ZFYVE27_uc001kok.1_RNA|ZFYVE27_uc001kol.1_Missense_Mutation_p.E310K|ZFYVE27_uc001kom.1_Missense_Mutation_p.E303K	NM_144588	NP_653189	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27 isoform	310	Extracellular (Potential).				cell death|nerve growth factor receptor signaling pathway|neuron projection development|protein localization in plasma membrane	axon|dendrite|endoplasmic reticulum membrane|growth cone membrane|integral to membrane|recycling endosome membrane	metal ion binding|protein binding			ovary(1)	1		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		GTGCCCAGCAGAGGATGAGCT	0.647													7	9	---	---	---	---	PASS
OR51D1	390038	broad.mit.edu	37	11	4661302	4661302	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4661302G>T	uc010qyk.1	+	1	282	c.282G>T	c.(280-282)ATG>ATT	p.M94I		NM_001004751	NP_001004751	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D,	94	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGCCCAAGATGGCCAGTCTTT	0.532													12	54	---	---	---	---	PASS
TCP11L1	55346	broad.mit.edu	37	11	33097696	33097696	+	Intron	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33097696T>C	uc001muf.1	+						LOC283267_uc001mug.3_RNA	NM_018393		Q9NUJ3	T11L1_HUMAN	t-complex 11 (mouse) like 1												0						TTCACCTCCATCAGTGAGATC	0.502													8	33	---	---	---	---	PASS
PAAF1	80227	broad.mit.edu	37	11	73638349	73638349	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73638349A>T	uc001ouk.1	+	12	1155	c.1121A>T	c.(1120-1122)CAG>CTG	p.Q374L	PAAF1_uc001oul.1_Missense_Mutation_p.Q357L|PAAF1_uc009ytx.1_RNA|PAAF1_uc001oum.1_Missense_Mutation_p.Q357L|PAAF1_uc001oun.1_RNA	NM_025155	NP_079431	Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1	374	WD 5.				interspecies interaction between organisms	proteasome complex	protein binding			ovary(1)|skin(1)	2	Breast(11;7.42e-05)					TGGGAGAAGCAGATCTACACA	0.458													13	58	---	---	---	---	PASS
ALG8	79053	broad.mit.edu	37	11	77812070	77812070	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77812070C>A	uc001oza.1	-	13	1586	c.1521G>T	c.(1519-1521)TGG>TGT	p.W507C	ALG8_uc001oyz.1_3'UTR|ALG8_uc009yux.1_Missense_Mutation_p.W405C	NM_024079	NP_076984	Q9BVK2	ALG8_HUMAN	dolichyl pyrophosphate Glc1Man9GlcNAc2	507	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)|pancreas(1)	3	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			ACAGTTTGAACCAAGCATATG	0.388													33	132	---	---	---	---	PASS
CHD4	1108	broad.mit.edu	37	12	6688041	6688041	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6688041T>G	uc001qpo.2	-	34	5116	c.4952A>C	c.(4951-4953)GAT>GCT	p.D1651A	CHD4_uc001qpn.2_Missense_Mutation_p.D1644A|CHD4_uc001qpp.2_Missense_Mutation_p.D1676A|uc001qpq.1_Intron	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1651	Required for interaction with PCNT.				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2						AGGGGTCAGATCTATTGCTGA	0.438													13	60	---	---	---	---	PASS
PLEKHA5	54477	broad.mit.edu	37	12	19410396	19410396	+	Silent	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19410396T>C	uc001reb.2	+	6	548	c.462T>C	c.(460-462)AAT>AAC	p.N154N	PLEKHA5_uc010sie.1_Silent_p.N154N|PLEKHA5_uc001rea.2_Silent_p.N154N|PLEKHA5_uc009zin.2_5'UTR|PLEKHA5_uc010sif.1_Silent_p.N46N|PLEKHA5_uc010sig.1_Silent_p.N46N|PLEKHA5_uc010sih.1_Silent_p.N46N	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A	154							1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					AAGTTCATAATTTTGGAAAGA	0.318													47	142	---	---	---	---	PASS
OR8S1	341568	broad.mit.edu	37	12	48921863	48921863	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48921863G>A	uc010slu.1	+	2	1057	c.1057G>A	c.(1057-1059)GCG>ACG	p.A353T		NM_001005203	NP_001005203	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S,	353	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						CGCGCTGCGCGCGGCGCCCAC	0.662													4	4	---	---	---	---	PASS
KRT85	3891	broad.mit.edu	37	12	52756641	52756641	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52756641G>T	uc001sag.2	-	6	1194	c.1074C>A	c.(1072-1074)TGC>TGA	p.C358*		NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85	358	Rod.|Coil 2.				epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		ACCCCACCTGGCACTTGGCAT	0.597													21	69	---	---	---	---	PASS
KRT1	3848	broad.mit.edu	37	12	53069018	53069018	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53069018C>T	uc001sau.1	-	9	1953	c.1894G>A	c.(1894-1896)GTG>ATG	p.V632M	KRT1_uc001sav.1_Missense_Mutation_p.V625M	NM_006121	NP_006112	P04264	K2C1_HUMAN	keratin 1	632	Gly/Ser-rich.|Tail.				complement activation, lectin pathway|epidermis development|fibrinolysis|regulation of angiogenesis|response to oxidative stress	plasma membrane	protein binding|receptor activity|structural constituent of cytoskeleton|sugar binding			ovary(1)|skin(1)	2						ACAAACTTCACGCTGGAACTG	0.517													57	156	---	---	---	---	PASS
ERBB3	2065	broad.mit.edu	37	12	56487573	56487573	+	Silent	SNP	A	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56487573A>G	uc001sjh.2	+	13	1699	c.1506A>G	c.(1504-1506)CCA>CCG	p.P502P	ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Silent_p.P443P|ERBB3_uc009zok.2_5'UTR|ERBB3_uc001sjk.2_5'Flank|ERBB3_uc001sjj.1_Silent_p.P70P	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	502	Extracellular (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TGTGTGACCCACTGTGCTCCT	0.567													25	117	---	---	---	---	PASS
TSPAN19	144448	broad.mit.edu	37	12	85421790	85421790	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85421790G>A	uc009zsj.2	-	4	252	c.151C>T	c.(151-153)CAC>TAC	p.H51Y		NM_001100917	NP_001094387	P0C672	TSN19_HUMAN	tetraspanin 19	51						integral to membrane				ovary(1)	1						ACTATGAAGTGATTATTTTCA	0.269													4	30	---	---	---	---	PASS
SLC7A1	6541	broad.mit.edu	37	13	30091722	30091722	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30091722T>C	uc001uso.2	-	10	1885	c.1498A>G	c.(1498-1500)ACC>GCC	p.T500A		NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid	500	Helical; (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	ATGAGGCTGGTTGAAATGTTC	0.498													27	216	---	---	---	---	PASS
PCDH9	5101	broad.mit.edu	37	13	67205519	67205519	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67205519G>A	uc001vik.2	-	4	3855	c.3163C>T	c.(3163-3165)CTC>TTC	p.L1055F	PCDH9_uc010aei.2_RNA|PCDH9_uc001vil.2_Missense_Mutation_p.L1021F|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	1055	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CCATCAGGGAGATGAAACGTA	0.502													8	54	---	---	---	---	PASS
IPO5	3843	broad.mit.edu	37	13	98654650	98654650	+	Intron	SNP	A	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98654650A>T	uc001vnf.1	+						IPO5_uc001vne.2_Intron|IPO5_uc010tik.1_Intron|IPO5_uc010til.1_Intron|IPO5_uc001vng.1_5'UTR	NM_002271	NP_002262	O00410	IPO5_HUMAN	importin 5						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)|skin(1)	3						GAACTTTTATACATCTCCCTC	0.274													5	37	---	---	---	---	PASS
FAM158A	51016	broad.mit.edu	37	14	24608257	24608257	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24608257G>C	uc001wmi.2	-	6	752	c.589C>G	c.(589-591)CAG>GAG	p.Q197E		NM_016049	NP_057133	Q9Y3B6	F158A_HUMAN	hypothetical protein LOC51016	197											0						CCAACCCACTGGGTGATTTGA	0.562													10	63	---	---	---	---	PASS
MAN2C1	4123	broad.mit.edu	37	15	75650634	75650634	+	Missense_Mutation	SNP	C	G	G	rs150703780		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75650634C>G	uc002baf.2	-	21	2472	c.2455G>C	c.(2455-2457)GTG>CTG	p.V819L	MAN2C1_uc002bag.2_Missense_Mutation_p.V819L|MAN2C1_uc002bah.2_Missense_Mutation_p.V836L|MAN2C1_uc010bkk.2_Missense_Mutation_p.V720L	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	819					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0						GAACTCCGCACGCGAGCAGGG	0.577													20	67	---	---	---	---	PASS
IL16	3603	broad.mit.edu	37	15	81589274	81589274	+	Silent	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81589274G>A	uc002bgh.3	+	13	2284	c.1908G>A	c.(1906-1908)GCG>GCA	p.A636A	IL16_uc010blq.1_Silent_p.A590A|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Silent_p.A678A|IL16_uc002bgg.2_Silent_p.A636A|IL16_uc002bgi.1_Silent_p.A26A|IL16_uc002bgj.2_Silent_p.A130A|IL16_uc002bgk.2_5'UTR|IL16_uc002bgl.1_5'UTR|IL16_uc010unq.1_5'Flank	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	636					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						CACAGGAAGCGAGAGAGCTGC	0.567													7	28	---	---	---	---	PASS
AXIN1	8312	broad.mit.edu	37	16	396290	396290	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:396290C>T	uc002cgp.1	-	2	913	c.736G>A	c.(736-738)GAA>AAA	p.E246K	AXIN1_uc002cgq.1_Missense_Mutation_p.E246K	NM_003502	NP_003493	O15169	AXIN1_HUMAN	axin 1 isoform a	246	Interaction with TP53 (By similarity).				activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CACTTCCATTCCTCATCTTCA	0.582													20	162	---	---	---	---	PASS
AXIN1	8312	broad.mit.edu	37	16	396291	396291	+	Silent	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:396291C>T	uc002cgp.1	-	2	912	c.735G>A	c.(733-735)GAG>GAA	p.E245E	AXIN1_uc002cgq.1_Silent_p.E245E	NM_003502	NP_003493	O15169	AXIN1_HUMAN	axin 1 isoform a	245	Interaction with TP53 (By similarity).				activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				ACTTCCATTCCTCATCTTCAT	0.582													21	160	---	---	---	---	PASS
SEC14L5	9717	broad.mit.edu	37	16	5050877	5050877	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5050877G>A	uc002cye.2	+	10	1261	c.1081G>A	c.(1081-1083)GGA>AGA	p.G361R		NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5	361	CRAL-TRIO.					integral to membrane|intracellular	transporter activity				0						CAACGAGGAAGGACAGAAGCG	0.627													4	13	---	---	---	---	PASS
ABCC6	368	broad.mit.edu	37	16	16244592	16244592	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16244592G>T	uc002den.3	-	30	4283	c.4246C>A	c.(4246-4248)CTT>ATT	p.L1416I	ABCC6_uc010bvo.2_RNA|ABCC6_uc002dem.2_Missense_Mutation_p.L168I	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	1416	Cytoplasmic (By similarity).|ABC transporter 2.				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		TTCCGGAGAAGGGCACGTGCC	0.612													5	27	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	32077410	32077410	+	RNA	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32077410G>T	uc010vft.1	+	1		c.25G>T			uc010vfu.1_5'Flank					Homo sapiens IGH mRNA for immunoglobulin heavy chain VHDJ region, partial cds, clone:aims0058h.																		GGAGTCTGGAGGAGGCTTGGT	0.562													58	396	---	---	---	---	PASS
HOXB1	3211	broad.mit.edu	37	17	46608210	46608210	+	Silent	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46608210G>T	uc002ink.1	-	1	63	c.57C>A	c.(55-57)CCC>CCA	p.P19P		NM_002144	NP_002135	P14653	HXB1_HUMAN	homeobox B1	19						nucleus	protein domain specific binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TGTAGGCGCTGGGTCCCCGGT	0.632													22	110	---	---	---	---	PASS
KIF2B	84643	broad.mit.edu	37	17	51900736	51900736	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51900736A>C	uc002iua.2	+	1	498	c.342A>C	c.(340-342)AAA>AAC	p.K114N	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	114					blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						CCGCCACGAAATGGGTTGCGA	0.597													35	92	---	---	---	---	PASS
TTYH2	94015	broad.mit.edu	37	17	72249930	72249930	+	Silent	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72249930C>T	uc002jkc.2	+	13	1513	c.1482C>T	c.(1480-1482)TAC>TAT	p.Y494Y	TTYH2_uc010wqw.1_Silent_p.Y473Y|TTYH2_uc002jkd.2_Silent_p.Y173Y	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1	494	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						ACCCACGCTACGAGAACGTGC	0.493													21	109	---	---	---	---	PASS
ILF3	3609	broad.mit.edu	37	19	10799269	10799269	+	Silent	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10799269C>T	uc002mpn.2	+	19	2783	c.2466C>T	c.(2464-2466)GGC>GGT	p.G822G	ILF3_uc002mpo.2_Silent_p.G826G|ILF3_uc002mpq.2_Missense_Mutation_p.A125V	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a	822	Interaction with PRMT1.				M phase|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleolus|ribonucleoprotein complex	DNA binding|double-stranded RNA binding|protein binding|protein binding			ovary(3)	3			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			ACAGCTACGGCTCAGGCGGGG	0.647													22	83	---	---	---	---	PASS
ZNF260	339324	broad.mit.edu	37	19	37004832	37004832	+	3'UTR	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37004832T>C	uc002oee.1	-	4					ZNF260_uc002oed.1_3'UTR|ZNF260_uc010eey.1_3'UTR|ZNF260_uc002oef.1_3'UTR	NM_001012756	NP_001012774	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.162)					GTAAAATGAATTTTCCAATAC	0.299													11	32	---	---	---	---	PASS
DHX34	9704	broad.mit.edu	37	19	47856562	47856562	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47856562C>T	uc010xyn.1	+	2	616	c.275C>T	c.(274-276)GCG>GTG	p.A92V	DHX34_uc010elc.1_Missense_Mutation_p.A92V	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	92						intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		AGCATCCCAGCGCTGGCCGAC	0.582													40	136	---	---	---	---	PASS
ZFP28	140612	broad.mit.edu	37	19	57065721	57065721	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57065721C>A	uc002qnj.2	+	8	1638	c.1567C>A	c.(1567-1569)CAC>AAC	p.H523N	uc002qnk.1_Intron	NM_020828	NP_065879	Q8NHY6	ZFP28_HUMAN	zinc finger protein 28	523	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		GCTTAATCAACACAGGAGAAT	0.423													15	66	---	---	---	---	PASS
FLRT3	23767	broad.mit.edu	37	20	14307334	14307334	+	Silent	SNP	G	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14307334G>C	uc002wov.1	-	3	1286	c.819C>G	c.(817-819)CTC>CTG	p.L273L	MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_Silent_p.L273L	NM_198391	NP_938205	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	273	Extracellular (Potential).|LRR 10.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			kidney(1)	1		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		CCAGTCGATAGAGCTGCCTTA	0.403													25	77	---	---	---	---	PASS
BACH1	571	broad.mit.edu	37	21	30693729	30693729	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30693729A>G	uc002ynj.2	+	2	243	c.128A>G	c.(127-129)CAG>CGG	p.Q43R	BACH1_uc002ynk.2_Missense_Mutation_p.Q43R|BACH1_uc002ynl.2_RNA	NM_001186	NP_001177	O14867	BACH1_HUMAN	BTB and CNC homology 1 transcription factor	43	BTB.					nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|liver(1)	2						GTGGAGGGACAGCGGTTCCGC	0.522													25	120	---	---	---	---	PASS
KRTAP13-2	337959	broad.mit.edu	37	21	31744251	31744251	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31744251G>A	uc002ynz.3	-	1	307	c.281C>T	c.(280-282)ACG>ATG	p.T94M		NM_181621	NP_853652	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	94	5 X 10 AA approximate repeats.|5.					intermediate filament					0						AGAGTAAGTCGTCTTGCAAGG	0.617													10	57	---	---	---	---	PASS
BRWD1	54014	broad.mit.edu	37	21	40590148	40590148	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40590148A>G	uc002yxk.1	-	31	3728	c.3589T>C	c.(3589-3591)TAC>CAC	p.Y1197H	BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Missense_Mutation_p.Y1197H|BRWD1_uc010god.1_Missense_Mutation_p.Y163H	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1197	Bromo 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				ACAGTACAGTACTTCGGGTAT	0.373													25	83	---	---	---	---	PASS
OTUD6A	139562	broad.mit.edu	37	X	69282742	69282742	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69282742G>T	uc004dxu.1	+	1	402	c.368G>T	c.(367-369)GGC>GTC	p.G123V		NM_207320	NP_997203	Q7L8S5	OTU6A_HUMAN	OTU domain containing 6A	123										lung(1)|skin(1)	2						CACCTGGCCGGCTTCAAGCGC	0.637													2	1	---	---	---	---	PASS
MORC4	79710	broad.mit.edu	37	X	106186437	106186437	+	Splice_Site	SNP	T	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106186437T>A	uc004emu.3	-	15	1929	c.1686_splice	c.e15-1	p.S562_splice	MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Splice_Site_p.S562_splice|MORC4_uc004emw.3_Splice_Site_p.S310_splice	NM_024657	NP_078933	Q8TE76	MORC4_HUMAN	zinc finger, CW type with coiled-coil domain 2								ATP binding|zinc ion binding			ovary(1)	1						TTGTACTTACTGCAAGAAGAG	0.423													9	63	---	---	---	---	PASS
LONRF3	79836	broad.mit.edu	37	X	118140161	118140161	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118140161A>G	uc004eqw.2	+	6	1524	c.1493A>G	c.(1492-1494)AAC>AGC	p.N498S	LONRF3_uc004eqx.2_Missense_Mutation_p.N457S|LONRF3_uc004eqy.2_RNA|LONRF3_uc004eqz.2_Missense_Mutation_p.N242S	NM_001031855	NP_001027026	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger	498	RING-type 2.				proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2						CTAGATCACAACGCAAAGTGT	0.348													83	124	---	---	---	---	PASS
FRMD7	90167	broad.mit.edu	37	X	131212433	131212433	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131212433T>G	uc004ewn.2	-	12	1790	c.1612A>C	c.(1612-1614)ATC>CTC	p.I538L	FRMD7_uc011muy.1_Missense_Mutation_p.I523L	NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	538	Potential.				regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TTCATTCTGATATTCCTTGGG	0.483													95	127	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14547	14547	+	RNA	SNP	T	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14547T>C	uc004cox.3	+	1		c.2211T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		AAAATTCAGAATAATAACACA	0.393													3	24	---	---	---	---	PASS
TARDBP	23435	broad.mit.edu	37	1	11077260	11077260	+	Intron	DEL	T	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11077260delT	uc001art.2	+						TARDBP_uc010oap.1_Intron	NM_007375	NP_031401	Q13148	TADBP_HUMAN	TAR DNA binding protein						3'-UTR-mediated mRNA stabilization|cell death|mRNA processing|negative regulation by host of viral transcription|RNA splicing|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)		GTTACCtttcttttttttttt	0.025													4	2	---	---	---	---	
TCTEX1D1	200132	broad.mit.edu	37	1	67242261	67242262	+	Intron	DEL	TA	-	-	rs60960124		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67242261_67242262delTA	uc001dcv.2	+						TCTEX1D1_uc009wau.2_Intron|TCTEX1D1_uc009wav.2_Intron	NM_152665	NP_689878	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1												0						tgtgtgtgtgtATATACATAAA	0.233													4	3	---	---	---	---	
KDM5B	10765	broad.mit.edu	37	1	202725354	202725355	+	Intron	INS	-	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202725354_202725355insA	uc001gyf.2	-						KDM5B_uc009xag.2_Intron|KDM5B_uc001gyg.1_Intron	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B						negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						TTCTGTAGGCTCTTTCTACTTT	0.312													16	7	---	---	---	---	
ATP2B4	493	broad.mit.edu	37	1	203593358	203593365	+	5'Flank	DEL	GAAGGAAG	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203593358_203593365delGAAGGAAG	uc001gzw.2	+						ATP2B4_uc001gzv.2_5'Flank	NM_001684	NP_001675	P23634	AT2B4_HUMAN	plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			aagaaagaaagaaggaaggaaggaagga	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203872719	203872719	+	IGR	DEL	G	-	-	rs144470926		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203872719delG								SNRPE (32441 upstream) : C1orf157 (128856 downstream)																							CTGATGTTGTGTTTTTTTTTT	0.249													4	6	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42760223	42760223	+	Intron	DEL	C	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42760223delC	uc002rso.1	+							NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						GTGGGGCAttctttttttttt	0.239													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91764930	91764935	+	IGR	DEL	TGTGTA	-	-	rs4005278		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91764930_91764935delTGTGTA								None (None upstream) : LOC654342 (40257 downstream)																							tgtgtgtgtgtgtgtatatatataca	0.015													5	4	---	---	---	---	
LYG2	254773	broad.mit.edu	37	2	99861575	99861575	+	Intron	DEL	A	-	-	rs5832869		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99861575delA	uc002szw.1	-						MRPL30_uc002szl.1_Intron|LYG2_uc010fip.1_Intron|LYG2_uc002szx.1_Intron	NM_175735	NP_783862	Q86SG7	LYG2_HUMAN	lysozyme G-like 2 precursor						cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity			ovary(1)	1						actccatctcaaaaaaaaaaa	0.199													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122067665	122067666	+	IGR	DEL	GT	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122067665_122067666delGT								TFCP2L1 (24887 upstream) : CLASP1 (27688 downstream)																							CCACATGAACgtgtgtgtgtgt	0.401													4	2	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10188202	10188202	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188202delC	uc003bvc.2	+	2	558	c.345delC	c.(343-345)CACfs	p.H115fs	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	115	Involved in binding to CCT complex.		H -> Q (in VHLD; type II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.H115N(5)|p.?(3)|p.H115Y(3)|p.H115fs*44(3)|p.H115D(1)|p.H115fs*41(1)|p.H115fs*42(1)|p.H115P(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CGATAGGTCACCTTTGGCTCT	0.338		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				130	56	---	---	---	---	
C3orf19	51244	broad.mit.edu	37	3	14706745	14706746	+	Intron	INS	-	ATTG	ATTG	rs142447115	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14706745_14706746insATTG	uc003byw.2	+						C3orf19_uc010hei.1_Intron|C3orf19_uc010hej.2_Intron	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244												0						AGTAAGGAGATattgattgatt	0.386													5	3	---	---	---	---	
KAT2B	8850	broad.mit.edu	37	3	20141236	20141237	+	Intron	DEL	TG	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20141236_20141237delTG	uc003cbq.2	+							NM_003884	NP_003875	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B						cell cycle arrest|cellular response to insulin stimulus|chromatin remodeling|histone H3 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|negative regulation of cell proliferation|transcription initiation from RNA polymerase I promoter	Ada2/Gcn5/Ada3 transcription activator complex|chromatin remodeling complex|PCAF complex	cyclin-dependent protein kinase inhibitor activity|histone acetyltransferase activity|histone deacetylase binding|protein kinase binding|transcription coactivator activity|transcription factor binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						CTTTAAAGGCTGTGTGTGTGTG	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115178759	115178760	+	IGR	INS	-	TCC	TCC	rs143809672	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115178759_115178760insTCC								ZBTB20 (312632 upstream) : GAP43 (163391 downstream)																							aagctttctcttcctcctcctc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137009703	137009704	+	IGR	INS	-	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137009703_137009704insT								IL20RB (279783 upstream) : SOX14 (473875 downstream)																							tccttccttccttccttccttc	0.000													5	3	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	171759202	171759213	+	Intron	DEL	TCCTTCCTTCCT	-	-	rs68136138		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171759202_171759213delTCCTTCCTTCCT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fhx.2_Intron	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		tccttctctctccttccttccttccttccttc	0.123													5	4	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3139908	3139911	+	Intron	DEL	GCCT	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3139908_3139911delGCCT	uc011bvq.1	+							NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		tccccttcccgcctgcctgcctgc	0.015													4	6	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7545631	7545634	+	Intron	DEL	CCAC	-	-	rs149040748	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7545631_7545634delCCAC	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						atccatccatccacccatccaccc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12637717	12637717	+	IGR	DEL	T	-	-	rs142332040		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12637717delT								None (None upstream) : HSP90AB2P (697320 downstream)																							ATAGGCTAGCTTTTTTTTTTT	0.209													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13234603	13234618	+	IGR	DEL	GAAAGAAAGAAAAAGG	-	-	rs71167697	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13234603_13234618delGAAAGAAAGAAAAAGG								None (None upstream) : HSP90AB2P (100419 downstream)																							aagaaagaaagaaagaaagaaaaaggaaggaaggaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72581181	72581182	+	IGR	INS	-	AGGA	AGGA	rs5859285		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72581181_72581182insAGGA								SLC4A4 (143378 upstream) : GC (26231 downstream)																							ggaaggaaggaaggcaggCAAG	0.218													10	5	---	---	---	---	
DKK2	27123	broad.mit.edu	37	4	108087414	108087414	+	Intron	DEL	A	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108087414delA	uc010ilw.1	-									Q9UBU2	DKK2_HUMAN	Homo sapiens dickkopf-2 mRNA, complete cds.						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ggaaggaaggaaggaaggaag	0.095													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	112582755	112582756	+	IGR	INS	-	TGTA	TGTA			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112582755_112582756insTGTA								MIR297 (800952 upstream) : C4orf32 (483797 downstream)																							gtgtgtgtgtgtgtgtgtgtgt	0.248													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189107787	189107788	+	IGR	INS	-	TG	TG	rs150229165	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189107787_189107788insTG								TRIML1 (39138 upstream) : None (None downstream)																							atagttacctctgtgtgtgtgt	0.030													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8287043	8287046	+	IGR	DEL	CTCC	-	-	rs139964067		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8287043_8287046delCTCC								MTRR (385810 upstream) : SEMA5A (748092 downstream)																							tccctctcctctccctcccttcct	0.103													3	3	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19747498	19747499	+	Intron	INS	-	T	T			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19747498_19747499insT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CTTTTCTGCAGTTTTTTTTTTT	0.287													8	4	---	---	---	---	
HMGCS1	3157	broad.mit.edu	37	5	43297941	43297941	+	Intron	DEL	A	-	-	rs75413713		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43297941delA	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						actcggtctcaaaaaaaaaaa	0.000													4	4	---	---	---	---	
ERBB2IP	55914	broad.mit.edu	37	5	65279617	65279617	+	Intron	DEL	C	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65279617delC	uc003juk.1	+						ERBB2IP_uc003juh.1_Intron|ERBB2IP_uc003jui.1_Intron|ERBB2IP_uc003juj.1_Intron|ERBB2IP_uc011cqx.1_Intron|ERBB2IP_uc011cqy.1_Intron|ERBB2IP_uc011cqz.1_Intron	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2						basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		TCTCAGGGCACCCCCCCCAAC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	103837871	103837872	+	IGR	DEL	TT	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103837871_103837872delTT								NUDT12 (939381 upstream) : RAB9BP1 (597303 downstream)																							tttctttctctttctttctttc	0.015													3	4	---	---	---	---	
TSLP	85480	broad.mit.edu	37	5	110409085	110409086	+	Intron	DEL	CT	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110409085_110409086delCT	uc003kpb.2	+						TSLP_uc003kpa.2_Intron|TSLP_uc010jbt.1_5'UTR	NM_033035	NP_149024	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin isoform 1							extracellular space	cytokine activity				0		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		TTCTCTCTGACTCTCGACTTGT	0.574													36	22	---	---	---	---	
MYOT	9499	broad.mit.edu	37	5	137213081	137213083	+	Intron	DEL	TAG	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137213081_137213083delTAG	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412	Q9UBF9	MYOTI_HUMAN	myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			aaaaaaaaaaTAGAATCTATCAT	0.143													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177398373	177398396	+	IGR	DEL	AGGACGAAGAGCTGGAGAGCGCCA	-	-	rs145131557		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177398373_177398396delAGGACGAAGAGCTGGAGAGCGCCA								LOC728554 (87106 upstream) : PROP1 (20840 downstream)																							GTCCCCGGGGAGGACGAAGAGCTGGAGAGCGCCAAGGACGACGA	0.531													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	12628850	12628865	+	IGR	DEL	CCTCCCTCCCTCCCTT	-	-	rs146594740		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12628850_12628865delCCTCCCTCCCTCCCTT								EDN1 (331424 upstream) : PHACTR1 (88023 downstream)																							ttccttcctccctccctccctcccttccttccttcc	0.102													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16972712	16972712	+	IGR	DEL	A	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16972712delA								ATXN1 (210991 upstream) : RBM24 (309097 downstream)																							ggaaggaaggaaggaaggaag	0.025													4	2	---	---	---	---	
HLA-C	3107	broad.mit.edu	37	6	31239271	31239275	+	Intron	DEL	ATCCA	-	-	rs72558142		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31239271_31239275delATCCA	uc003nsy.2	-						HLA-C_uc011dnj.1_Intron|HLA-C_uc003nsx.2_5'UTR|HLA-C_uc003nsz.2_Intron|HLA-C_uc010jsl.2_Intron|HLA-C_uc003nta.2_Intron|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron|HLA-C_uc011dnl.1_Intron|HLA-B_uc003ntf.2_Intron	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0						GGTTCCGCAGATCCACCTTGGGGTG	0.683													7	4	---	---	---	---	
MED20	9477	broad.mit.edu	37	6	41888527	41888527	+	Intron	DEL	A	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41888527delA	uc003ork.2	-						MED20_uc003orj.2_Intron|MED20_uc011duh.1_Intron|MED20_uc011dui.1_Intron|MED20_uc011duj.1_Intron|BYSL_uc003orl.2_5'Flank	NM_004275	NP_004266	Q9H944	MED20_HUMAN	Trf (TATA binding protein-related						regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	mediator complex	DNA-directed RNA polymerase activity|protein binding				0	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000367)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			aaaacaaaacaaaaaaaaaaC	0.279													4	2	---	---	---	---	
C6orf165	154313	broad.mit.edu	37	6	88125702	88125702	+	Intron	DEL	A	-	-	rs34892535		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88125702delA	uc003plv.2	+						C6orf165_uc003plw.2_Intron|C6orf165_uc010kbv.1_Intron|C6orf165_uc003plu.1_Intron	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1											central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		TTTTTATCTGAAAAAAAAAAA	0.279													6	3	---	---	---	---	
ALDH8A1	64577	broad.mit.edu	37	6	135265198	135265199	+	Intron	INS	-	TTTTG	TTTTG	rs146661388	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135265198_135265199insTTTTG	uc003qew.2	-						ALDH8A1_uc003qex.2_Intron|ALDH8A1_uc010kgh.2_Intron|ALDH8A1_uc011ecx.1_Intron	NM_022568	NP_072090	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8A1 isoform 1						retinal metabolic process	cytoplasm	retinal dehydrogenase activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		ACACACCTCATttttgttttgt	0.243													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153133134	153133135	+	IGR	DEL	TC	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153133134_153133135delTC								VIP (52236 upstream) : FBXO5 (158525 downstream)																							tcctcttctttctctttccttc	0.000													5	3	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163697000	163697000	+	Intron	DEL	T	-	-	rs79000543		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163697000delT	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)		AGAGTATTGCTTTTTTTTTTT	0.040													5	3	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37053771	37053773	+	Intron	DEL	CTC	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37053771_37053773delCTC	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						GGTCCCTACTctcctcctcctcc	0.394													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64532452	64532452	+	Intron	DEL	T	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64532452delT	uc003ttt.1	+						uc010kzt.1_Intron					Homo sapiens cDNA clone IMAGE:4215179, partial cds.																		atgcccagccttttttttttt	0.119													9	4	---	---	---	---	
LOC100128542	100128542	broad.mit.edu	37	7	150451251	150451252	+	Intron	INS	-	GAAA	GAAA	rs72059403		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150451251_150451252insGAAA	uc011kuw.1	+							NM_001162367	NP_001155839			hypothetical protein LOC100128542												0						aaggagggaaggaaaggaagga	0.094													4	3	---	---	---	---	
DNAJB6	10049	broad.mit.edu	37	7	157178362	157178362	+	Intron	DEL	A	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157178362delA	uc003wnk.2	+						DNAJB6_uc003wnj.2_3'UTR|DNAJB6_uc003wnl.2_Intron|DNAJB6_uc011kvy.1_Intron|DNAJB6_uc011kvz.1_Intron|DNAJB6_uc010lqt.2_3'UTR	NM_058246	NP_490647	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6						intermediate filament organization|negative regulation of caspase activity|protein folding|response to unfolded protein	nucleus|perinuclear region of cytoplasm	ATPase activator activity|chaperone binding|heat shock protein binding|unfolded protein binding			ovary(2)	2	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		CACTTAACAGAAATGTTAAAC	0.353													63	43	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30841837	30841837	+	IGR	DEL	C	-	-	rs34137012		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30841837delC								TEX15 (95615 upstream) : PURG (11484 downstream)																							CTTCCCCAttctttttttttt	0.229													4	2	---	---	---	---	
ZNF704	619279	broad.mit.edu	37	8	81553805	81553805	+	Intron	DEL	A	-	-	rs78833157	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81553805delA	uc003yby.1	-							NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			GTGAGGGAGGAAAAAAAAAAA	0.239													4	3	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110460747	110460747	+	Intron	DEL	T	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110460747delT	uc003yne.2	+							NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			gtttgtttggttttttttttt	0.090										HNSCC(38;0.096)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69876385	69876386	+	IGR	INS	-	TCT	TCT			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69876385_69876386insTCT								LOC100133920 (211436 upstream) : FOXD4L5 (299323 downstream)																							TTCTTCTCTTCTCTTCTTGTTT	0.277													4	2	---	---	---	---	
SLC27A4	10999	broad.mit.edu	37	9	131117233	131117233	+	Intron	DEL	A	-	-	rs151315045		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131117233delA	uc004but.2	+						SLC27A4_uc004buu.2_Intron	NM_005094	NP_005085	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid						long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0						actccgtctcaaaaaaaaaaa	0.259													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4159644	4159645	+	IGR	INS	-	A	A			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4159644_4159645insA								KLF6 (332171 upstream) : LOC100216001 (461799 downstream)																							aggaaggaaggagaaagacaga	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	34220055	34220056	+	IGR	INS	-	TTCCTTCCTTCC	TTCCTTCCTTCC			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34220055_34220056insTTCCTTCCTTCC								NRP1 (596049 upstream) : PARD3 (180042 downstream)																							AGATAAGTGGAttccttccttc	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	97878499	97878500	+	IGR	DEL	GC	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97878499_97878500delGC								CCNJ (57876 upstream) : ZNF518A (10972 downstream)																							tgtaacctgagcatgcgcagat	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42010455	42010462	+	IGR	DEL	AAAAGAAA	-	-	rs72331687		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42010455_42010462delAAAAGAAA								LRRC4C (529132 upstream) : None (None downstream)																							agaaagaaagaaaagaaagaaagaaaga	0.130													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45764950	45764965	+	IGR	DEL	AAGGAAGGAAGGAAGA	-	-	rs56170165	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45764950_45764965delAAGGAAGGAAGGAAGA								CHST1 (77778 upstream) : DKFZp779M0652 (28018 downstream)																							ggaaggaaggaaggaaggaaggaagagagagagaga	0.000													5	3	---	---	---	---	
ATL3	25923	broad.mit.edu	37	11	63400292	63400293	+	Intron	INS	-	CAAAA	CAAAA			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63400292_63400293insCAAAA	uc001nxk.1	-						ATL3_uc010rms.1_Intron|ATL3_uc010rmr.1_Intron	NM_015459	NP_056274	Q6DD88	ATLA3_HUMAN	atlastin 3						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			pancreas(1)	1						TATTTGCTATTcaaaacaaaac	0.257													8	5	---	---	---	---	
MAP4K2	5871	broad.mit.edu	37	11	64559791	64559792	+	Intron	INS	-	C	C	rs145440016	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64559791_64559792insC	uc001obh.2	-						MAP4K2_uc001obg.2_Intron|MAP4K2_uc001obi.2_Intron	NM_004579	NP_004570	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|immune response|positive regulation of JNK cascade|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2						GGCCTGCGCTGCCCCCCACCAG	0.688													7	4	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70445967	70445970	+	Intron	DEL	AAAA	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70445967_70445970delAAAA	uc001oqc.2	-						SHANK2_uc010rqn.1_Intron|SHANK2_uc001opz.2_Intron|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			agaaagaaataaaaagaaagaaag	0.000													5	3	---	---	---	---	
BCL9L	283149	broad.mit.edu	37	11	118774003	118774014	+	In_Frame_Del	DEL	CGCCCCCGCCCC	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118774003_118774014delCGCCCCCGCCCC	uc001pug.2	-	4	1645_1656	c.680_691delGGGGCGGGGGCG	c.(679-693)GGGGGCGGGGGCGTC>GTC	p.GGGG227del	BCL9L_uc009zal.2_In_Frame_Del_p.GGGG222del	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	227_230					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TTTCCGGGGAcgcccccgcccccgcccccgcc	0.575													3	3	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	2016881	2016882	+	Intron	INS	-	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2016881_2016882insG	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GCGTGTCTGGTGGACGGCCTGG	0.668													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4058013	4058020	+	IGR	DEL	TCCCTCCC	-	-	rs606595		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4058013_4058020delTCCCTCCC								PARP11 (75405 upstream) : CCND2 (324882 downstream)																							cttccttccttccctccctccctccctc	0.024													4	3	---	---	---	---	
ACSM4	341392	broad.mit.edu	37	12	7476752	7476752	+	Intron	DEL	A	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7476752delA	uc001qsx.1	+							NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0						actctgtctcaaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	33452396	33452397	+	IGR	INS	-	AAGG	AAGG	rs143444187	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33452396_33452397insAAGG								PKP2 (402616 upstream) : SYT10 (75951 downstream)																							gaaagaaaggaaaggaaggaag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92707077	92707080	+	IGR	DEL	TGTG	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92707077_92707080delTGTG								BTG1 (167404 upstream) : CLLU1OS (106790 downstream)																							TGTTTGACTTtgtgtgtgtgtgtg	0.093													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965130	117965131	+	Intron	DEL	AG	-	-	rs58270726		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965130_117965131delAG	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	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119145968	119145969	+	IGR	INS	-	AT	AT			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119145968_119145969insAT								SUDS3 (290129 upstream) : SRRM4 (273427 downstream)																							tggtggtgatggtgatgatggt	0.000													8	4	---	---	---	---	
PABPN1	8106	broad.mit.edu	37	14	23790967	23790969	+	In_Frame_Del	DEL	GAG	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23790967_23790969delGAG	uc001wjk.2	+	1	1571_1573	c.289_291delGAG	c.(289-291)GAGdel	p.E101del	PABPN1_uc001wjh.3_Intron|PABPN1_uc001wjj.2_In_Frame_Del_p.E101del	NM_004643	NP_004634	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	101	Interacts with SKIP.				modification by virus of host mRNA processing|mRNA 3'-end processing|muscle contraction|nuclear mRNA splicing, via spliceosome|poly(A)+ mRNA export from nucleus|termination of RNA polymerase II transcription|viral infectious cycle	cytoplasm|nucleoplasm|ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CGGCAGCCAAGAGGAGGAGGAGG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	52754387	52754387	+	IGR	DEL	A	-	-	rs72414119		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52754387delA								PTGDR (10946 upstream) : PTGER2 (26629 downstream)																							aaagtataataaaaaaaaaaa	0.095													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	59435614	59435615	+	IGR	INS	-	CTTCCTTCCTTCCTTC	CTTCCTTCCTTCCTTC	rs150857658	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59435614_59435615insCTTCCTTCCTTCCTTC								DACT1 (320578 upstream) : DAAM1 (219784 downstream)																							ttccttcctttcttccttcctt	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	86538163	86538164	+	IGR	INS	-	GAGAGAGAGAAA	GAGAGAGAGAAA	rs140881841	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86538163_86538164insGAGAGAGAGAAA								FLRT2 (443894 upstream) : None (None downstream)																							aggaagaaagggagagagagaa	0.084													9	4	---	---	---	---	
BUB1B	701	broad.mit.edu	37	15	40498204	40498205	+	Intron	INS	-	G	G			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40498204_40498205insG	uc001zkx.3	+						BUB1B_uc010ucl.1_Intron	NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		CTTCCTGGTACATTTTTTGGAT	0.312			Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				4	2	---	---	---	---	
GOLGA6L5	374650	broad.mit.edu	37	15	85055754	85055756	+	RNA	DEL	CTC	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85055754_85055756delCTC	uc002bkm.2	-	6		c.804_806delGAG				NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CACGTAGCCTCTCCTCCTGTTCA	0.547													6	4	---	---	---	---	
ARRDC4	91947	broad.mit.edu	37	15	98508660	98508661	+	Intron	DEL	CG	-	-	rs28380454	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98508660_98508661delCG	uc010bom.2	+						ARRDC4_uc002bui.3_Intron	NM_183376	NP_899232	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4						signal transduction						0	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			CATAGACACACGCACACACACC	0.203													4	2	---	---	---	---	
MLST8	64223	broad.mit.edu	37	16	2255805	2255805	+	Intron	DEL	G	-	-	rs3214648		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2255805delG	uc002coz.2	+						MLST8_uc002coy.2_Intron|MLST8_uc002cpa.2_Intron|MLST8_uc002cpb.2_Intron|MLST8_uc010uvx.1_Intron|MLST8_uc002cpc.2_Intron|MLST8_uc002cpd.2_Intron|MLST8_uc002cpe.2_5'UTR|MLST8_uc010uvy.1_5'UTR|MLST8_uc002cpg.2_5'UTR|MLST8_uc002cph.2_RNA|MLST8_uc002cpf.2_5'UTR	NM_022372	NP_071767	Q9BVC4	LST8_HUMAN	G protein beta subunit-like						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|T cell costimulation	cytosol	protein binding				0						CTGCGGAGGTGGGGGGGGGAC	0.512													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19906275	19906275	+	IGR	DEL	C	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19906275delC								GPRC5B (9443 upstream) : GPR139 (136768 downstream)																							tcctcctcctcctcTCTCTCT	0.294													4	2	---	---	---	---	
TNFSF12-TNFSF13	407977	broad.mit.edu	37	17	7451453	7451454	+	5'Flank	INS	-	GTCC	GTCC			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7451453_7451454insGTCC	uc002ghi.1	+						TNFSF12_uc002ghg.2_5'Flank|TNFSF12_uc002ghh.2_5'Flank	NM_172089	NP_742086	Q8IZK7	Q8IZK7_HUMAN	TNFSF12-TNFSF13 protein						immune response	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0		Prostate(122;0.157)				agccAATTTTGGtccttccttc	0.010													5	4	---	---	---	---	
FBXW10	10517	broad.mit.edu	37	17	18673619	18673620	+	Intron	INS	-	T	T	rs111256666		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18673619_18673620insT	uc002guk.2	+						FBXW10_uc002guj.2_Intron|FBXW10_uc002gul.2_Intron|FBXW10_uc010cqh.1_Intron	NM_031456	NP_113644	Q5XX13	FBW10_HUMAN	F-box and WD-40 domain protein 10											ovary(1)	1						TTCATTTTGACttttttttttt	0.218													5	3	---	---	---	---	
RHOT1	55288	broad.mit.edu	37	17	30527795	30527795	+	Intron	DEL	A	-	-	rs80009584		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30527795delA	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron	NM_018307	NP_060777	Q8IXI2	MIRO1_HUMAN	ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				cctatctttcaaaaaaaaaaa	0.149													3	3	---	---	---	---	
TBC1D3	729873	broad.mit.edu	37	17	36370035	36370036	+	Intron	DEL	GT	-	-	rs3987840		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36370035_36370036delGT	uc010wdn.1	-						uc002hpx.2_Intron			Q8IZP1	TBC3A_HUMAN	Homo sapiens TBC1D3 mRNA for TBC1 domain family, member 3, complete cds.							intracellular	Rab GTPase activator activity				0	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		agattaTGTCgtgtgtgtgtgt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39856173	39856174	+	Intron	INS	-	CCTT	CCTT	rs72362251		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39856173_39856174insCCTT	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		TCTGGGCTGGCccttccttcct	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57429217	57429218	+	IGR	DEL	AG	-	-	rs141641247	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57429217_57429218delAG								CCBE1 (64573 upstream) : PMAIP1 (137974 downstream)																							AAAAAAAAAAAGAGGAAGACAG	0.243													4	2	---	---	---	---	
ZNF699	374879	broad.mit.edu	37	19	9415943	9415944	+	5'Flank	DEL	AC	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9415943_9415944delAC	uc002mlc.1	-							NM_198535	NP_940937	Q32M78	ZN699_HUMAN	zinc finger protein 699						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CAAAacacatacacacacacac	0.381													4	2	---	---	---	---	
CEACAM1	634	broad.mit.edu	37	19	43031783	43031783	+	Intron	DEL	G	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43031783delG	uc002otv.2	-						uc010eif.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron|CEACAM1_uc002otw.2_Intron|CEACAM1_uc010eij.2_Intron|CEACAM1_uc002otx.2_Intron|CEACAM1_uc002oty.2_Intron|CEACAM1_uc002otz.2_Intron|CEACAM1_uc010eik.2_Intron|CEACAM1_uc002oua.2_Intron|CEACAM1_uc002oub.2_Intron|CEACAM1_uc002ouc.2_Intron	NM_001712	NP_001703	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion						angiogenesis|cell migration|homophilic cell adhesion|integrin-mediated signaling pathway	extracellular region|integral to plasma membrane|membrane fraction				ovary(1)|central_nervous_system(1)	2		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	cccttccccagggatccgcat	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	44917382	44917383	+	IGR	DEL	TT	-	-	rs36015912		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44917382_44917383delTT								ZFP112 (11605 upstream) : ZNF229 (13043 downstream)																							tgggaaaccatttttttttttt	0.050													3	3	---	---	---	---	
ISOC2	79763	broad.mit.edu	37	19	55964546	55964547	+	3'UTR	INS	-	C	C	rs139098245	by1000genomes	TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55964546_55964547insC	uc002qlb.2	-	6					ISOC2_uc002qla.2_3'UTR|ISOC2_uc002qlc.2_3'UTR	NM_001136201	NP_001129673	Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2 isoform 1						protein destabilization	mitochondrion|nucleus	catalytic activity|protein binding			ovary(1)	1	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		GCAGCACCCTGCCCCCCCCACA	0.639													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	23604976	23604977	+	IGR	INS	-	GGAAGGAAGGGAGGAAGGAAGGAAGGAAGGAAGGAAGGAA	GGAAGGAAGGGAGGAAGGAAGGAAGGAAGGAAGGAAGGAA	rs13046240		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23604976_23604977insGGAAGGAAGGGAGGAAGGAAGGAAGGAAGGAAGGAAGGAA								NCAM2 (693762 upstream) : None (None downstream)																							GCAGCaaagagggaaggaaggg	0.168													8	4	---	---	---	---	
LSS	4047	broad.mit.edu	37	21	47632005	47632006	+	Intron	INS	-	C	C			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47632005_47632006insC	uc002zij.2	-						LSS_uc011afv.1_Intron|LSS_uc002zil.2_Intron|LSS_uc002zik.2_Intron	NM_001001438	NP_001001438	P48449	ERG7_HUMAN	lanosterol synthase isoform 1						cholesterol biosynthetic process	endoplasmic reticulum membrane	lanosterol synthase activity				0	Breast(49;0.214)					gggcagggaggccagggcCTGC	0.371													4	2	---	---	---	---	
HUWE1	10075	broad.mit.edu	37	X	53629650	53629651	+	Intron	DEL	AT	-	-	rs35692881		TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53629650_53629651delAT	uc004dsp.2	-							NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1						base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						AGCAAAAGAAATATATATATAT	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9996490	9996490	+	IGR	DEL	A	-	-			TCGA-BP-4989-01A-01D-1462-08	TCGA-BP-4989-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9996490delA								TTTY22 (345636 upstream) : None (None downstream)																							gaagtcctacatagaataatt	0.000													6	3	---	---	---	---	
