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
SNHG3-RCC1	751867	broad.mit.edu	37	1	28835180	28835180	+	Intron	SNP	T	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28835180T>C	uc001bqa.1	+						SNHG3-RCC1_uc001bqb.1_Intron|SNHG3-RCC1_uc001bqc.1_Intron	NM_001048197	NP_001041662			regulator of chromosome condensation 1												0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|READ - Rectum adenocarcinoma(331;0.0649)		acgttgaagatgaagctgggc	0.010													4	83	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62349973	62349973	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62349973G>C	uc001dab.2	+	22	3138	c.3024G>C	c.(3022-3024)AGG>AGC	p.R1008S	INADL_uc009waf.1_Missense_Mutation_p.R1008S|INADL_uc001daa.2_Missense_Mutation_p.R1008S|INADL_uc001dad.3_Missense_Mutation_p.R705S|INADL_uc001dac.2_RNA	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1008					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						TGGCTCAAAGGAGGGAGCAAG	0.463													8	234	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75037720	75037720	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75037720C>T	uc001dgg.2	-	14	3893	c.3674G>A	c.(3673-3675)GGA>GAA	p.G1225E		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1225	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						CTGCACCTTTCCTGCTGGCTC	0.627													21	87	---	---	---	---	PASS
DNTTIP2	30836	broad.mit.edu	37	1	94343391	94343391	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94343391G>T	uc001dqf.2	-	2	138	c.100C>A	c.(100-102)CAT>AAT	p.H34N	DNTTIP2_uc010otm.1_RNA|DNTTIP2_uc009wdo.1_Intron	NM_014597	NP_055412	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal,	34					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CTTTCTGGATGCGCTTGAATC	0.443													11	40	---	---	---	---	PASS
KCND3	3752	broad.mit.edu	37	1	112524490	112524490	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112524490C>T	uc001ebu.1	-	2	1339	c.859G>A	c.(859-861)GTC>ATC	p.V287I	KCND3_uc001ebv.1_Missense_Mutation_p.V287I	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related	287	Helical; Voltage-sensor; Name=Segment S4; (Potential).					sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		CGGAGCGTGACGAAGGCGCCG	0.597													14	69	---	---	---	---	PASS
HMGCS2	3158	broad.mit.edu	37	1	120307117	120307117	+	Silent	SNP	C	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120307117C>A	uc001eid.2	-	2	288	c.237G>T	c.(235-237)GTG>GTT	p.V79V	HMGCS2_uc010oxj.1_Silent_p.V79V|HMGCS2_uc001eie.2_5'UTR	NM_005518	NP_005509	P54868	HMCS2_HUMAN	hydroxymethylglutaryl-CoA synthase 2 isoform 1	79					acetoacetic acid biosynthetic process|cholesterol biosynthetic process|isoprenoid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA synthase activity			ovary(2)	2	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TTCCTGCTTCCACATTGTTAT	0.542													40	125	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142713944	142713944	+	Intron	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142713944C>T	uc001eiw.1	+						uc001eix.1_RNA					Homo sapiens PNAS-130 mRNA, complete cds.																		TGATTACCTCCGAAGTTAAAG	0.308													7	27	---	---	---	---	PASS
ZBTB41	360023	broad.mit.edu	37	1	197169423	197169423	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197169423T>C	uc001gtx.1	-	1	250	c.181A>G	c.(181-183)AGA>GGA	p.R61G	ZBTB41_uc009wyz.1_RNA|CRB1_uc010poz.1_5'Flank	NM_194314	NP_919290	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	61					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2						AAAAGCTTTCTCTGATCTGGA	0.383													33	105	---	---	---	---	PASS
TEKT4	150483	broad.mit.edu	37	2	95542539	95542539	+	3'UTR	SNP	G	A	A	rs80350895	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95542539G>A	uc002stw.1	+	6					uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN	tektin 4						cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|breast(1)|skin(1)	3						CTTCCCCCCAGTCCCCCAAAT	0.602													3	26	---	---	---	---	PASS
ANKRD36	375248	broad.mit.edu	37	2	97869931	97869931	+	Missense_Mutation	SNP	A	T	T	rs76309140		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-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	29	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128757921	128757921	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128757921G>A	uc002tpp.2	-	8	1187	c.1055C>T	c.(1054-1056)GCA>GTA	p.A352V	SAP130_uc002tpn.2_Missense_Mutation_p.A113V|SAP130_uc002tpo.2_Missense_Mutation_p.A97V|SAP130_uc010fmd.2_Missense_Mutation_p.A352V|SAP130_uc002tpq.1_Missense_Mutation_p.A325V	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	352					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CGTCCCTAATGCAGGGTGAGA	0.473													7	128	---	---	---	---	PASS
WNT7A	7476	broad.mit.edu	37	3	13921263	13921263	+	Silent	SNP	G	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13921263G>T	uc003bye.1	-	1	356	c.51C>A	c.(49-51)GGC>GGA	p.G17G		NM_004625	NP_004616	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family,	17					activation of JUN kinase activity|anterior/posterior pattern formation|canonical Wnt receptor signaling pathway|cell proliferation in forebrain|cellular response to transforming growth factor beta stimulus|central nervous system vasculogenesis|cerebellar granule cell differentiation|dorsal/ventral pattern formation|embryonic axis specification|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic leg morphogenesis|lens fiber cell development|negative regulation of neurogenesis|palate development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of JNK cascade|positive regulation of synaptogenesis|positive regulation of transcription from RNA polymerase II promoter|regulation of axon diameter|satellite cell activation|satellite cell maintenance involved in skeletal muscle regeneration|sex differentiation|uterus development|Wnt receptor signaling pathway involved in wound healing, spreading of epidermal cells|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	cytokine activity|frizzled binding|receptor agonist activity|signal transducer activity			ovary(2)|breast(1)	3						GGTAGACCATGCCCAGGCTGA	0.547													3	30	---	---	---	---	PASS
MAP4	4134	broad.mit.edu	37	3	47957988	47957988	+	Silent	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47957988C>T	uc003csb.2	-	7	1855	c.1329G>A	c.(1327-1329)GAG>GAA	p.E443E	MAP4_uc003csc.3_Silent_p.E443E|MAP4_uc011bbf.1_Silent_p.E420E|MAP4_uc003csf.3_Silent_p.E460E	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1	443	11.|17 X 14 AA tandem repeats.				negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		CCAGGGCTACCTCTGTTTCTG	0.493													42	88	---	---	---	---	PASS
GMPS	8833	broad.mit.edu	37	3	155655512	155655512	+	3'UTR	SNP	G	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155655512G>T	uc003faq.2	+	16					GMPS_uc011bom.1_3'UTR	NM_003875	NP_003866	P49915	GUAA_HUMAN	guanine monophosphate synthetase						glutamine metabolic process|purine base biosynthetic process	cytosol	ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity			ovary(2)|lung(1)	3			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	AGTACCGTGTGCAGTTTAAAT	0.378			T	MLL	AML								9	47	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	94751143	94751143	+	IGR	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94751143G>A								ATOH1 (1 upstream) : SMARCAD1 (377616 downstream)																							GGCAAGTTAGGAAGGTGACAG	0.522													22	90	---	---	---	---	PASS
METTL14	57721	broad.mit.edu	37	4	119631494	119631494	+	3'UTR	SNP	C	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119631494C>A	uc003icf.2	+	11					METTL14_uc003icg.2_3'UTR	NM_020961	NP_066012	Q9HCE5	MTL14_HUMAN	methyltransferase like 14							nucleus	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity				0						CCTCCTCTAACCTTCTTTATT	0.418													11	17	---	---	---	---	PASS
SLC12A2	6558	broad.mit.edu	37	5	127466804	127466804	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127466804G>T	uc003kus.2	+	5	1258	c.1094G>T	c.(1093-1095)GGT>GTT	p.G365V	SLC12A2_uc010jdf.2_RNA|SLC12A2_uc010jdg.2_Missense_Mutation_p.G365V	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12	365	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAGAATTTGGTGGTGCAATT	0.373													58	283	---	---	---	---	PASS
FSTL4	23105	broad.mit.edu	37	5	132585226	132585226	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132585226A>G	uc003kyn.1	-	7	988	c.770T>C	c.(769-771)GTG>GCG	p.V257A		NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor	257	Ig-like 1.					extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CACTGTGGTCACACTGACCCT	0.627											OREG0005128	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	12	63	---	---	---	---	PASS
PCDHGA1	56114	broad.mit.edu	37	5	140710369	140710369	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140710369G>T	uc003lji.1	+	1	118	c.118G>T	c.(118-120)GAC>TAC	p.D40Y	PCDHGA1_uc011dan.1_Missense_Mutation_p.D40Y	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	40	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAGAGACAGACAAAGGTTC	0.577													11	181	---	---	---	---	PASS
SLC35A1	10559	broad.mit.edu	37	6	88218629	88218629	+	Intron	SNP	C	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88218629C>G	uc011dzj.1	+						SLC35A1_uc003plx.2_Intron|SLC35A1_uc010kbw.2_Intron|SLC35A1_uc003plz.2_Intron|SLC35A1_uc011dzi.1_Intron|SLC35A1_uc003ply.2_Intron|SLC35A1_uc010kbx.2_Intron|SLC35A1_uc010kby.2_Intron|SLC35A1_uc011dzk.1_RNA	NM_006416	NP_006407	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid						carbohydrate metabolic process|protein modification process	Golgi membrane|integral to plasma membrane	CMP-N-acetylneuraminate transmembrane transporter activity|sugar:hydrogen symporter activity				0		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;0.0429)		TCAGATGGCTCCTTCTAAGGA	0.353													3	14	---	---	---	---	PASS
STEAP2	261729	broad.mit.edu	37	7	89866345	89866345	+	3'UTR	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89866345C>T	uc003ujz.2	+	5					STEAP2_uc010len.2_3'UTR|STEAP2_uc003uka.2_3'UTR|STEAP2_uc003ukb.2_3'UTR|STEAP2_uc003ukc.2_3'UTR|STEAP2_uc003ukd.2_3'UTR	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the						electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)					tgagtgttggccagtgagatg	0.100													3	38	---	---	---	---	PASS
SAMD9	54809	broad.mit.edu	37	7	92730525	92730525	+	3'UTR	SNP	G	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92730525G>C	uc003umf.2	-	3					SAMD9_uc003umg.2_3'UTR	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9							cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TGCATGTACAGATCTGAAGAG	0.343													8	53	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100680563	100680563	+	Missense_Mutation	SNP	C	A	A	rs117408972	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100680563C>A	uc003uxp.1	+	3	5919	c.5866C>A	c.(5866-5868)CCT>ACT	p.P1956T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1956	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|31.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					CACCAGGACACCTGTGACCAC	0.483													14	332	---	---	---	---	PASS
COPG2	26958	broad.mit.edu	37	7	130295934	130295934	+	Silent	SNP	A	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130295934A>G	uc003vqh.1	-	9	717	c.627T>C	c.(625-627)CTT>CTC	p.L209L		NM_012133	NP_036265	Q9UBF2	COPG2_HUMAN	coatomer protein complex, subunit gamma 2	209					intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)					TGGAAACAGCAAGTCGATCAT	0.373													18	67	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151851228	151851228	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151851228G>T	uc003wla.2	-	48	12362	c.12143C>A	c.(12142-12144)TCA>TAA	p.S4048*	MLL3_uc003wkz.2_Nonsense_Mutation_p.S3166*|MLL3_uc003wkx.2_Nonsense_Mutation_p.S206*|MLL3_uc003wky.2_Nonsense_Mutation_p.S1612*	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	4048					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		TCTTGATTCTGAACCTTTAAA	0.338			N		medulloblastoma								19	99	---	---	---	---	PASS
GPAA1	8733	broad.mit.edu	37	8	145138388	145138388	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145138388G>C	uc003zax.2	+	3	461	c.351G>C	c.(349-351)GAG>GAC	p.E117D	GPAA1_uc003zav.1_5'UTR|GPAA1_uc003zaw.1_Missense_Mutation_p.E57D	NM_003801	NP_003792	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment	117	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|protein complex assembly|protein retention in ER lumen	GPI-anchor transamidase complex	tubulin binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCCCAGATGAGACCCACGAGC	0.632													14	64	---	---	---	---	PASS
PDCD1LG2	80380	broad.mit.edu	37	9	5570162	5570162	+	3'UTR	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5570162C>T	uc003zjg.3	+	7					C9orf46_uc003zjd.2_Intron|PDCD1LG2_uc011lmc.1_3'UTR|PDCD1LG2_uc011lmd.1_3'UTR	NM_025239	NP_079515	Q9BQ51	PD1L2_HUMAN	programmed cell death 1 ligand 2 precursor						immune response|T cell costimulation	endomembrane system|extracellular region|integral to membrane|plasma membrane	receptor activity				0	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000767)|Lung(218;0.112)		TCTGGACTCACCTCTGGAGCC	0.488													8	10	---	---	---	---	PASS
ASTN2	23245	broad.mit.edu	37	9	119802150	119802150	+	Silent	SNP	A	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119802150A>G	uc004bjs.1	-	6	1472	c.1371T>C	c.(1369-1371)TGT>TGC	p.C457C	ASTN2_uc004bjr.1_Silent_p.C457C|ASTN2_uc004bjt.1_Silent_p.C406C	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	457	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						CAGTGAGTGGACAAGACATCT	0.537													9	34	---	---	---	---	PASS
KIF20B	9585	broad.mit.edu	37	10	91476196	91476196	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91476196T>C	uc001kgs.1	+	9	1016	c.944T>C	c.(943-945)CTA>CCA	p.L315P	KIF20B_uc001kgr.1_Missense_Mutation_p.L315P	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	315	Kinesin-motor.				cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						TTTAAAGATCTACAATGGATT	0.294													12	46	---	---	---	---	PASS
RRP12	23223	broad.mit.edu	37	10	99120376	99120376	+	Splice_Site	SNP	C	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99120376C>A	uc001knf.2	-	31	3707	c.3568_splice	c.e31-1	p.K1190_splice	RRP12_uc001kne.2_Splice_Site_p.K205_splice|RRP12_uc009xvl.2_Splice_Site_p.K307_splice|RRP12_uc009xvm.2_Splice_Site_p.K908_splice|RRP12_uc010qou.1_Splice_Site_p.K1129_splice|RRP12_uc009xvn.2_Splice_Site_p.K1090_splice	NM_015179	NP_055994	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog isoform 1							integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GGTGCTTTTTCTATAGAGAGA	0.547													28	90	---	---	---	---	PASS
HSPA12A	259217	broad.mit.edu	37	10	118464696	118464696	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118464696A>G	uc001lct.2	-	3	325	c.220T>C	c.(220-222)TTC>CTC	p.F74L	HSPA12A_uc001lcu.2_5'UTR	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	74							ATP binding			ovary(1)	1				all cancers(201;0.0158)		TCCTTGGTGAAGCTGTAGGCA	0.587													13	58	---	---	---	---	PASS
PRLHR	2834	broad.mit.edu	37	10	120353582	120353582	+	3'UTR	SNP	G	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120353582G>T	uc001ldp.1	-	2						NM_004248	NP_004239	P49683	PRLHR_HUMAN	G protein-coupled receptor 10						female pregnancy	integral to plasma membrane	neuropeptide Y receptor activity				0		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		GATTGACCTCGAGTGGTGCCC	0.557													14	41	---	---	---	---	PASS
OSBPL5	114879	broad.mit.edu	37	11	3150289	3150289	+	Silent	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3150289C>T	uc001lxk.2	-	2	248	c.90G>A	c.(88-90)CGG>CGA	p.R30R	OSBPL5_uc010qxq.1_5'Flank|OSBPL5_uc009ydw.2_Silent_p.R30R|OSBPL5_uc001lxl.2_Silent_p.R30R|OSBPL5_uc009ydx.2_Silent_p.R54R|OSBPL5_uc001lxm.1_RNA	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	30					cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GGAGCAAGTTCCGGGTGAGCT	0.667													4	11	---	---	---	---	PASS
SLC35C1	55343	broad.mit.edu	37	11	45832463	45832463	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45832463C>A	uc001nbp.2	+	2	1384	c.672C>A	c.(670-672)GAC>GAA	p.D224E	SLC35C1_uc001nbo.2_Missense_Mutation_p.D211E|SLC35C1_uc010rgm.1_Missense_Mutation_p.D211E	NM_018389	NP_060859	Q96A29	FUCT1_HUMAN	GDP-fucose transporter 1 isoform a	224						Golgi membrane|integral to membrane	GDP-fucose transmembrane transporter activity				0				GBM - Glioblastoma multiforme(35;0.227)		CGGCGGTGGACGGCAGCATCT	0.637													3	38	---	---	---	---	PASS
MARK2	2011	broad.mit.edu	37	11	63668343	63668343	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63668343G>A	uc001nxw.2	+	10	1559	c.980G>A	c.(979-981)CGG>CAG	p.R327Q	MARK2_uc001nxx.2_Missense_Mutation_p.R327Q|MARK2_uc001nxy.2_Missense_Mutation_p.R327Q|MARK2_uc001nxv.3_Missense_Mutation_p.R327Q|MARK2_uc001nxz.3_Missense_Mutation_p.R294Q|MARK2_uc009yoy.2_Missense_Mutation_p.R294Q	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	327	UBA.				cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3						AAGGACCCCCGGCGGACAGGT	0.547													45	115	---	---	---	---	PASS
PCF11	51585	broad.mit.edu	37	11	82877718	82877718	+	Silent	SNP	T	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82877718T>C	uc001ozx.3	+	5	2124	c.1779T>C	c.(1777-1779)TCT>TCC	p.S593S	PCF11_uc010rsu.1_Silent_p.S593S	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	593					mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1						GTTCCAAGTCTGCCAAAAGAT	0.363													35	120	---	---	---	---	PASS
DDI1	414301	broad.mit.edu	37	11	103907540	103907540	+	5'UTR	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103907540G>A	uc001phr.2	+	1					PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1						proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|upper_aerodigestive_tract(1)|pancreas(1)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		cggcccgcccgggcccccgcc	0.562													26	108	---	---	---	---	PASS
ZNF770	54989	broad.mit.edu	37	15	35274804	35274804	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35274804A>T	uc001ziw.2	-	3	1143	c.832T>A	c.(832-834)TCT>ACT	p.S278T		NM_014106	NP_054825	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		TTCTCCTCAGATTCACCAATC	0.388													19	89	---	---	---	---	PASS
UACA	55075	broad.mit.edu	37	15	70994283	70994283	+	Intron	SNP	G	A	A	rs6494889	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70994283G>A	uc002asr.2	-						UACA_uc010uke.1_Intron|UACA_uc002asq.2_5'UTR|UACA_uc010bin.1_5'UTR	NM_018003	NP_060473	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4						TGTTGCTAATGGCAAACTACT	0.393													4	90	---	---	---	---	PASS
MYO9A	4649	broad.mit.edu	37	15	72300251	72300251	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72300251G>C	uc002atl.3	-	8	1769	c.1296C>G	c.(1294-1296)ATC>ATG	p.I432M	MYO9A_uc010biq.2_Missense_Mutation_p.I27M|MYO9A_uc002ato.2_Missense_Mutation_p.I432M|MYO9A_uc002atn.1_Missense_Mutation_p.I413M	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	432	Myosin head-like 1.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3						TTTTGTAACAGATATTACCCA	0.358													25	108	---	---	---	---	PASS
ACAN	176	broad.mit.edu	37	15	89395179	89395179	+	Silent	SNP	T	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89395179T>A	uc010upo.1	+	11	2555	c.2181T>A	c.(2179-2181)ACT>ACA	p.T727T	ACAN_uc010upp.1_Silent_p.T727T|ACAN_uc002bna.2_RNA	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor	727					cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GGGAGACTACTGCCATCCTAG	0.582													6	19	---	---	---	---	PASS
ANPEP	290	broad.mit.edu	37	15	90340889	90340889	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90340889A>G	uc002bop.3	-	15	2366	c.2074T>C	c.(2074-2076)TAC>CAC	p.Y692H		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	692	Extracellular.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)|skin(1)	4	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)	CAGGGCATGTACTGTCTCTCT	0.562													38	137	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102292785	102292785	+	Missense_Mutation	SNP	C	G	G	rs143389223		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102292785C>G	uc010usj.1	+	4	432	c.373C>G	c.(373-375)CAG>GAG	p.Q125E	uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		TGCTGCTTCTCAGAGCTGCTG	0.602													3	21	---	---	---	---	PASS
VWA3A	146177	broad.mit.edu	37	16	22162103	22162103	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22162103G>A	uc010vbq.1	+	30	3313	c.3217G>A	c.(3217-3219)GTC>ATC	p.V1073I	VWA3A_uc010bxd.2_RNA|VWA3A_uc002dkg.3_Missense_Mutation_p.V151I|VWA3A_uc010bxe.1_Missense_Mutation_p.V175I	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	1073	VWFA 2.					extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		CCTAAATGAAGTCCAAAAACT	0.448													5	22	---	---	---	---	PASS
CHD3	1107	broad.mit.edu	37	17	7806304	7806304	+	Silent	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7806304C>T	uc002gje.2	+	22	3570	c.3420C>T	c.(3418-3420)GGC>GGT	p.G1140G	CHD3_uc002gjd.2_Silent_p.G1199G|CHD3_uc002gjf.2_Silent_p.G1140G|CHD3_uc002gjh.2_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1140	Helicase C-terminal.				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|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)				GAGCTGGGGGCCTGGGCATCA	0.547													10	94	---	---	---	---	PASS
DLX4	1748	broad.mit.edu	37	17	48051147	48051147	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48051147C>T	uc002ipv.2	+	3	834	c.563C>T	c.(562-564)CCT>CTT	p.P188L	DLX4_uc002ipw.2_Missense_Mutation_p.P116L	NM_138281	NP_612138	Q92988	DLX4_HUMAN	distal-less homeobox 4 isoform a	188					multicellular organismal development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GGGGACTTCCCTGGGAGGACC	0.577													6	164	---	---	---	---	PASS
CXXC1	30827	broad.mit.edu	37	18	47808972	47808972	+	Silent	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47808972G>A	uc002leq.3	-	15	2695	c.1962C>T	c.(1960-1962)GCC>GCT	p.A654A	MBD1_uc002leg.2_5'Flank|MBD1_uc010dow.1_5'Flank|MBD1_uc010xdi.1_5'Flank|MBD1_uc002leh.3_5'Flank|MBD1_uc002len.2_5'Flank|MBD1_uc002lei.3_5'Flank|MBD1_uc002lej.3_5'Flank|MBD1_uc002lek.3_5'Flank|MBD1_uc002lel.3_5'Flank|MBD1_uc002lem.3_5'Flank|MBD1_uc010xdj.1_5'Flank|MBD1_uc010xdk.1_5'Flank|MBD1_uc010dox.1_5'Flank|MBD1_uc002leo.2_5'Flank|CXXC1_uc002lep.3_Silent_p.A511A|CXXC1_uc002ler.3_Silent_p.A658A|CXXC1_uc010doy.2_3'UTR	NM_014593	NP_055408	Q9P0U4	CXXC1_HUMAN	CXXC finger 1 (PHD domain) isoform 2	654					histone H3-K4 methylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|Set1C/COMPASS complex	protein binding|unmethylated CpG binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						CTCAGCGGTCGGCACTGGAGC	0.647													42	90	---	---	---	---	PASS
SERPINB5	5268	broad.mit.edu	37	18	61154215	61154215	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61154215G>A	uc002liz.3	+	3	347	c.205G>A	c.(205-207)GGA>AGA	p.G69R	SERPINB5_uc002liy.2_Missense_Mutation_p.G69R	NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	69					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1						TGTACCCTTTGGATTTCAAAC	0.373													23	137	---	---	---	---	PASS
ZNF557	79230	broad.mit.edu	37	19	7075062	7075062	+	5'UTR	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7075062C>T	uc002mgb.2	+	3					ZNF557_uc002mga.2_5'UTR|ZNF557_uc002mgc.2_5'UTR	NM_001044388	NP_001037853	Q8N988	ZN557_HUMAN	zinc finger protein 557 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2				Lung(535;0.179)		TTCCCGGCTGCCCTGTTGCTG	0.632													20	49	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39964875	39964875	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39964875T>C	uc002olo.3	+	27	2832	c.2653T>C	c.(2653-2655)TAC>CAC	p.Y885H	SUPT5H_uc002olp.3_Missense_Mutation_p.Y885H|SUPT5H_uc002olq.3_Missense_Mutation_p.Y881H|SUPT5H_uc002oln.3_Missense_Mutation_p.Y885H|SUPT5H_uc002olr.3_Missense_Mutation_p.Y885H|SUPT5H_uc002ols.1_Missense_Mutation_p.Y508H	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	885	10 X 8 AA approximate tandem repeats of P-[TS]-P-S-P-[QA]-[SG]-Y, motif CTR2.|Pro-rich.|CTR2-4; half-length.				cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TCTCTGCAGGTACAACACAGA	0.632											OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	81	---	---	---	---	PASS
ZNF283	284349	broad.mit.edu	37	19	44352238	44352238	+	Silent	SNP	C	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44352238C>T	uc002oxr.3	+	7	1753	c.1485C>T	c.(1483-1485)ACC>ACT	p.T495T	ZNF283_uc002oxp.3_Silent_p.T356T	NM_181845	NP_862828	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	495	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				GCGGAAAGACCTTTTGTAGTG	0.413													8	174	---	---	---	---	PASS
KIR3DL1	3811	broad.mit.edu	37	19	55341753	55341753	+	3'UTR	SNP	A	G	G	rs12985492	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55341753A>G	uc002qhk.3	+	9					KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR3DL1_uc010yfn.1_3'UTR|KIR3DL1_uc010esf.2_3'UTR|KIR3DL1_uc010yfo.1_3'UTR|KIR3DL1_uc002qhl.3_Intron|KIR2DS4_uc010esg.1_5'Flank|KIR2DS4_uc002qhm.1_5'Flank	NM_013289	NP_037421	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three						immune response|regulation of immune response	integral to plasma membrane	HLA-B specific inhibitory MHC class I receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1)	5				GBM - Glioblastoma multiforme(193;0.0192)		GGCCTTGAGGACGTCTTCTAG	0.522													9	242	---	---	---	---	PASS
DEFB123	245936	broad.mit.edu	37	20	30028442	30028442	+	5'UTR	SNP	T	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30028442T>A	uc002wvy.2	+	1						NM_153324	NP_697019	Q8N688	DB123_HUMAN	defensin, beta 123 precursor						defense response to bacterium	extracellular region					0	Lung NSC(7;0.000139)|all_lung(7;0.000197)|all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GGCACTCTCCTTCTCCCATTA	0.567													15	251	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11014987	11014987	+	RNA	SNP	A	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11014987A>G	uc002yis.1	-	7		c.1459T>C						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTATAGTTTCAATAGCAGACT	0.388													5	59	---	---	---	---	PASS
FAM116B	414918	broad.mit.edu	37	22	50752245	50752245	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50752245T>G	uc011aru.1	-	15	1273	c.1201A>C	c.(1201-1203)AAG>CAG	p.K401Q	FAM116B_uc011arv.1_Missense_Mutation_p.K401Q	NM_001001794	NP_001001794	Q8NEG7	F116B_HUMAN	family with sequence similarity 116, member B	401											0		all_cancers(38;4.34e-09)|all_epithelial(38;3.03e-08)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCATATACCTTGAGCAGCCGT	0.677													5	12	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2700	2700	+	5'Flank	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2700G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		ccgtgaagaggcgggcatgac	0.109													3	2	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	10686	10686	+	RNA	SNP	G	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:10686G>A	uc004cov.3	+	1		c.109G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		GCGAAGCAGCGGTGGGCCTAG	0.468													3	1	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	12954	12954	+	RNA	SNP	T	C	C			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:12954T>C	uc004cox.3	+	1		c.618T>C			uc004coy.2_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CTTCTAAACGCTAATCCAAGC	0.512													2	11	---	---	---	---	PASS
WDR3	10885	broad.mit.edu	37	1	118491215	118491216	+	Intron	INS	-	T	T	rs67677152		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118491215_118491216insT	uc010oxe.1	+						WDR3_uc001ehi.2_Intron	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3							nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		AAAGCCTGAGGTTTTTTTTTTT	0.371													10	7	---	---	---	---	
TBX15	6913	broad.mit.edu	37	1	119436109	119436112	+	Intron	DEL	GAAA	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119436109_119436112delGAAA	uc001ehl.1	-						TBX15_uc009whj.1_Intron	NM_152380	NP_689593	Q96SF7	TBX15_HUMAN	T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		aggaaggaaggaaagaaagaaaga	0.000													4	3	---	---	---	---	
FAM5B	57795	broad.mit.edu	37	1	177250855	177250856	+	3'UTR	INS	-	AC	AC	rs144473187	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177250855_177250856insAC	uc001glf.2	+	8					FAM5B_uc001glg.2_3'UTR	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B							extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						CGCGcacgcatacacacacaca	0.441													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199878832	199878832	+	IGR	DEL	A	-	-	rs34433898		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199878832delA								None (None upstream) : NR5A2 (117938 downstream)																							GCTTGTTTTTAAAAAAAAAAA	0.318													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	234919752	234919753	+	IGR	INS	-	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234919752_234919753insA								IRF2BP2 (174481 upstream) : TOMM20 (352907 downstream)																							aaaactccatcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236732199	236732200	+	Intron	INS	-	C	C	rs76883267		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236732199_236732200insC	uc001hyd.1	-						HEATR1_uc009xgh.1_Intron	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			aaaaaaaaacaaaaaaaaaaaa	0.262													5	3	---	---	---	---	
SFRS7	6432	broad.mit.edu	37	2	38973132	38973132	+	Intron	DEL	A	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38973132delA	uc002rqz.2	-						SFRS7_uc002rra.2_Intron|SFRS7_uc010ynp.1_Intron	NM_001031684	NP_001026854	Q16629	SRSF7_HUMAN	splicing factor, arginine/serine-rich 7						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)				TTACTGAATCAAAAAAAAAAA	0.303													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57947592	57947593	+	IGR	INS	-	G	G			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57947592_57947593insG								None (None upstream) : VRK2 (187193 downstream)																							gaaggaaggaagaaggaaggaa	0.084													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96593321	96593321	+	Intron	DEL	T	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96593321delT	uc002sva.1	-						uc010yug.1_Intron|uc002svc.1_5'Flank					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		AGAAATACACTGAAAAAAAAG	0.338													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129393430	129393437	+	IGR	DEL	CCTTCCTT	-	-	rs72091728		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129393430_129393437delCCTTCCTT								HS6ST1 (317259 upstream) : None (None downstream)																							tccctccctcccttccttccttccttcc	0.192													6	5	---	---	---	---	
NUP35	129401	broad.mit.edu	37	2	183993328	183993329	+	Intron	DEL	AA	-	-	rs71407008		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183993328_183993329delAA	uc002upf.2	+						NUP35_uc010zfs.1_Intron|NUP35_uc010zft.1_Intron|NUP35_uc002upg.2_Intron	NM_138285	NP_612142	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	intermediate filament cytoskeleton|nuclear membrane|nuclear pore|plasma membrane					0						ctgatgagctaaaaaaaaaaaa	0.000													7	4	---	---	---	---	
STK17B	9262	broad.mit.edu	37	2	197008112	197008113	+	Intron	INS	-	CAATA	CAATA	rs142415504	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197008112_197008113insCAATA	uc002utk.2	-						STK17B_uc010fsh.2_Intron	NM_004226	NP_004217	O94768	ST17B_HUMAN	serine/threonine kinase 17B						apoptosis|induction of apoptosis|intracellular protein kinase cascade	nucleus	ATP binding|protein serine/threonine kinase activity			lung(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.141)			ATACTTTTATTCATTTCATTTA	0.282													2	5	---	---	---	---	
ALS2CR11	151254	broad.mit.edu	37	2	202439758	202439758	+	Intron	DEL	A	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202439758delA	uc002uye.2	-						ALS2CR11_uc002uyf.2_Intron|ALS2CR11_uc010fti.2_Intron	NM_152525	NP_689738	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3						ACCATTTAGCAaaaaaaaaaa	0.254													4	2	---	---	---	---	
PECR	55825	broad.mit.edu	37	2	216916025	216916027	+	Intron	DEL	AAG	-	-	rs148608726		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216916025_216916027delAAG	uc002vft.2	-						PECR_uc010zjq.1_Intron|PECR_uc002vfr.2_Intron|PECR_uc002vfs.2_Intron	NM_018441	NP_060911	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase						fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	aaaaaaaaaaaagaaaaTTAGGC	0.138													5	4	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10183714	10183720	+	Frame_Shift_Del	DEL	CGTGCTG	-	-	rs5030651		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183714_10183720delCGTGCTG	uc003bvc.2	+	1	396_402	c.183_189delCGTGCTG	c.(181-189)CCCGTGCTGfs	p.P61fs	VHL_uc003bvd.2_Frame_Shift_Del_p.P61fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	61_63			L -> P (in pheochromocytoma).		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.V62fs*5(7)|p.P61P(4)|p.?(2)|p.V62fs*68(2)|p.L63fs*4(2)|p.P59_P61del(1)|p.E52_S65del(1)|p.P61fs(1)|p.R60fs*35(1)|p.R64fs*63(1)|p.P61fs*70(1)|p.P61fs*61(1)|p.R60fs*70(1)|p.V62fs*3(1)|p.V62fs*1(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)		GGCCGCGGCCCGTGCTGCGCTCGGTGA	0.729		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				8	4	---	---	---	---	
ANKRD28	23243	broad.mit.edu	37	3	15720643	15720643	+	Intron	DEL	T	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15720643delT	uc003caj.1	-						ANKRD28_uc003cai.1_Intron|ANKRD28_uc011avz.1_Intron|ANKRD28_uc003cak.1_Intron|ANKRD28_uc011awa.1_Intron|ANKRD28_uc011avy.1_5'Flank	NM_015199	NP_056014	O15084	ANR28_HUMAN	ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1						catcatgcacttttttttttt	0.000													12	6	---	---	---	---	
CACNA1D	776	broad.mit.edu	37	3	53760700	53760701	+	Intron	INS	-	T	T	rs149095851	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53760700_53760701insT	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Intron	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	TAATAAGGTTATTTTTTTTCAC	0.178													1	5	---	---	---	---	
FLNB	2317	broad.mit.edu	37	3	58092739	58092742	+	Intron	DEL	TTTG	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58092739_58092742delTTTG	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CAGGCCTGCAtttgtttgtttgtt	0.255													4	2	---	---	---	---	
DCBLD2	131566	broad.mit.edu	37	3	98519697	98519698	+	Intron	INS	-	T	T	rs148543159		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98519697_98519698insT	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron	NM_080927	NP_563615	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3						TATAATCCAACTTTTTTTTTTT	0.327													10	6	---	---	---	---	
DIRC2	84925	broad.mit.edu	37	3	122525555	122525556	+	Intron	INS	-	T	T	rs35035359		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122525555_122525556insT	uc003efw.3	+						DIRC2_uc010hrl.2_Intron|DIRC2_uc010hrm.2_Intron	NM_032839	NP_116228	Q96SL1	DIRC2_HUMAN	disrupted in renal carcinoma 2						transport	integral to membrane					0				GBM - Glioblastoma multiforme(114;0.0614)		AGGGTTCGTTGTTTTTTTTTTT	0.163													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186204359	186204360	+	Intron	INS	-	G	G	rs111354223		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186204359_186204360insG	uc003fqd.1	-											Homo sapiens cDNA FLJ32735 fis, clone TESTI2001229.																		gaaggaaggaaggacagactac	0.000													5	3	---	---	---	---	
LIMCH1	22998	broad.mit.edu	37	4	41699388	41699388	+	3'UTR	DEL	T	-	-	rs113753743		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41699388delT	uc003gvu.3	+	27					LIMCH1_uc003gvv.3_3'UTR|LIMCH1_uc003gvw.3_3'UTR|LIMCH1_uc003gvx.3_3'UTR|LIMCH1_uc003gwe.3_3'UTR|LIMCH1_uc003gvy.3_3'UTR|LIMCH1_uc003gwa.3_3'UTR|LIMCH1_uc003gvz.3_3'UTR|LIMCH1_uc011byu.1_3'UTR|LIMCH1_uc003gwc.3_3'UTR|LIMCH1_uc003gwd.3_3'UTR|LIMCH1_uc011byv.1_3'UTR|LIMCH1_uc011byw.1_3'UTR|LIMCH1_uc010ifv.2_RNA	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						attgttttggttttttttttt	0.294													3	3	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47427395	47427396	+	Intron	DEL	CA	-	-	rs143317856		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47427395_47427396delCA	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	GAAGAAATACcacacacacaca	0.213													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	77840873	77840876	+	IGR	DEL	TTCC	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77840873_77840876delTTCC								ANKRD56 (21871 upstream) : SEPT11 (30019 downstream)																							gcctgcttctttccttccttcctt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3276430	3276430	+	IGR	DEL	G	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3276430delG								C5orf38 (520918 upstream) : IRX1 (319738 downstream)																							ggatgaaggagggaggggagg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30591165	30591170	+	IGR	DEL	ACACAC	-	-	rs36206495		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30591165_30591170delACACAC								None (None upstream) : CDH6 (602626 downstream)																							ctacacacagacacacacacacacac	0.180													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	61129109	61129110	+	IGR	INS	-	GAAG	GAAG	rs7707571	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61129109_61129110insGAAG								FLJ37543 (126747 upstream) : KIF2A (472879 downstream)																							aatgaatgaatgaaggaaggaa	0.149													7	5	---	---	---	---	
PPWD1	23398	broad.mit.edu	37	5	64880705	64880706	+	Intron	INS	-	AA	AA	rs10682457		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64880705_64880706insAA	uc003jtv.3	+						PPWD1_uc011cqv.1_Intron|PPWD1_uc011cqw.1_Intron	NM_015342	NP_056157	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TAGAGATTATGAAAAAAAAAAA	0.332													7	6	---	---	---	---	
SYCP2L	221711	broad.mit.edu	37	6	10964195	10964195	+	Intron	DEL	T	-	-	rs149829365		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10964195delT	uc003mzo.2	+						SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			AACTTCTCCAttttttttttt	0.224													5	3	---	---	---	---	
PPT2	9374	broad.mit.edu	37	6	32123887	32123888	+	Intron	INS	-	TT	TT			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32123887_32123888insTT	uc003nzx.2	+						uc003nzv.3_5'Flank|PPT2_uc003nzw.2_Intron|PPT2_uc011dpi.1_Intron|PPT2_uc003nzy.1_Intron|PPT2_uc003nzz.2_Intron|PPT2_uc003oaa.2_Intron|PPT2_uc010jtu.1_Intron	NM_005155	NP_005146	Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2 isoform a						protein modification process	lysosome	palmitoyl-(protein) hydrolase activity				0						TCTGTTCAGAAttttttttttt	0.193													4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32557612	32557612	+	5'Flank	DEL	G	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32557612delG	uc003obk.3	-						HLA-DRB1_uc003obp.3_5'Flank	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CCAAGTTATAGGGAGGAAGTT	0.507													15	7	---	---	---	---	
FKBP5	2289	broad.mit.edu	37	6	35582932	35582933	+	Intron	INS	-	AC	AC	rs148530740	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35582932_35582933insAC	uc011dte.1	-						FKBP5_uc003okx.2_Intron|FKBP5_uc011dtf.1_Intron|FKBP5_uc003oky.2_Intron|FKBP5_uc003okz.2_Intron	NM_001145776	NP_001139248	Q13451	FKBP5_HUMAN	FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1						caacaacaactacacacacaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112286286	112286288	+	IGR	DEL	GGA	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112286286_112286288delGGA								FYN (91659 upstream) : WISP3 (88990 downstream)																							GTCaggaggcggaggaggaggag	0.113													4	2	---	---	---	---	
ENPP3	5169	broad.mit.edu	37	6	132014471	132014471	+	Intron	DEL	G	-	-	rs3841511		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132014471delG	uc003qcu.3	+						ENPP3_uc010kfq.2_Intron|ENPP3_uc003qcv.2_Intron	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		CTAATAACTAGGGGGATCTGA	0.239													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160319646	160319648	+	IGR	DEL	CTT	-	-	rs403644	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160319646_160319648delCTT								PNLDC1 (77911 upstream) : MAS1 (8326 downstream)																							cttcctcctccttcctcctcctc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17125263	17125263	+	IGR	DEL	T	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17125263delT								AGR3 (203650 upstream) : AHR (213013 downstream)																							TCCTTCCttcttttttttttt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24497556	24497559	+	IGR	DEL	AGGA	-	-	rs148435103		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24497556_24497559delAGGA								NPY (166079 upstream) : MPP6 (115526 downstream)																							Taagggaaggaggaaggaaggaag	0.191													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	31404676	31404676	+	IGR	DEL	A	-	-	rs35317967		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31404676delA								NEUROD6 (24138 upstream) : CCDC129 (149009 downstream)																							actctgtctcaaaaaaaaaaa	0.000													5	4	---	---	---	---	
GTF2IRD2	84163	broad.mit.edu	37	7	74239418	74239418	+	Intron	DEL	A	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74239418delA	uc003ubd.1	-						GTF2IRD2_uc011kfi.1_Intron|GTF2IRD2_uc003ubf.1_Intron|GTF2IRD2_uc003ubg.1_Intron	NM_173537	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						actccatctcaaaaaaaaaaa	0.174													3	3	---	---	---	---	
PXDNL	137902	broad.mit.edu	37	8	52656468	52656469	+	Intron	INS	-	AAGG	AAGG	rs67558657		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52656468_52656469insAAGG	uc003xqu.3	-							NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCTGAGAGagaaaggaaggaag	0.178													2	5	---	---	---	---	
C9orf114	51490	broad.mit.edu	37	9	131586559	131586560	+	Intron	DEL	GT	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131586559_131586560delGT	uc004bwd.2	-						C9orf114_uc004bwe.2_Intron|C9orf114_uc010mym.2_Intron	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490												0						GAGCtgtgtggtgtgtgtgtgt	0.500													4	2	---	---	---	---	
DHTKD1	55526	broad.mit.edu	37	10	12132423	12132423	+	Intron	DEL	C	-	-	rs57211373		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12132423delC	uc001ild.3	+							NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			ttccttccttcctttttcctt	0.095													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	96769295	96769296	+	IGR	INS	-	T	T			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96769295_96769296insT								CYP2C9 (20148 upstream) : CYP2C8 (27234 downstream)																							TCGTACAGTTGTTTTTTTTTTC	0.297													4	2	---	---	---	---	
SFXN4	119559	broad.mit.edu	37	10	120914415	120914415	+	Intron	DEL	T	-	-	rs34654417		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120914415delT	uc001leb.2	-						SFXN4_uc001ldy.2_Intron|SFXN4_uc001ldz.2_Intron|SFXN4_uc001lea.2_Intron	NM_213649	NP_998814	Q6P4A7	SFXN4_HUMAN	sideroflexin 4						iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		atgcCCCATCTTATCAGGGGG	0.239													2	4	---	---	---	---	
HRAS	3265	broad.mit.edu	37	11	534404	534415	+	Intron	DEL	CCCAGGCCCAGC	-	-	rs45443193		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:534404_534415delCCCAGGCCCAGC	uc001lpv.2	-						HRAS_uc010qvw.1_Intron|HRAS_uc010qvx.1_Intron|HRAS_uc010qvy.1_Intron	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene						activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding			urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	CTCAGCCAGGCCCAGGCCCAGCCCCAGGCCCC	0.698		6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			6	3	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11470179	11470183	+	Intron	DEL	AGGAA	-	-	rs72161646		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11470179_11470183delAGGAA	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		tggctgaagcaggaaagggacccaa	0.156													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	41592764	41592765	+	IGR	DEL	AC	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41592764_41592765delAC								LRRC4C (111441 upstream) : None (None downstream)																							gtgtgtgtgtacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	104315825	104315826	+	IGR	INS	-	TTCA	TTCA			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104315825_104315826insTTCA								PDGFD (280798 upstream) : CASP12 (440616 downstream)																							tccttccttccttgcttgtttc	0.104													4	2	---	---	---	---	
DHX37	57647	broad.mit.edu	37	12	125465270	125465272	+	In_Frame_Del	DEL	CTC	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125465270_125465272delCTC	uc001ugy.2	-	4	601_603	c.502_504delGAG	c.(502-504)GAGdel	p.E168del		NM_032656	NP_116045	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	168							ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CCGATTCCGActcctcctcctcc	0.601													4	2	---	---	---	---	
DCLK1	9201	broad.mit.edu	37	13	36532204	36532206	+	Intron	DEL	CAC	-	-	rs138785659		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36532204_36532206delCAC	uc001uvf.2	-							NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		taaccactagcaccaccaccact	0.000													4	2	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95657758	95657759	+	3'UTR	INS	-	C	C	rs60112171		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95657758_95657759insC	uc001yef.2	-	13						NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		AAAAAAAAAAACCACAATAGCG	0.446													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98480465	98480470	+	IGR	DEL	TCTTTC	-	-	rs72290183		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98480465_98480470delTCTTTC								C14orf64 (36004 upstream) : C14orf177 (697480 downstream)																							ttccttcctttctttctctttctttc	0.000													3	3	---	---	---	---	
KIAA0125	9834	broad.mit.edu	37	14	106385208	106385217	+	Intron	DEL	TTCAGTGGGG	-	-	rs71406526		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106385208_106385217delTTCAGTGGGG	uc001ysq.2	+						ADAM6_uc010tyt.1_Intron|KIAA0125_uc001ysr.2_Intron|KIAA0125_uc001yss.2_Intron|KIAA0125_uc001yst.2_Intron					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0						GTCCTCACCATTCAGTGGGGTTCAGTGGGG	0.657													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22566684	22566684	+	IGR	DEL	A	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22566684delA								MIR1268 (53404 upstream) : GOLGA8DP (135601 downstream)																							GTAAAGCGTGAACAAGTAAGA	0.299													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23098652	23098655	+	Intron	DEL	TTCT	-	-	rs3057778		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23098652_23098655delTTCT	uc001yvf.2	-											Homo sapiens cDNA clone IMAGE:5275816.																		tgagtcctacttctctctccatct	0.211													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48198789	48198790	+	IGR	DEL	AC	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48198789_48198790delAC								SEMA6D (132370 upstream) : SLC24A5 (214379 downstream)																							tttcttgcttacacacacacac	0.010													4	2	---	---	---	---	
SIN3A	25942	broad.mit.edu	37	15	75708196	75708197	+	Intron	DEL	AA	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75708196_75708197delAA	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5						cggtctcaggaaaaaaaaaaaa	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90701000	90701001	+	IGR	INS	-	A	A			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90701000_90701001insA								IDH2 (55292 upstream) : SEMA4B (27151 downstream)																							aggaaggaaggagaaagaaaga	0.089													4	2	---	---	---	---	
GDE1	51573	broad.mit.edu	37	16	19522426	19522427	+	Intron	DEL	TT	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19522426_19522427delTT	uc002dgh.2	-						GDE1_uc002dgi.2_Intron	NM_016641	NP_057725	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1						glycerol metabolic process|lipid metabolic process	cytoplasm|integral to membrane	glycerophosphodiester phosphodiesterase activity|glycerophosphoinositol glycerophosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3						TACTTTAAGAtttttttttttt	0.163													3	3	---	---	---	---	
CIAPIN1	57019	broad.mit.edu	37	16	57464912	57464912	+	Intron	DEL	T	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57464912delT	uc002ell.1	-						CIAPIN1_uc002elk.1_Intron|CIAPIN1_uc002elm.1_Intron|CIAPIN1_uc002eln.1_Intron|CIAPIN1_uc010cda.1_Intron|CIAPIN1_uc002elo.1_Intron	NM_020313	NP_064709	Q6FI81	CPIN1_HUMAN	cytokine induced apoptosis inhibitor 1						anti-apoptosis|apoptosis	cytoplasm|nucleolus					0						gcctggctaattttttttttt	0.085													4	3	---	---	---	---	
ZFPM1	161882	broad.mit.edu	37	16	88593211	88593211	+	Intron	DEL	T	-	-	rs35678431		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88593211delT	uc002fkv.2	+							NM_153813	NP_722520	Q8IX07	FOG1_HUMAN	zinc finger protein, multitype 1						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|transcription factor binding|zinc ion binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GTTCCTACCCTCCCCCCCCAG	0.687													3	3	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2703722	2703743	+	Intron	DEL	GGCTGTCCCGGGGACTCCTCCA	-	-	rs72122107		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2703722_2703743delGGCTGTCCCGGGGACTCCTCCA	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						TGGTGGTTTGGGCTGTCCCGGGGACTCCTCCATACAGATGCT	0.595													4	4	---	---	---	---	
FLCN	201163	broad.mit.edu	37	17	17119744	17119744	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17119744delA	uc002gra.3	-	11	1754	c.1250delT	c.(1249-1251)TTCfs	p.F417fs	PLD6_uc010cpn.2_RNA	NM_144997	NP_659434	Q8NFG4	FLCN_HUMAN	folliculin isoform 1	417					regulation of protein phosphorylation	cytoplasm|nucleus|plasma membrane	protein binding			thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	3						GAGCCCCAGGAAGTTGCACCG	0.667									Birt-Hogg-Dub__syndrome|Familial_Non-VHL_Clear_Cell_Renal_Cancer				23	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75068178	75068181	+	IGR	DEL	TTCC	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75068178_75068181delTTCC								MGAT5B (121708 upstream) : C17orf86 (16544 downstream)																							tccttcttctttccttccttcctt	0.029													4	2	---	---	---	---	
CYB5A	1528	broad.mit.edu	37	18	71930382	71930382	+	Intron	DEL	A	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71930382delA	uc002lli.2	-						CYB5A_uc002llh.2_Intron	NM_148923	NP_683725	P00167	CYB5_HUMAN	cytochrome b-5 isoform 1						electron transport chain|water-soluble vitamin metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane	aldo-keto reductase (NADP) activity|cytochrome-c oxidase activity|enzyme binding|heme binding				0		Esophageal squamous(42;0.0749)|Prostate(75;0.157)|Melanoma(33;0.211)			Methoxyflurane(DB01028)	gacctgtctcaaaaaaaaaaa	0.124													6	4	---	---	---	---	
SPPL2B	56928	broad.mit.edu	37	19	2324113	2324114	+	Intron	INS	-	C	C	rs140121434	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2324113_2324114insC	uc010dsw.1	+						LSM7_uc002lvp.3_Intron			Q8TCT7	PSL1_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000371624;							Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCGGCCGCCACCCCACTCACC	0.678													4	2	---	---	---	---	
MYO9B	4650	broad.mit.edu	37	19	17302113	17302114	+	Intron	DEL	CT	-	-	rs138603930		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17302113_17302114delCT	uc010eak.2	+						MYO9B_uc002nfi.2_Intron|MYO9B_uc002nfj.1_Intron	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1						actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1						CCCAGGGCCACTCTCTGAAACA	0.634													3	3	---	---	---	---	
HAPLN4	404037	broad.mit.edu	37	19	19379018	19379018	+	Intron	DEL	T	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19379018delT	uc002nmc.2	-						TM6SF2_uc002nmd.1_Intron	NM_023002	NP_075378	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4						cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			pancreas(1)	1			Epithelial(12;0.00575)			ttcttttttcttttttttttt	0.159													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29283474	29283476	+	IGR	DEL	TTC	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29283474_29283476delTTC								LOC148189 (998626 upstream) : LOC148145 (172564 downstream)																							TTCTCAGAGGTTCTTCTTCTTCT	0.360													4	2	---	---	---	---	
FCGBP	8857	broad.mit.edu	37	19	40384321	40384324	+	Intron	DEL	AGAA	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40384321_40384324delAGAA	uc002omp.3	-							NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor							extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			gaggacacagagaaagaaatggga	0.088													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46846767	46846769	+	IGR	DEL	TCC	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46846767_46846769delTCC								HIF3A (78 upstream) : PPP5C (3525 downstream)																							TTTTTTTTTttccttccttcctt	0.271													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55080103	55080108	+	IGR	DEL	GAAAGG	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55080103_55080108delGAAAGG								KIR3DX1 (24908 upstream) : LILRA2 (4374 downstream)																							gaaagaaagagaaaggaagaaaggaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57577481	57577481	+	IGR	DEL	A	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57577481delA								MIMT1 (217559 upstream) : USP29 (54028 downstream)																							GGCAAAGACTAAAGAACTTGC	0.378													4	2	---	---	---	---	
DLGAP4	22839	broad.mit.edu	37	20	35055905	35055908	+	Intron	DEL	GGAA	-	-			TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35055905_35055908delGGAA	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				agggagggagggaaggaaggaagg	0.000													4	2	---	---	---	---	
STX16	8675	broad.mit.edu	37	20	57246492	57246493	+	Intron	DEL	GG	-	-	rs35720492		TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57246492_57246493delGG	uc002xzi.2	+						STX16_uc010zzq.1_Intron|STX16_uc002xzk.2_Intron|STX16_uc002xzm.2_Intron|STX16_uc002xzj.2_Intron|STX16_uc002xzl.2_Intron	NM_001001433	NP_001001433	O14662	STX16_HUMAN	syntaxin 16 isoform a						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|microsome|SNARE complex	SNAP receptor activity			ovary(1)	1	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			Atgtgtgtgtgggtgtgtgtgt	0.223													16	7	---	---	---	---	
SEC14L3	266629	broad.mit.edu	37	22	30863234	30863235	+	Intron	INS	-	CATCCATC	CATCCATC	rs151165173	by1000genomes	TCGA-BP-4961-01A-01D-1462-08	TCGA-BP-4961-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30863234_30863235insCATCCATC	uc003ahy.2	-						SEC14L3_uc003ahz.2_Intron|SEC14L3_uc003aia.2_Intron|SEC14L3_uc003aib.2_Intron	NM_174975	NP_777635	Q9UDX4	S14L3_HUMAN	SEC14-like 3							integral to membrane|intracellular	lipid binding|transporter activity			ovary(3)|pancreas(1)|skin(1)	5					Vitamin E(DB00163)	ccatccatccacatccatccat	0.218													3	3	---	---	---	---	
