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	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	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
SLC35E2B	728661	broad.mit.edu	37	1	1668255	1668256	+	Intron	INS	-	AG	AG	rs113531126		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1668255_1668256insAG	uc001ahh.3	-						SLC35E2_uc009vkm.1_Intron|SLC35E2_uc001ahy.2_Intron|SLC35E2_uc001ahz.2_Intron|SLC35E2_uc001aib.1_Intron	NM_001110781	NP_001104251			similar to solute carrier family 35, member E2							integral to membrane					0																		---	---	---	---
DARS2	55157	broad.mit.edu	37	1	173819744	173819744	+	Intron	DEL	T	-	-	rs66665709		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173819744delT	uc001gjh.1	+							NM_018122	NP_060592			aspartyl-tRNA synthetase 2, mitochondrial						tRNA aminoacylation for protein translation	mitochondrial matrix|nucleus	aspartate-tRNA ligase activity|ATP binding|nucleic acid binding			central_nervous_system(2)	2					L-Aspartic Acid(DB00128)													---	---	---	---
ATP2C1	27032	broad.mit.edu	37	3	130637835	130637836	+	Intron	INS	-	AAAC	AAAC			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130637835_130637836insAAAC	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron	NM_014382	NP_055197			calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)									Hailey-Hailey_disease				---	---	---	---
CRIPAK	285464	broad.mit.edu	37	4	1388946	1388976	+	Frame_Shift_Del	DEL	GGAGTGTTCGCCTGCTCACACGTGCCGATGC	-	-	rs140577610	byFrequency;by1000genomes;byFrequency;byFrequency;byFrequency;byFrequency	TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1388946_1388976delGGAGTGTTCGCCTGCTCACACGTGCCGATGC	uc003gdf.2	+	1	3607_3637	c.647_677delGGAGTGTTCGCCTGCTCACACGTGCCGATGC	c.(646-678)TGGAGTGTTCGCCTGCTCACACGTGCCGATGCGfs	p.W216fs		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	216_226					ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)															---	---	---	---
LETM1	3954	broad.mit.edu	37	4	1837947	1837950	+	Intron	DEL	AAAT	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1837947_1837950delAAAT	uc003gdv.2	-						LETM1_uc010icc.2_Intron|LETM1_uc011bvg.1_Intron	NM_012318	NP_036450			leucine zipper-EF-hand containing transmembrane						cristae formation	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			central_nervous_system(1)	1			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)															---	---	---	---
ELF2	1998	broad.mit.edu	37	4	139983328	139983329	+	Intron	INS	-	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139983328_139983329insT	uc003ihp.1	-						ELF2_uc003ihm.1_Intron|ELF2_uc003ihn.1_Intron|ELF2_uc003iho.1_Intron|ELF2_uc011chc.1_5'UTR	NM_201999	NP_973728			E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
GALNT7	51809	broad.mit.edu	37	4	174235080	174235081	+	Intron	DEL	AT	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174235080_174235081delAT	uc003isz.3	+						GALNT7_uc011ckb.1_Intron	NM_017423	NP_059119			polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183673226	183673227	+	Intron	INS	-	A	A	rs5864797		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183673226_183673227insA	uc003ivd.1	+						ODZ3_uc003ive.1_Intron	NM_001080477	NP_001073946			odz, odd Oz/ten-m homolog 3						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)														---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14481080	14481080	+	Intron	DEL	A	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14481080delA	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
C5orf34	375444	broad.mit.edu	37	5	43496685	43496693	+	Intron	DEL	TTTTTTTTT	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43496685_43496693delTTTTTTTTT	uc003jnz.1	-							NM_198566	NP_940968			hypothetical protein LOC375444											breast(1)	1	Lung NSC(6;2.07e-05)																	---	---	---	---
CCDC125	202243	broad.mit.edu	37	5	68599933	68599933	+	Intron	DEL	T	-	-	rs35098133		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68599933delT	uc003jvv.1	-						CCDC125_uc003jvx.1_Intron|CCDC125_uc003jvy.1_Intron|CCDC125_uc003jvw.2_Intron	NM_176816	NP_789786			coiled-coil domain containing 125							cytoplasm					0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	128901170	128901171	+	IGR	DEL	TG	-	-	rs113280241		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128901170_128901171delTG								PTPRK (59300 upstream) : LAMA2 (303115 downstream)																																			---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5800900	5800901	+	Intron	INS	-	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5800900_5800901insA	uc003soy.1	-						RNF216_uc010ksz.1_5'Flank|RNF216_uc010kta.1_5'Flank|RNF216_uc011jwj.1_5'Flank|RNF216_uc003sox.1_Intron	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	22813177	22813178	+	IGR	INS	-	C	C	rs145036723	by1000genomes	TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22813177_22813178insC								IL6 (41558 upstream) : TOMM7 (39076 downstream)																																			---	---	---	---
HOXA5	3202	broad.mit.edu	37	7	27185066	27185075	+	5'Flank	DEL	GTTTTGTTTT	-	-	rs70994631		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27185066_27185075delGTTTTGTTTT	uc003syn.1	-						uc003syp.1_5'Flank	NM_019102	NP_061975			homeobox A5						negative regulation of angiogenesis|negative regulation of erythrocyte differentiation|positive regulation of apoptosis|positive regulation of myeloid cell differentiation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123924715	123924715	+	Intron	DEL	T	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123924715delT	uc004bkx.1	+						CEP110_uc004blb.1_Intron|CEP110_uc010mvp.1_Intron	NM_007018	NP_008949			centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	127956856	127956856	+	IGR	DEL	G	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127956856delG								PPP6C (4638 upstream) : RABEPK (5961 downstream)																																			---	---	---	---
HYOU1	10525	broad.mit.edu	37	11	118916978	118916979	+	Intron	DEL	TT	-	-	rs144229837		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118916978_118916979delTT	uc001puu.2	-						HYOU1_uc001put.2_Intron|HYOU1_uc010ryu.1_Intron|HYOU1_uc010ryv.1_Intron|HYOU1_uc001pux.3_Intron	NM_006389	NP_006380			hypoxia up-regulated 1 precursor							endoplasmic reticulum lumen	ATP binding|protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)														---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	492920	492921	+	Intron	INS	-	T	T	rs71839973		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:492920_492921insT	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	12	53280185	53280186	+	IGR	INS	-	T	T	rs34054821		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53280185_53280186insT								KRT78 (37407 upstream) : KRT8 (10785 downstream)																																			---	---	---	---
USP44	84101	broad.mit.edu	37	12	95911790	95911790	+	3'UTR	DEL	A	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95911790delA	uc001teg.2	-	6					USP44_uc001teh.2_3'UTR|USP44_uc009zte.2_3'UTR	NM_001042403	NP_001035862			ubiquitin thiolesterase 44						anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
HMGB1	3146	broad.mit.edu	37	13	31037926	31037929	+	Intron	DEL	TTAT	-	-	rs35116094		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31037926_31037929delTTAT	uc001usw.2	-						HMGB1_uc001usz.2_Intron|HMGB1_uc001usv.2_5'UTR|HMGB1_uc001usx.2_Intron|HMGB1_uc001usy.2_Intron|HMGB1_uc001uta.1_Intron	NM_002128	NP_002119			high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
C13orf37	440145	broad.mit.edu	37	13	73301718	73301728	+	Frame_Shift_Del	DEL	CCAGCACCGCT	-	-	rs142438556	by1000genomes;by1000genomes	TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73301718_73301728delCCAGCACCGCT	uc001viu.2	-	1	211_221	c.13_23delAGCGGTGCTGG	c.(13-24)AGCGGTGCTGGGfs	p.S5fs	C13orf34_uc010thq.1_5'Flank|C13orf34_uc001viv.1_5'Flank|C13orf34_uc010aen.1_5'Flank|C13orf34_uc010thr.1_5'Flank|C13orf34_uc001viw.1_5'Flank	NM_001071775	NP_001065243	Q08AG7	MZT1_HUMAN	hypothetical protein LOC440145	5_8	Poly-Ala.				gamma-tubulin complex localization	centrosome|gamma-tubulin ring complex|spindle	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	20081407	20081408	+	IGR	DEL	AC	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20081407_20081408delAC								P704P (61135 upstream) : OR4Q3 (134179 downstream)																																			---	---	---	---
AP4E1	23431	broad.mit.edu	37	15	51221549	51221550	+	Intron	INS	-	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51221549_51221550insT	uc001zyx.1	+						AP4E1_uc010ufi.1_Intron|AP4E1_uc010ufj.1_Intron|AP4E1_uc010ufk.1_Intron	NM_007347	NP_031373			adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)														---	---	---	---
ARID3B	10620	broad.mit.edu	37	15	74865018	74865018	+	Intron	DEL	A	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74865018delA	uc002aye.2	+						ARID3B_uc002ayc.2_Intron|ARID3B_uc002ayd.2_Intron	NM_006465	NP_006456			AT rich interactive domain 3B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
C16orf70	80262	broad.mit.edu	37	16	67165083	67165084	+	Intron	INS	-	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67165083_67165084insT	uc002erc.2	+						C16orf70_uc002erd.2_Intron|C16orf70_uc002ere.1_Intron	NM_025187	NP_079463			lin-10											ovary(2)	2		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)														---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70351677	70351678	+	Intron	INS	-	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70351677_70351678insA	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron|uc002eyt.2_Intron	NM_007242	NP_009173			DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2888572	2888573	+	Intron	DEL	TG	-	-	rs146159488		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2888572_2888573delTG	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			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																		---	---	---	---
TP53	7157	broad.mit.edu	37	17	7577594	7577595	+	Frame_Shift_Del	DEL	AC	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577594_7577595delAC	uc002gim.2	-	7	880_881	c.686_687delGT	c.(685-687)TGTfs	p.C229fs	TP53_uc002gig.1_Frame_Shift_Del_p.C229fs|TP53_uc002gih.2_Frame_Shift_Del_p.C229fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.C97fs|TP53_uc010cng.1_Frame_Shift_Del_p.C97fs|TP53_uc002gii.1_Frame_Shift_Del_p.C97fs|TP53_uc010cnh.1_Frame_Shift_Del_p.C229fs|TP53_uc010cni.1_Frame_Shift_Del_p.C229fs|TP53_uc002gij.2_Frame_Shift_Del_p.C229fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.C136fs|TP53_uc002gio.2_Frame_Shift_Del_p.C97fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	229	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		C -> Y (in sporadic cancers; somatic mutation).|C -> G (in a sporadic cancer; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> S (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.C229fs*10(10)|p.0?(7)|p.C229*(3)|p.C229S(2)|p.C229R(2)|p.C229Y(2)|p.C229_H233delCTTIH(2)|p.T230fs*9(1)|p.C229fs*1(1)|p.C229fs*18(1)|p.C229_T230insX(1)|p.C229C(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.C229G(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)			111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	7858584	7858584	+	IGR	DEL	A	-	-	rs78611358		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7858584delA								CNTROB (5689 upstream) : GUCY2D (47404 downstream)																																			---	---	---	---
C17orf53	78995	broad.mit.edu	37	17	42229795	42229796	+	Intron	INS	-	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42229795_42229796insA	uc002ifi.1	+						C17orf53_uc010czq.1_Intron|C17orf53_uc002ifj.1_Intron|C17orf53_uc002ifk.1_Intron	NM_024032	NP_076937			hypothetical protein LOC78995												0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)														---	---	---	---
ZNF555	148254	broad.mit.edu	37	19	2851297	2851297	+	Intron	DEL	A	-	-	rs10713166		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2851297delA	uc002lwo.2	+						ZNF555_uc002lwn.3_Intron	NM_152791	NP_690004			zinc finger protein 555						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				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)														---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62074331	62074333	+	Intron	DEL	CAC	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074331_62074333delCAC	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105			potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)													---	---	---	---
ERG	2078	broad.mit.edu	37	21	39774634	39774634	+	Intron	DEL	C	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39774634delC	uc010gnw.2	-						ERG_uc002yxa.2_Intron|ERG_uc011aek.1_Intron|ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc011aem.1_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gny.1_Intron	NM_001136155	NP_001129627			ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)																---	---	---	---
DGCR5	26220	broad.mit.edu	37	22	18976301	18976324	+	Intron	DEL	TATTTATTTATTTATTTATTTATT	-	-	rs111433751		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18976301_18976324delTATTTATTTATTTATTTATTTATT	uc002zom.1	+						DGCR5_uc002zon.1_Intron	NR_002733				Homo sapiens mRNA for KIAA1647 protein, partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	40767693	40767693	+	IGR	DEL	A	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40767693delA								LOC100132831 (75244 upstream) : USP9X (177195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42384560	42384561	+	IGR	DEL	AA	-	-			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42384560_42384561delAA								CASK (602273 upstream) : PPP1R2P9 (252058 downstream)																																			---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117676484	117676485	+	Intron	DEL	TG	-	-	rs113602759		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117676484_117676485delTG	uc004eqp.2	+							NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
PRAMEF10	343071	broad.mit.edu	37	1	12954419	12954419	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12954419G>A	uc001auo.2	-	3	937	c.864C>T	c.(862-864)CTC>CTT	p.L288L		NM_001039361	NP_001034450	O60809	PRA10_HUMAN	PRAME family member 10	288											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
FLG	2312	broad.mit.edu	37	1	152280076	152280076	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152280076C>T	uc001ezu.1	-	3	7322	c.7286G>A	c.(7285-7287)GGA>GAA	p.G2429E		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2429	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
FLG	2312	broad.mit.edu	37	1	152281163	152281163	+	Missense_Mutation	SNP	G	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152281163G>T	uc001ezu.1	-	3	6235	c.6199C>A	c.(6199-6201)CCC>ACC	p.P2067T		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2067	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
DARC	2532	broad.mit.edu	37	1	159175316	159175316	+	Silent	SNP	C	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159175316C>A	uc001fto.2	+	2	327	c.87C>A	c.(85-87)TCC>TCA	p.S29S	DARC_uc001ftp.3_Silent_p.S31S	NM_002036	NP_002027	Q16570	DUFFY_HUMAN	Duffy blood group antigen isoform b	29	Extracellular (Potential).				defense response	integral to membrane|plasma membrane	C-C chemokine binding|chemokine receptor activity			ovary(1)|lung(1)	2	all_hematologic(112;0.0429)																	---	---	---	---
KIAA1614	57710	broad.mit.edu	37	1	180885845	180885845	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180885845G>A	uc001gok.2	+	2	673	c.606G>A	c.(604-606)CTG>CTA	p.L202L		NM_020950	NP_066001	Q5VZ46	K1614_HUMAN	hypothetical protein LOC57710	202										ovary(3)|skin(1)	4																		---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49295370	49295370	+	Missense_Mutation	SNP	T	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49295370T>C	uc002rww.2	-	2	286	c.212A>G	c.(211-213)GAC>GGC	p.D71G	FSHR_uc002rwx.2_Missense_Mutation_p.D71G|FSHR_uc010fbn.2_Missense_Mutation_p.D71G|FSHR_uc010fbo.1_RNA	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	71	Extracellular (Potential).|LRR 1.				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
CCDC85A	114800	broad.mit.edu	37	2	56420153	56420153	+	Missense_Mutation	SNP	C	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56420153C>G	uc002rzn.2	+	2	1320	c.818C>G	c.(817-819)GCA>GGA	p.A273G		NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	273	His-rich.									breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141283892	141283892	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141283892C>T	uc002tvj.1	-	48	8762	c.7790G>A	c.(7789-7791)CGC>CAC	p.R2597H		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2597	Extracellular (Potential).|LDL-receptor class A 13.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167055546	167055546	+	Missense_Mutation	SNP	A	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167055546A>C	uc010fpl.2	-	27	5911	c.5570T>G	c.(5569-5571)ATG>AGG	p.M1857R	uc002udp.2_Intron	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	1868						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170060760	170060760	+	Silent	SNP	A	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170060760A>C	uc002ues.2	-	42	7950	c.7737T>G	c.(7735-7737)ACT>ACG	p.T2579T		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	2579	LDL-receptor class B 28.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
TTN	7273	broad.mit.edu	37	2	179654210	179654210	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179654210G>A	uc010zfg.1	-	13	2177	c.1953C>T	c.(1951-1953)GCC>GCT	p.A651A	TTN_uc010zfh.1_Silent_p.A605A|TTN_uc010zfi.1_Silent_p.A605A|TTN_uc010zfj.1_Silent_p.A605A|TTN_uc002unb.2_Silent_p.A651A|TTN_uc010frg.1_Silent_p.A233A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	651							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)															---	---	---	---
SP110	3431	broad.mit.edu	37	2	231067427	231067427	+	Missense_Mutation	SNP	G	A	A	rs148304482		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231067427G>A	uc002vqh.3	-	9	1156	c.916C>T	c.(916-918)CAC>TAC	p.H306Y	SP110_uc002vqg.3_Missense_Mutation_p.H306Y|SP110_uc002vqi.3_Missense_Mutation_p.H306Y|SP110_uc010fxk.2_Missense_Mutation_p.H304Y|SP110_uc010fxj.2_Intron	NM_004509	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein isoform a	306					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)														---	---	---	---
PLXNB1	5364	broad.mit.edu	37	3	48448490	48448490	+	Silent	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48448490C>T	uc003csw.2	-	35	6366	c.6096G>A	c.(6094-6096)CCG>CCA	p.P2032P	PLXNB1_uc003cst.2_Silent_p.P482P|PLXNB1_uc003csu.2_Silent_p.P1849P|PLXNB1_uc003csx.2_Silent_p.P2032P	NM_002673	NP_002664	O43157	PLXB1_HUMAN	plexin B1 precursor	2032	Cytoplasmic (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)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	55107475	55107475	+	Silent	SNP	C	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55107475C>G	uc003dhf.2	+	36	3039	c.2991C>G	c.(2989-2991)TCC>TCG	p.S997S	CACNA2D3_uc003dhg.1_Silent_p.S903S|CACNA2D3_uc003dhh.1_RNA	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha	997	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120975996	120975996	+	Intron	SNP	G	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120975996G>C	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795			syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
SLC15A2	6565	broad.mit.edu	37	3	121648191	121648191	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121648191G>A	uc003eep.2	+	17	1702	c.1549G>A	c.(1549-1551)GTG>ATG	p.V517M	SLC15A2_uc011bjn.1_Missense_Mutation_p.V486M	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	517					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)													---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175473204	175473204	+	Silent	SNP	T	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175473204T>C	uc003fit.2	+	13	2274	c.2187T>C	c.(2185-2187)TAT>TAC	p.Y729Y		NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	729	Extracellular (Potential).				proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)														---	---	---	---
PDHA2	5161	broad.mit.edu	37	4	96761832	96761832	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96761832G>A	uc003htr.3	+	1	594	c.531G>A	c.(529-531)CTG>CTA	p.L177L		NM_005390	NP_005381	P29803	ODPAT_HUMAN	pyruvate dehydrogenase E1 alpha 2 precursor	177					glycolysis	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	NADH(DB00157)													---	---	---	---
TNPO1	3842	broad.mit.edu	37	5	72178338	72178338	+	Missense_Mutation	SNP	A	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72178338A>G	uc003kck.3	+	10	1112	c.965A>G	c.(964-966)GAT>GGT	p.D322G	TNPO1_uc011csi.1_RNA|TNPO1_uc011csj.1_Missense_Mutation_p.D272G|TNPO1_uc003kch.2_Missense_Mutation_p.D314G|TNPO1_uc003kci.3_Missense_Mutation_p.D314G|TNPO1_uc003kcg.3_Missense_Mutation_p.D314G	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1	322					interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111601943	111601943	+	Silent	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111601943C>T	uc003kpv.1	-	5	694	c.420G>A	c.(418-420)GCG>GCA	p.A140A	EPB41L4A_uc003kpw.1_Silent_p.A140A	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4	140	FERM.					cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132272875	132272875	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132272875G>A	uc003kyd.2	-	2	415	c.7C>T	c.(7-9)CGT>TGT	p.R3C	AFF4_uc011cxk.1_5'UTR|AFF4_uc003kye.1_Missense_Mutation_p.R3C|AFF4_uc003kyf.3_Missense_Mutation_p.R3C	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	3					transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
NR3C1	2908	broad.mit.edu	37	5	142689712	142689712	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142689712C>A	uc003lmz.2	-	4	1910	c.1418G>T	c.(1417-1419)TGC>TTC	p.C473F	NR3C1_uc003lmy.2_Missense_Mutation_p.C474F|NR3C1_uc003lna.2_Missense_Mutation_p.C473F|NR3C1_uc003lnb.2_Missense_Mutation_p.C473F|NR3C1_uc011dbk.1_Missense_Mutation_p.C76F|NR3C1_uc003lnc.2_Missense_Mutation_p.C473F|NR3C1_uc003lnd.2_Missense_Mutation_p.C473F|NR3C1_uc003lne.2_Missense_Mutation_p.C473F|NR3C1_uc003lnf.2_Missense_Mutation_p.C474F	NM_000176	NP_000167	P04150	GCR_HUMAN	glucocorticoid receptor isoform alpha	473	NR C4-type.|Nuclear receptor.				chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)													---	---	---	---
SAP30L	79685	broad.mit.edu	37	5	153833058	153833058	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153833058G>A	uc003lvk.2	+	3	1069	c.421G>A	c.(421-423)GAA>AAA	p.E141K	SAP30L_uc003lvm.3_RNA|SAP30L_uc011ddc.1_Missense_Mutation_p.E100K|SAP30L_uc011ddd.1_Missense_Mutation_p.E95K	NM_024632	NP_078908	Q9HAJ7	SP30L_HUMAN	SAP30-like isoform 1	141					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|metal ion binding				0	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)															---	---	---	---
FBXW11	23291	broad.mit.edu	37	5	171305130	171305130	+	Missense_Mutation	SNP	A	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171305130A>G	uc003mbm.1	-	7	1164	c.793T>C	c.(793-795)TGG>CGG	p.W265R	FBXW11_uc011dey.1_Missense_Mutation_p.W233R|FBXW11_uc003mbl.1_Missense_Mutation_p.W252R|FBXW11_uc003mbn.1_Missense_Mutation_p.W231R	NM_012300	NP_036432	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11 isoform	265	WD 1.				cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31729612	31729612	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31729612G>A	uc003nwv.1	+	23	2278	c.2199G>A	c.(2197-2199)GAG>GAA	p.E733E	MSH5_uc003nwt.1_Silent_p.E750E|MSH5_uc003nwu.1_Silent_p.E734E|MSH5_uc003nww.1_Silent_p.E733E|MSH5_uc003nwx.1_Silent_p.E751E|MSH5_uc011dof.1_Silent_p.E432E|MSH5_uc003nwy.1_Silent_p.E407E|MSH5_uc003nwz.3_RNA|C6orf26_uc003nxa.3_5'Flank	NM_172166	NP_751898	O43196	MSH5_HUMAN	mutS homolog 5 isoform c	733					chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3													Direct_reversal_of_damage|MMR					---	---	---	---
Unknown	0	broad.mit.edu	37	6	153603648	153603648	+	IGR	SNP	T	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603648T>A								RGS17 (151259 upstream) : OPRM1 (727988 downstream)																																			---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77998505	77998505	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77998505G>A	uc003ugx.2	-	7	1325	c.1071C>T	c.(1069-1071)ATC>ATT	p.I357I	MAGI2_uc003ugy.2_Silent_p.I357I|MAGI2_uc010ldx.1_5'UTR|MAGI2_uc010ldy.1_5'UTR|MAGI2_uc011kgr.1_Silent_p.I189I|MAGI2_uc011kgs.1_Silent_p.I194I	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	357	WW 2.|Interaction with DDN.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
KRIT1	889	broad.mit.edu	37	7	91864762	91864762	+	Silent	SNP	A	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91864762A>G	uc003ulq.1	-	6	855	c.684T>C	c.(682-684)TGT>TGC	p.C228C	KRIT1_uc010lev.1_Silent_p.C21C|KRIT1_uc003ulr.1_Silent_p.C228C|KRIT1_uc003uls.1_Silent_p.C228C|KRIT1_uc003ult.1_Silent_p.C228C|KRIT1_uc003ulu.1_Silent_p.C228C|KRIT1_uc003ulv.1_Silent_p.C228C	NM_194456	NP_919438	O00522	KRIT1_HUMAN	krev interaction trapped 1 isoform 1	228					angiogenesis|cell redox homeostasis|negative regulation of angiogenesis|negative regulation of endothelial cell apoptosis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|regulation of establishment of cell polarity|small GTPase mediated signal transduction	cell-cell junction|cytoskeleton	protein binding|small GTPase regulator activity			ovary(2)|lung(1)	3	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)											Familial_Cerebral_Cavernous_Angioma				---	---	---	---
PILRB	29990	broad.mit.edu	37	7	99956991	99956991	+	Silent	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99956991C>T	uc003uuk.2	+	17	2982	c.486C>T	c.(484-486)AGC>AGT	p.S162S	PILRB_uc003uul.2_Nonsense_Mutation_p.Q93*|PILRB_uc003uun.2_Silent_p.S162S	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta	162	Extracellular (Potential).				activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121608163	121608163	+	Missense_Mutation	SNP	A	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121608163A>C	uc003vjy.2	+	3	678	c.283A>C	c.(283-285)ATT>CTT	p.I95L	PTPRZ1_uc003vjz.2_Missense_Mutation_p.I95L	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	95	Extracellular (Potential).|Alpha-carbonic anhydrase.				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9																		---	---	---	---
PINX1	54984	broad.mit.edu	37	8	10623284	10623284	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10623284G>A	uc003wth.2	-	7	647	c.614C>T	c.(613-615)ACG>ATG	p.T205M	SOX7_uc011kwz.1_Intron|PINX1_uc003wti.2_3'UTR	NM_017884	NP_060354	Q96BK5	PINX1_HUMAN	PIN2-interacting protein 1	205				T -> A (in Ref. 6; AAS19507).	mitotic metaphase plate congression|negative regulation of cell proliferation	chromosome, telomeric region|condensed chromosome kinetochore|mitochondrion|nuclear chromosome|nucleolus|spindle	protein binding|telomerase inhibitor activity|telomeric RNA binding			lung(1)|kidney(1)|skin(1)	3				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)														---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113276010	113276010	+	Silent	SNP	A	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113276010A>G	uc003ynu.2	-	61	9879	c.9720T>C	c.(9718-9720)TCT>TCC	p.S3240S	CSMD3_uc003yns.2_Silent_p.S2442S|CSMD3_uc003ynt.2_Silent_p.S3200S|CSMD3_uc011lhx.1_Silent_p.S3071S	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3240	Sushi 25.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116426974	116426974	+	Missense_Mutation	SNP	A	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116426974A>C	uc003ynz.2	-	6	3582	c.3123T>G	c.(3121-3123)AGT>AGG	p.S1041R	TRPS1_uc011lhy.1_Missense_Mutation_p.S1045R|TRPS1_uc003yny.2_Missense_Mutation_p.S1054R|TRPS1_uc010mcy.2_Missense_Mutation_p.S1041R	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	1041	Mediates interaction with RNF4 (By similarity).				negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8518230	8518230	+	Silent	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8518230C>T	uc003zkk.2	-	20	1872	c.1161G>A	c.(1159-1161)TCG>TCA	p.S387S	PTPRD_uc003zkp.2_Silent_p.S387S|PTPRD_uc003zkq.2_Silent_p.S387S|PTPRD_uc003zkr.2_Silent_p.S381S|PTPRD_uc003zks.2_Silent_p.S377S|PTPRD_uc003zkl.2_Silent_p.S387S|PTPRD_uc003zkm.2_Silent_p.S374S|PTPRD_uc003zkn.2_Silent_p.S387S|PTPRD_uc003zko.2_Silent_p.S384S	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	387	Fibronectin type-III 1.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140437210	140437210	+	Missense_Mutation	SNP	T	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140437210T>G	uc004cnf.2	-	6	812	c.475A>C	c.(475-477)AAA>CAA	p.K159Q	PNPLA7_uc010ncj.1_Missense_Mutation_p.K184Q	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	159	cNMP 1.				lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)														---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27400956	27400956	+	Missense_Mutation	SNP	C	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27400956C>G	uc001iti.2	-	20	2454	c.2272G>C	c.(2272-2274)GCC>CCC	p.A758P	YME1L1_uc001itj.2_Missense_Mutation_p.A701P|YME1L1_uc010qdl.1_Missense_Mutation_p.A668P|YME1L1_uc009xkv.2_RNA	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1	758					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64967507	64967507	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64967507G>A	uc001jmn.2	-	10	4222	c.3922C>T	c.(3922-3924)CGT>TGT	p.R1308C	JMJD1C_uc001jml.2_Missense_Mutation_p.R1089C|JMJD1C_uc001jmm.2_Missense_Mutation_p.R1020C|JMJD1C_uc010qiq.1_Missense_Mutation_p.R1126C|JMJD1C_uc009xpi.2_Missense_Mutation_p.R1126C|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc009xpk.1_Missense_Mutation_p.R345C	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	1308					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
NT5C2	22978	broad.mit.edu	37	10	104859733	104859733	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104859733G>A	uc001kwo.2	-	9	769	c.583C>T	c.(583-585)CGG>TGG	p.R195W	NT5C2_uc010qqp.1_Missense_Mutation_p.R166W|NT5C2_uc001kwq.2_Missense_Mutation_p.R195W|NT5C2_uc001kwp.2_Missense_Mutation_p.R42W	NM_012229	NP_036361	P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	195					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)													---	---	---	---
TDRD1	56165	broad.mit.edu	37	10	115963311	115963311	+	Missense_Mutation	SNP	G	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115963311G>C	uc001lbg.1	+	8	1119	c.966G>C	c.(964-966)AAG>AAC	p.K322N	TDRD1_uc001lbf.2_Missense_Mutation_p.K313N|TDRD1_uc001lbh.1_Missense_Mutation_p.K313N|TDRD1_uc001lbi.1_Missense_Mutation_p.K313N|TDRD1_uc010qsc.1_Missense_Mutation_p.K31N|TDRD1_uc001lbj.2_Missense_Mutation_p.K31N	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	322	Tudor 1.				DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)														---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132944909	132944909	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132944909G>A	uc001lkp.2	-	7	1135	c.1049C>T	c.(1048-1050)ACG>ATG	p.T350M	TCERG1L_uc009yax.1_RNA	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	350	WW 2.									large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
KDM4D	55693	broad.mit.edu	37	11	94731792	94731792	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94731792G>A	uc001pfe.2	+	3	2088	c.1256G>A	c.(1255-1257)CGG>CAG	p.R419Q		NM_018039	NP_060509	Q6B0I6	KDM4D_HUMAN	jumonji domain containing 2D	419					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107299860	107299860	+	Silent	SNP	A	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107299860A>G	uc010rvp.1	-	8	1128	c.1098T>C	c.(1096-1098)GCT>GCC	p.A366A	CWF19L2_uc001pjh.3_RNA|CWF19L2_uc009yxo.2_RNA	NM_152434	NP_689647	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control	366							catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
SIDT2	51092	broad.mit.edu	37	11	117059426	117059426	+	Missense_Mutation	SNP	C	T	T	rs141277106		TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117059426C>T	uc001pqh.1	+	13	1203	c.1162C>T	c.(1162-1164)CGC>TGC	p.R388C	SIDT2_uc010rxe.1_Missense_Mutation_p.R388C|SIDT2_uc001pqg.2_Missense_Mutation_p.R409C|SIDT2_uc001pqi.1_Intron	NM_001040455	NP_001035545	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2 precursor	388	Cytoplasmic (Potential).					integral to membrane|lysosomal membrane					0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)														---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41967067	41967067	+	Missense_Mutation	SNP	A	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41967067A>T	uc010skn.1	+	10	1957	c.1889A>T	c.(1888-1890)TAC>TTC	p.Y630F	PDZRN4_uc001rmq.3_Missense_Mutation_p.Y571F|PDZRN4_uc009zjz.2_Missense_Mutation_p.Y569F|PDZRN4_uc001rmr.2_Missense_Mutation_p.Y456F	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2	829							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
KIAA0748	9840	broad.mit.edu	37	12	55356738	55356738	+	Missense_Mutation	SNP	A	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55356738A>C	uc001sgn.3	-	9	1054	c.944T>G	c.(943-945)GTT>GGT	p.V315G	KIAA0748_uc001sgl.3_Missense_Mutation_p.V177G|KIAA0748_uc001sgm.3_Missense_Mutation_p.V62G|KIAA0748_uc010spb.1_Missense_Mutation_p.V62G|KIAA0748_uc010spc.1_Missense_Mutation_p.V177G|KIAA0748_uc010spd.1_Missense_Mutation_p.V315G|KIAA0748_uc001sgo.3_RNA	NM_001098815	NP_001092285	A2RU30	K0748_HUMAN	hypothetical protein LOC9840	315										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111785892	111785892	+	Missense_Mutation	SNP	G	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111785892G>T	uc001tsa.1	+	22	4377	c.4224G>T	c.(4222-4224)ATG>ATT	p.M1408I		NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2	1408	Pro-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42442545	42442545	+	Missense_Mutation	SNP	C	G	G	rs144180077	byFrequency	TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42442545C>G	uc001uyj.2	-	10	1219	c.1149G>C	c.(1147-1149)ATG>ATC	p.M383I	KIAA0564_uc001uyk.2_Missense_Mutation_p.M383I	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	383						extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76245989	76245989	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76245989C>A	uc001xrx.2	+	24	2664	c.2459C>A	c.(2458-2460)ACT>AAT	p.T820N	TTLL5_uc010ask.1_Missense_Mutation_p.T834N|TTLL5_uc001xrz.2_Missense_Mutation_p.T395N|TTLL5_uc001xry.1_RNA	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	820					protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
DLK1	8788	broad.mit.edu	37	14	101193435	101193435	+	Silent	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101193435C>T	uc001yhs.3	+	1	183	c.30C>T	c.(28-30)GTC>GTT	p.V10V	DLK1_uc001yhu.3_Silent_p.V10V	NM_003836	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog precursor	10					multicellular organismal development	extracellular space|integral to membrane|soluble fraction				ovary(2)|breast(1)|skin(1)	4		Melanoma(154;0.155)																---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	31776401	31776401	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31776401C>A	uc001zfq.2	-	11	1970	c.1877G>T	c.(1876-1878)CGC>CTC	p.R626L	OTUD7A_uc001zfr.2_Missense_Mutation_p.R633L	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A	626						cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43067923	43067923	+	Splice_Site	SNP	T	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43067923T>C	uc001zqo.2	-	13	1849	c.1410_splice	c.e13-1	p.C470_splice	TTBK2_uc010bcy.2_Splice_Site_p.C401_splice	NM_173500	NP_775771			tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48788332	48788332	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48788332C>T	uc001zwx.1	-	20	2712	c.2384G>A	c.(2383-2385)GGA>GAA	p.G795E		NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	795	EGF-like 12; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62299687	62299687	+	Intron	SNP	C	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62299687C>G	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
PPL	5493	broad.mit.edu	37	16	4934484	4934484	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4934484C>T	uc002cyd.1	-	22	4262	c.4172G>A	c.(4171-4173)CGG>CAG	p.R1391Q		NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin	1391	Potential.				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
ERN2	10595	broad.mit.edu	37	16	23706580	23706580	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23706580C>T	uc002dma.3	-	15	2054	c.1885G>A	c.(1885-1887)GAG>AAG	p.E629K	ERN2_uc010bxp.2_Missense_Mutation_p.E577K	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	581	Protein kinase.|Cytoplasmic (Potential).				apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity	p.E580*(1)		large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)														---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24196897	24196897	+	Intron	SNP	A	G	G	rs140933898	by1000genomes	TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24196897A>G	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8397045	8397045	+	Intron	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8397045G>A	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
CCDC47	57003	broad.mit.edu	37	17	61830101	61830101	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61830101C>T	uc002jbs.3	-	10	1429	c.1093G>A	c.(1093-1095)GTG>ATG	p.V365M	CCDC47_uc010ddx.2_Missense_Mutation_p.V365M|CCDC47_uc002jbt.2_Missense_Mutation_p.V365M	NM_020198	NP_064583	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47 precursor	365						integral to membrane	protein binding				0																OREG0031500	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66899633	66899633	+	Silent	SNP	A	G	G			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66899633A>G	uc002jhp.2	-	18	2465	c.2286T>C	c.(2284-2286)GCT>GCC	p.A762A	ABCA8_uc002jhq.2_Silent_p.A802A|ABCA8_uc010wqq.1_Silent_p.A802A|ABCA8_uc010wqr.1_Silent_p.A741A|ABCA8_uc002jhr.2_Silent_p.A802A	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	762						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)																	---	---	---	---
SERPINB8	5271	broad.mit.edu	37	18	61649024	61649024	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61649024G>T	uc002ljv.2	+	4	545	c.376G>T	c.(376-378)GAA>TAA	p.E126*	SERPINB8_uc002ljs.1_Nonsense_Mutation_p.E126*|SERPINB8_uc002ljt.2_Nonsense_Mutation_p.E126*|SERPINB8_uc002lju.2_Nonsense_Mutation_p.E126*|SERPINB8_uc010xex.1_5'UTR	NM_198833	NP_942130	P50452	SPB8_HUMAN	serine (or cysteine) proteinase inhibitor, clade	126					regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
DPF1	8193	broad.mit.edu	37	19	38709248	38709248	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38709248C>T	uc002ohl.2	-	5	589	c.562G>A	c.(562-564)GAC>AAC	p.D188N	DPF1_uc002ohm.2_Missense_Mutation_p.D188N|DPF1_uc002ohn.2_Missense_Mutation_p.D106N|DPF1_uc010xtu.1_Missense_Mutation_p.D162N|DPF1_uc010xtv.1_Missense_Mutation_p.D162N|DPF1_uc010xtw.1_Missense_Mutation_p.D162N	NM_004647	NP_004638	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1 isoform	188					induction of apoptosis|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nBAF complex	zinc ion binding				0	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49671854	49671854	+	Silent	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49671854C>T	uc002pmw.2	+	6	729	c.657C>T	c.(655-657)GAC>GAT	p.D219D	TRPM4_uc010emu.2_Silent_p.D219D|TRPM4_uc010yak.1_Translation_Start_Site|TRPM4_uc002pmx.2_Silent_p.D45D|TRPM4_uc010emv.2_Silent_p.D104D|TRPM4_uc010yal.1_Translation_Start_Site	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,	219	Cytoplasmic (Potential).				dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)														---	---	---	---
UBE2V1	7335	broad.mit.edu	37	20	48732031	48732031	+	5'Flank	SNP	G	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48732031G>T	uc002xva.2	-						TMEM189-UBE2V1_uc002xvf.2_Intron|UBE2V1_uc002xvb.2_5'Flank|UBE2V1_uc002xvc.2_Missense_Mutation_p.F10L|UBE2V1_uc002xvd.2_Missense_Mutation_p.H28N|UBE2V1_uc002xve.2_Missense_Mutation_p.H28N	NM_001032288	NP_001027459			ubiquitin-conjugating enzyme E2 variant 1						cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein K63-linked ubiquitination|regulation of DNA repair|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-UEV1A complex|ubiquitin ligase complex	acid-amino acid ligase activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(9;4.74e-06)															---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51872060	51872060	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51872060C>A	uc002xwo.2	+	2	3019	c.2063C>A	c.(2062-2064)GCC>GAC	p.A688D		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	688					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32617948	32617948	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32617948G>A	uc002yow.1	-	7	1912	c.1440C>T	c.(1438-1440)GAC>GAT	p.D480D	TIAM1_uc011adk.1_Silent_p.D480D|TIAM1_uc011adl.1_Silent_p.D480D|TIAM1_uc002yox.1_Silent_p.D88D	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	480	PH 1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38538093	38538093	+	Missense_Mutation	SNP	G	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38538093G>C	uc002yvz.2	+	33	3682	c.3577G>C	c.(3577-3579)GAA>CAA	p.E1193Q	TTC3_uc011aee.1_Missense_Mutation_p.E883Q|TTC3_uc002ywa.2_Missense_Mutation_p.E1193Q|TTC3_uc002ywb.2_Missense_Mutation_p.E1193Q|TTC3_uc010gnf.2_Missense_Mutation_p.E958Q|TTC3_uc002ywc.2_Missense_Mutation_p.E883Q|TTC3_uc002ywd.1_Missense_Mutation_p.E257Q	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1193					protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)																---	---	---	---
ASMT	438	broad.mit.edu	37	X	1743214	1743214	+	Silent	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1743214G>A	uc004cqd.2	+	4	442	c.297G>A	c.(295-297)CCG>CCA	p.P99P	ASMT_uc010ncy.2_Silent_p.P99P|ASMT_uc004cqe.2_Silent_p.P99P	NM_004043	NP_004034	P46597	HIOM_HUMAN	acetylserotonin O-methyltransferase	99					melatonin biosynthetic process|translation	cytosol	acetylserotonin O-methyltransferase activity|S-methyltransferase activity			skin(1)	1		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
HEPH	9843	broad.mit.edu	37	X	65476001	65476001	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65476001G>T	uc011moz.1	+	17	2794	c.2734G>T	c.(2734-2736)GAG>TAG	p.E912*	HEPH_uc004dwn.2_Nonsense_Mutation_p.E912*|HEPH_uc004dwo.2_Nonsense_Mutation_p.E642*|HEPH_uc010nkr.2_Nonsense_Mutation_p.E720*|HEPH_uc011mpa.1_Nonsense_Mutation_p.E912*|HEPH_uc010nks.2_Nonsense_Mutation_p.E201*	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	909	Extracellular (Potential).				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9																		---	---	---	---
AR	367	broad.mit.edu	37	X	66941727	66941727	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66941727C>A	uc004dwu.1	+	6	3486	c.2371C>A	c.(2371-2373)CTC>ATC	p.L791I	AR_uc004dwv.1_Missense_Mutation_p.L259I	NM_000044	NP_000035	P10275	ANDR_HUMAN	androgen receptor isoform 1	790	Ligand-binding.|Interaction with MYST2.		L -> F (in AIS).		cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)									Androgen_Insensitivity_Syndrome				---	---	---	---
PDZD11	51248	broad.mit.edu	37	X	69508031	69508031	+	Intron	SNP	A	C	C			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69508031A>C	uc004dyd.1	-						KIF4A_uc004dyg.2_5'Flank|KIF4A_uc010nkw.2_5'Flank|PDZD11_uc004dye.1_Intron|KIF4A_uc004dyf.1_5'Flank	NM_016484	NP_057568			PDZ domain containing 11							basolateral plasma membrane|cytosol|extracellular region	protein C-terminus binding				0																		---	---	---	---
SEPT6	23157	broad.mit.edu	37	X	118767373	118767373	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118767373C>T	uc004erv.2	-	8	1304	c.1039G>A	c.(1039-1041)GTC>ATC	p.V347I	SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Missense_Mutation_p.V347I|SEPT6_uc004ert.2_Missense_Mutation_p.V347I|SEPT6_uc004eru.2_Missense_Mutation_p.V347I|SEPT6_uc004erw.2_Missense_Mutation_p.V289I|SEPT6_uc011mtv.1_Missense_Mutation_p.V289I|SEPT6_uc011mtw.1_Missense_Mutation_p.V377I	NM_015129	NP_055944	Q14141	SEPT6_HUMAN	septin 6 isoform B	347	Potential.				cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			lung(1)|ovary(1)|prostate(1)|kidney(1)	4																		---	---	---	---
GLUD2	2747	broad.mit.edu	37	X	120182259	120182259	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5732-01	TCGA-CG-5732-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120182259G>A	uc004eto.2	+	1	798	c.721G>A	c.(721-723)GCC>ACC	p.A241T		NM_012084	NP_036216	P49448	DHE4_HUMAN	glutamate dehydrogenase 2 precursor	241					glutamate biosynthetic process|glutamate catabolic process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding			pancreas(1)	1					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
