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
CHD5	26038	broad.mit.edu	37	1	6219643	6219643	+	Intron	DEL	A	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6219643delA	uc001amb.1	-							NM_015557	NP_056372			chromodomain helicase DNA binding protein 5						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17229298	17229303	+	Intron	DEL	ATAATA	-	-	rs77418498		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17229298_17229303delATAATA	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22235083	22235083	+	Intron	DEL	A	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22235083delA	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron	NM_005529	NP_005520			heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
FAM73A	374986	broad.mit.edu	37	1	78319393	78319394	+	Intron	INS	-	AC	AC			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78319393_78319394insAC	uc001dhx.2	+						FAM73A_uc010ork.1_Intron|FAM73A_uc010orl.1_Intron|FAM73A_uc001dhy.1_Intron	NM_198549	NP_940951			hypothetical protein LOC374986							integral to membrane				ovary(1)	1				Colorectal(170;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	90623317	90623320	+	IGR	DEL	TTCC	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90623317_90623320delTTCC								ZNF326 (129223 upstream) : BARHL2 (554260 downstream)																																			---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120612224	120612226	+	5'UTR	DEL	GCC	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120612224_120612226delGCC	uc001eik.2	-	1					NOTCH2_uc001eil.2_5'UTR|NOTCH2_uc001eim.3_5'UTR	NM_024408	NP_077719			notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
ARNT	405	broad.mit.edu	37	1	150849072	150849073	+	5'UTR	DEL	CC	-	-	rs71749764		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150849072_150849073delCC	uc001evr.1	-	1					ARNT_uc001evs.1_5'UTR|ARNT_uc009wmb.1_5'UTR|ARNT_uc009wmc.1_5'UTR|ARNT_uc009wmd.1_5'UTR|ARNT_uc009wme.1_5'UTR|ARNT_uc010pcl.1_5'UTR	NM_001668	NP_001659			aryl hydrocarbon receptor nuclear translocator						positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia		aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity			skin(4)|lung(3)|central_nervous_system(1)|kidney(1)	9	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)					T	ETV6	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	1	204363978	204363979	+	IGR	INS	-	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204363978_204363979insA								LOC127841 (25131 upstream) : PPP1R15B (8515 downstream)																																			---	---	---	---
CMPK2	129607	broad.mit.edu	37	2	7001234	7001235	+	Intron	DEL	CG	-	-	rs3085147		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001234_7001235delCG	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198			UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
NEB	4703	broad.mit.edu	37	2	152495880	152495880	+	Intron	DEL	A	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152495880delA	uc010fnx.2	-						NEB_uc002txu.2_Frame_Shift_Del_p.W74fs	NM_004543	NP_004534			nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	155098762	155098763	+	Intron	INS	-	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155098762_155098763insT	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron	NM_052917	NP_443149			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
PSMD14	10213	broad.mit.edu	37	2	162227558	162227559	+	Intron	INS	-	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162227558_162227559insG	uc002ubu.2	+							NM_005805	NP_005796			proteasome 26S subunit, non-ATPase 14						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K63-linked deubiquitination|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	endopeptidase activator activity|metal ion binding|metallopeptidase activity|proteasome binding|ubiquitin thiolesterase activity			breast(1)	1																		---	---	---	---
FAM171B	165215	broad.mit.edu	37	2	187608158	187608158	+	Intron	DEL	T	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187608158delT	uc002ups.2	+						FAM171B_uc002upr.1_Intron	NM_177454	NP_803237			KIAA1946							integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10																		---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200173298	200173299	+	Intron	DEL	CA	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200173298_200173299delCA	uc002uuy.1	-						SATB2_uc010fsq.1_Intron|SATB2_uc002uuz.1_Intron|SATB2_uc002uva.1_Intron	NM_015265	NP_056080			SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
BARD1	580	broad.mit.edu	37	2	215657183	215657183	+	Intron	DEL	A	-	-	rs71399150		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215657183delA	uc002veu.2	-						BARD1_uc010zjm.1_Intron	NM_000465	NP_000456			BRCA1 associated RING domain 1						cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)										Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	237209274	237209275	+	IGR	INS	-	TCCT	TCCT	rs59878840		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237209274_237209275insTCCT								ASB18 (36286 upstream) : IQCA1 (23519 downstream)																																			---	---	---	---
NKTR	4820	broad.mit.edu	37	3	42642634	42642635	+	Intron	INS	-	C	C	rs151282511	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42642634_42642635insC	uc003clo.2	+						SEC22C_uc003cli.2_5'Flank|NKTR_uc003cll.1_Intron|NKTR_uc003clm.1_Intron|NKTR_uc003clp.2_Intron|NKTR_uc011azp.1_Intron	NM_005385	NP_005376			natural killer-tumor recognition sequence						protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	48332852	48332852	+	IGR	DEL	T	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48332852delT								ZNF589 (3739 upstream) : NME6 (2739 downstream)																																			---	---	---	---
DZIP3	9666	broad.mit.edu	37	3	108373204	108373205	+	Intron	INS	-	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108373204_108373205insT	uc003dxd.2	+						DZIP3_uc003dxf.1_Intron|DZIP3_uc011bhm.1_Intron|DZIP3_uc003dxg.1_Frame_Shift_Ins_p.G472fs	NM_014648	NP_055463			DAZ interacting protein 3, zinc finger						protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126222662	126222663	+	Intron	DEL	GT	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126222662_126222663delGT	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240			urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
LPP	4026	broad.mit.edu	37	3	188242759	188242760	+	Intron	INS	-	T	T	rs11393215		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188242759_188242760insT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14481080	14481080	+	Intron	DEL	A	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									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)																	---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16679926	16679927	+	Intron	INS	-	C	C	rs139264862	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16679926_16679927insC	uc003jft.3	-						MYO10_uc011cnb.1_Intron|MYO10_uc011cnc.1_Intron|MYO10_uc011cnd.1_Intron|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
GOLPH3	64083	broad.mit.edu	37	5	32126121	32126124	+	3'UTR	DEL	TTAA	-	-	rs77366940		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32126121_32126124delTTAA	uc003jhp.1	-	4						NM_022130	NP_071413			golgi phosphoprotein 3						cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1																		---	---	---	---
AP3S1	1176	broad.mit.edu	37	5	115177668	115177669	+	5'UTR	INS	-	AGGC	AGGC	rs144226661	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115177668_115177669insAGGC	uc003krl.2	+	1					AP3S1_uc003krk.2_5'UTR|AP3S1_uc003krm.2_5'UTR|ATG12_uc003krh.2_5'Flank|ATG12_uc003kri.2_5'Flank|ATG12_uc003krj.2_5'Flank	NM_001284	NP_001275			adaptor-related protein complex 3, sigma 1						insulin receptor signaling pathway|intracellular protein transport|vesicle-mediated transport	AP-type membrane coat adaptor complex|cytoplasmic vesicle membrane|Golgi apparatus|transport vesicle	protein binding|protein transporter activity				0		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)														---	---	---	---
CLTB	1212	broad.mit.edu	37	5	175823608	175823609	+	Intron	DEL	AG	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175823608_175823609delAG	uc003meh.2	-						CLTB_uc003mei.2_Intron|CLTB_uc011dfn.1_Intron	NM_007097	NP_009028			clathrin, light polypeptide isoform b						intracellular protein transport|vesicle-mediated transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle	protein binding|structural molecule activity				0	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.098)														---	---	---	---
HCG4	54435	broad.mit.edu	37	6	29760353	29760373	+	RNA	DEL	GCGGGCGCCGTGGATGGAGCA	-	-	rs146714150		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29760353_29760373delGCGGGCGCCGTGGATGGAGCA	uc003nns.2	-	1		c.478_498delTGCTCCATCCACGGCGCCCGC			uc010jrm.1_In_Frame_Del_p.AGAVDGA111del|uc003nnt.2_In_Frame_Del_p.RAPWMEQ147del|uc011dma.1_5'Flank	NR_002139				Homo sapiens clone HCG IV.9 unknown mRNA.												0																		---	---	---	---
UHRF1BP1	54887	broad.mit.edu	37	6	34791333	34791334	+	Intron	DEL	TC	-	-	rs79872775	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34791333_34791334delTC	uc003oju.3	+						UHRF1BP1_uc010jvm.1_Intron|UHRF1BP1_uc010jvn.2_Intron	NM_017754	NP_060224			ICBP90 binding protein 1											ovary(3)	3																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103193953	103193953	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103193953delG	uc003vca.2	-	40	6187	c.6027delC	c.(6025-6027)ACCfs	p.T2009fs	RELN_uc010liz.2_Frame_Shift_Del_p.T2009fs	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2009					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)														---	---	---	---
NOXA1	10811	broad.mit.edu	37	9	140320927	140320928	+	Intron	INS	-	GGGTC	GGGTC	rs145312088	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140320927_140320928insGGGTC	uc004cmv.2	+						C9orf167_uc011mew.1_Intron|NOXA1_uc004cmu.2_Intron|NOXA1_uc010nch.2_Intron	NM_006647	NP_006638			NADPH oxidase activator 1						regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|superoxide metabolic process	cytoplasm|NADPH oxidase complex	Rac GTPase binding|superoxide-generating NADPH oxidase activator activity				0	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000238)|Epithelial(140;0.000982)														---	---	---	---
MSRB2	22921	broad.mit.edu	37	10	23384788	23384788	+	Intron	DEL	C	-	-	rs72126625		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23384788delC	uc001iro.2	+							NM_012228	NP_036360			methionine sulfoxide reductase B2 precursor						protein repair	mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0					L-Methionine(DB00134)													---	---	---	---
CCDC7	221016	broad.mit.edu	37	10	32745152	32745153	+	Intron	DEL	TT	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32745152_32745153delTT	uc001iwj.2	+						CCDC7_uc009xlu.1_Intron|CCDC7_uc001iwk.2_Intron|CCDC7_uc009xlv.2_Intron|CCDC7_uc009xlw.1_Intron|CCDC7_uc009xlx.1_Intron|CCDC7_uc009xly.1_Intron	NM_145023	NP_659460			coiled-coil domain containing 7												0		Breast(68;0.000207)|Prostate(175;0.0107)																---	---	---	---
NXF1	10482	broad.mit.edu	37	11	62564556	62564556	+	Intron	DEL	C	-	-	rs111331941		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62564556delC	uc001nvf.1	-						NXF1_uc001nvg.1_Intron|NXF1_uc009yog.1_Intron	NM_006362	NP_006353			nuclear RNA export factor 1 isoform 1						gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3																		---	---	---	---
BBS1	582	broad.mit.edu	37	11	66282291	66282291	+	Intron	DEL	T	-	-	rs72050815		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66282291delT	uc001oij.1	+						BBS1_uc001oii.1_Intron|BBS1_uc010rpf.1_Intron|BBS1_uc010rpg.1_Intron|BBS1_uc001oik.1_Intron|BBS1_uc001oil.1_Intron	NM_024649	NP_078925			Bardet-Biedl syndrome 1						nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
ME3	10873	broad.mit.edu	37	11	86280402	86280402	+	Intron	DEL	C	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86280402delC	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_Intron	NM_001014811	NP_001014811			mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	113662516	113662516	+	IGR	DEL	T	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113662516delT								CLDN25 (11309 upstream) : USP28 (6082 downstream)																																			---	---	---	---
GRAMD1B	57476	broad.mit.edu	37	11	123455101	123455102	+	Intron	INS	-	G	G	rs140088482	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123455101_123455102insG	uc001pyx.2	+						GRAMD1B_uc001pyw.2_Intron|GRAMD1B_uc010rzw.1_Intron|GRAMD1B_uc010rzx.1_Intron|GRAMD1B_uc009zbe.1_Intron	NM_020716	NP_065767			GRAM domain containing 1B							integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)														---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2303597	2303597	+	Intron	DEL	C	-	-	rs34167706		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2303597delC	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
HEBP1	50865	broad.mit.edu	37	12	13153127	13153142	+	5'UTR	DEL	GGCGGCAGGGCGGCAG	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13153127_13153142delGGCGGCAGGGCGGCAG	uc001rbd.2	-	1					HEBP1_uc001rbf.2_5'UTR|HTR7P1_uc010shq.1_5'Flank|HTR7P1_uc001rbh.2_5'Flank	NM_015987	NP_057071			heme binding protein 1						circadian rhythm	extracellular region				breast(1)	1		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)														---	---	---	---
TARBP2	6895	broad.mit.edu	37	12	53895601	53895602	+	Intron	INS	-	C	C	rs138441746	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53895601_53895602insC	uc001sdo.2	+						MAP3K12_uc001sdm.1_5'Flank|MAP3K12_uc001sdn.1_5'Flank|TARBP2_uc009znb.2_Intron|TARBP2_uc001sdp.2_Intron|TARBP2_uc001sdq.2_Intron|TARBP2_uc001sdr.2_Intron|TARBP2_uc001sds.2_Intron|TARBP2_uc001sdt.2_Intron|TARBP2_uc001sdu.2_Intron|TARBP2_uc001sdv.2_Intron	NM_134323	NP_599150			TAR RNA binding protein 2 isoform a						miRNA loading onto RISC involved in gene silencing by miRNA|negative regulation of defense response to virus by host|negative regulation of protein kinase activity|positive regulation of viral genome replication|pre-miRNA processing|production of siRNA involved in RNA interference|regulation of transcription from RNA polymerase II promoter|regulation of translation|regulation of viral transcription|targeting of mRNA for destruction involved in RNA interference	cytosol|nucleus|perinuclear region of cytoplasm|RNA-induced silencing complex	double-stranded RNA binding|protein homodimerization activity|siRNA binding			central_nervous_system(1)	1																		---	---	---	---
GNS	2799	broad.mit.edu	37	12	65133419	65133419	+	Intron	DEL	A	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65133419delA	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067			glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)														---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104131353	104131354	+	Intron	DEL	TC	-	-	rs141425461		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104131353_104131354delTC	uc001tjw.2	+						STAB2_uc009zug.2_Intron	NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133363542	133363543	+	Intron	INS	-	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133363542_133363543insT	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886			Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
PARP4	143	broad.mit.edu	37	13	25000864	25000864	+	Intron	DEL	A	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25000864delA	uc001upl.2	-							NM_006437	NP_006428			poly (ADP-ribose) polymerase family, member 4						cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77644557	77644557	+	Intron	DEL	T	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77644557delT	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron|MYCBP2_uc001vke.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	114025814	114025814	+	IGR	DEL	C	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114025814delC								GRTP1 (7351 upstream) : ADPRHL1 (50446 downstream)																																			---	---	---	---
ALDH6A1	4329	broad.mit.edu	37	14	74535797	74535798	+	Intron	DEL	AC	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74535797_74535798delAC	uc001xpo.2	-						C14orf45_uc001xpm.1_Intron|ALDH6A1_uc010asa.2_Intron|ALDH6A1_uc010tuq.1_Intron	NM_005589	NP_005580			aldehyde dehydrogenase 6A1 precursor							mitochondrial matrix|nucleus	fatty-acyl-CoA binding|malonate-semialdehyde dehydrogenase (acetylating) activity|methylmalonate-semialdehyde dehydrogenase (acylating) activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00354)	NADH(DB00157)													---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18897122	18897123	+	Intron	INS	-	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18897122_18897123insA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71710658	71710659	+	Intron	INS	-	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71710658_71710659insT	uc002fax.2	-						PHLPP2_uc002fav.2_Intron|PHLPP2_uc010cgf.2_Intron	NM_015020	NP_055835			PH domain and leucine rich repeat protein							cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PLCG2	5336	broad.mit.edu	37	16	81954997	81954997	+	Intron	DEL	T	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81954997delT	uc002fgt.2	+						PLCG2_uc010chg.1_Frame_Shift_Del_p.N810fs	NM_002661	NP_002652			phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8																		---	---	---	---
UTP6	55813	broad.mit.edu	37	17	30216088	30216089	+	Intron	INS	-	A	A	rs76051459		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30216088_30216089insA	uc002hgr.2	-						UTP6_uc002hgq.2_5'Flank|UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_Intron	NM_018428	NP_060898			hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	72206117	72206117	+	IGR	DEL	C	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72206117delC								RPL38 (100 upstream) : MGC16275 (24 downstream)																																			---	---	---	---
TTYH2	94015	broad.mit.edu	37	17	72218928	72218928	+	Intron	DEL	T	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72218928delT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035			tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
LLGL2	3993	broad.mit.edu	37	17	73565883	73565884	+	Intron	DEL	AA	-	-	rs35146910		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73565883_73565884delAA	uc002joh.2	+						LLGL2_uc002joi.2_Intron|LLGL2_uc010dgg.1_Intron|LLGL2_uc002joj.2_Intron|LLGL2_uc010wsd.1_Intron	NM_001031803	NP_001026973			lethal giant larvae homolog 2 isoform c						cell cycle|cell division|exocytosis|regulation of establishment or maintenance of cell polarity	cytoplasm|intracellular membrane-bounded organelle	PDZ domain binding			ovary(2)	2	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)															---	---	---	---
QRICH2	84074	broad.mit.edu	37	17	74273604	74273605	+	Intron	DEL	CA	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74273604_74273605delCA	uc002jrd.1	-						QRICH2_uc010wsz.1_Intron|QRICH2_uc010dgw.1_Intron	NM_032134	NP_115510			glutamine rich 2								protein binding			ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77147525	77147527	+	Intron	DEL	GAG	-	-	rs63146461		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77147525_77147527delGAG	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044			hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)															---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3134953	3134954	+	Intron	INS	-	TT	TT			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3134953_3134954insTT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
ZFR2	23217	broad.mit.edu	37	19	3819298	3819299	+	Intron	INS	-	GGGCAGGT	GGGCAGGT	rs146619879	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3819298_3819299insGGGCAGGT	uc002lyw.2	-							NM_015174	NP_055989			zinc finger RNA binding protein 2 isoform 1							intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)														---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11129671	11129671	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11129671delC	uc002mqf.3	+	17	2761	c.2477delC	c.(2476-2478)GCCfs	p.A826fs	SMARCA4_uc010dxp.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxo.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc002mqg.1_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxq.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxr.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc002mqj.3_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxs.2_Frame_Shift_Del_p.A826fs|SMARCA4_uc010dxt.1_Frame_Shift_Del_p.A46fs|SMARCA4_uc002mqh.3_5'Flank|SMARCA4_uc002mqi.1_5'Flank	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	826	Helicase ATP-binding.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
CCDC159	126075	broad.mit.edu	37	19	11462456	11462456	+	Intron	DEL	G	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11462456delG	uc010xlw.1	+						CCDC159_uc010xls.1_Intron|CCDC159_uc010xlt.1_Intron|CCDC159_uc010xlv.1_Intron	NM_001080503	NP_001073972			coiled-coil domain-containing-like											ovary(1)	1																		---	---	---	---
SYMPK	8189	broad.mit.edu	37	19	46329782	46329782	+	Intron	DEL	T	-	-	rs28362500		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46329782delT	uc002pdn.2	-						SYMPK_uc002pdo.1_Intron|SYMPK_uc002pdp.1_Intron	NM_004819	NP_004810			symplekin						cell adhesion|mRNA processing	cytoplasm|cytoskeleton|nucleoplasm|tight junction	protein binding			ovary(1)	1		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)														---	---	---	---
STRN4	29888	broad.mit.edu	37	19	47249351	47249352	+	Intron	INS	-	GGCCG	GGCCG			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47249351_47249352insGGCCG	uc002pfl.2	-						STRN4_uc002pfm.2_Intron|STRN4_uc010xyf.1_Intron|STRN4_uc010xyg.1_Intron|FKRP_uc002pfn.2_Intron|FKRP_uc002pfp.2_Intron	NM_013403	NP_037535			zinedin isoform 1							cytoplasm|membrane	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)														---	---	---	---
MED25	81857	broad.mit.edu	37	19	50331485	50331486	+	Intron	INS	-	A	A	rs35999270		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50331485_50331486insA	uc002ppw.1	+						MED25_uc010ybe.1_Intron	NM_030973	NP_112235			mediator complex subunit 25						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)														---	---	---	---
CRELD2	79174	broad.mit.edu	37	22	50315936	50315973	+	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	-	rs71805922	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50315936_50315973delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	uc003bja.2	+						CRELD2_uc003biz.3_Intron|CRELD2_uc010haj.2_Intron|CRELD2_uc010hal.2_Splice_Site_p.V198_splice|CRELD2_uc010hak.2_Intron|CRELD2_uc010ham.2_Intron	NM_024324	NP_077300			cysteine-rich with EGF-like domains 2 isoform b							endoplasmic reticulum|extracellular region	calcium ion binding				0		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
MED14	9282	broad.mit.edu	37	X	40540221	40540221	+	Intron	DEL	A	-	-			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40540221delA	uc004dex.3	-							NM_004229	NP_004220			mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48136019	48136020	+	IGR	INS	-	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48136019_48136020insT								SSX1 (9140 upstream) : SSX3 (69843 downstream)																																			---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7724319	7724319	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7724319C>T	uc001aoi.2	+	9	1919	c.1712C>T	c.(1711-1713)TCG>TTG	p.S571L		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	571					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
MFN2	9927	broad.mit.edu	37	1	12049230	12049230	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12049230C>T	uc001atn.3	+	3	458	c.5C>T	c.(4-6)TCC>TTC	p.S2F	MFN2_uc009vni.2_Missense_Mutation_p.S2F	NM_014874	NP_055689	O95140	MFN2_HUMAN	mitofusin 2	2	Cytoplasmic (Potential).				blood coagulation|mitochondrial fusion|mitochondrial membrane organization|mitochondrion localization|negative regulation of Ras protein signal transduction|negative regulation of smooth muscle cell proliferation|protein targeting to mitochondrion	cytosol|integral to membrane|intrinsic to mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
TMEM82	388595	broad.mit.edu	37	1	16069534	16069534	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16069534G>A	uc001axc.2	+	3	319	c.181G>A	c.(181-183)GAA>AAA	p.E61K		NM_001013641	NP_001013663	A0PJX8	TMM82_HUMAN	transmembrane protein 82	61	Leu-rich.					integral to membrane				breast(1)|central_nervous_system(1)	2		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
MED18	54797	broad.mit.edu	37	1	28661175	28661175	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28661175C>T	uc001bpt.3	+	3	566	c.321C>T	c.(319-321)GAC>GAT	p.D107D	MED18_uc009vtg.2_Silent_p.D107D	NM_017638	NP_060108	Q9BUE0	MED18_HUMAN	mediator complex subunit 18	107					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	identical protein binding				0		Colorectal(325;0.000147)|Lung NSC(340;0.000818)|all_lung(284;0.000996)|Renal(390;0.00357)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0557)|Ovarian(437;0.113)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0141)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34117926	34117926	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34117926T>G	uc001bxn.1	-	28	4492	c.4463A>C	c.(4462-4464)AAC>ACC	p.N1488T	CSMD2_uc001bxm.1_Missense_Mutation_p.N1528T|CSMD2_uc001bxo.1_Missense_Mutation_p.N401T	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1488	CUB 9.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42047974	42047974	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42047974G>A	uc001cgz.3	-	4	3708	c.2495C>T	c.(2494-2496)CCA>CTA	p.P832L	HIVEP3_uc001cha.3_Missense_Mutation_p.P832L|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	832	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN (By similarity).				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75072302	75072302	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75072302T>C	uc001dgg.2	-	10	1691	c.1472A>G	c.(1471-1473)GAA>GGA	p.E491G	uc001dgh.2_Intron|C1orf173_uc001dgi.3_Missense_Mutation_p.E285G	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	491	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
TGFBR3	7049	broad.mit.edu	37	1	92200388	92200388	+	Silent	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92200388A>T	uc001doh.2	-	5	979	c.513T>A	c.(511-513)GTT>GTA	p.V171V	TGFBR3_uc009wde.2_5'UTR|TGFBR3_uc010osy.1_Silent_p.V129V|TGFBR3_uc001doi.2_Silent_p.V171V|TGFBR3_uc001doj.2_Silent_p.V171V	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	171	Extracellular (Potential).				BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103488523	103488523	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103488523T>G	uc001dul.2	-	8	1338	c.1020A>C	c.(1018-1020)GAA>GAC	p.E340D	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dum.2_Missense_Mutation_p.E352D|COL11A1_uc001dun.2_Missense_Mutation_p.E301D|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	340	Nonhelical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
C1orf59	113802	broad.mit.edu	37	1	109198327	109198327	+	Intron	SNP	A	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109198327A>G	uc001dvt.3	-						C1orf59_uc001dvu.3_Intron|C1orf59_uc009wer.2_Intron	NM_001102592	NP_001096062			hypothetical protein LOC113802						gene silencing by RNA|piRNA metabolic process	P granule	metal ion binding|O-methyltransferase activity|RNA binding|RNA methyltransferase activity				0		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0152)|Lung(183;0.0895)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.163)														---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150935146	150935146	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150935146G>C	uc001evu.2	+	18	3432	c.3242G>C	c.(3241-3243)AGT>ACT	p.S1081T	SETDB1_uc001evv.2_Missense_Mutation_p.S1081T|SETDB1_uc009wmg.1_Missense_Mutation_p.S1081T	NM_001145415	NP_001138887	Q15047	SETB1_HUMAN	SET domain, bifurcated 1 isoform 1	1081	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
FLG2	388698	broad.mit.edu	37	1	152328939	152328939	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152328939C>T	uc001ezw.3	-	3	1396	c.1323G>A	c.(1321-1323)GGG>GGA	p.G441G	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	441	Filaggrin 2.|Ser-rich.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176675535	176675535	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176675535G>A	uc001gkz.2	+	10	4570	c.3406G>A	c.(3406-3408)GGA>AGA	p.G1136R	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1136					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181764163	181764163	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181764163G>A	uc001gow.2	+	45	6227	c.6062G>A	c.(6061-6063)CGC>CAC	p.R2021H	CACNA1E_uc009wxs.2_Missense_Mutation_p.R1909H|CACNA1E_uc009wxt.2_Missense_Mutation_p.R1290H	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	2064	Cytoplasmic (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CFH	3075	broad.mit.edu	37	1	196695999	196695999	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196695999C>T	uc001gtj.3	+	14	2405	c.2165C>T	c.(2164-2166)TCA>TTA	p.S722L		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	722	Sushi 12.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233388478	233388478	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233388478G>A	uc001hvl.2	-	6	2126	c.1891C>T	c.(1891-1893)CAC>TAC	p.H631Y	PCNXL2_uc009xfu.2_RNA|PCNXL2_uc009xfv.1_RNA|PCNXL2_uc001hvq.1_5'Flank	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	631						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15676657	15676657	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15676657C>T	uc002rcc.1	-	8	558	c.532G>A	c.(532-534)GAC>AAC	p.D178N	NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	178										ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
SOCS5	9655	broad.mit.edu	37	2	46986557	46986557	+	Silent	SNP	A	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46986557A>G	uc002rvf.2	+	2	1052	c.888A>G	c.(886-888)TTA>TTG	p.L296L	SOCS5_uc010yoe.1_Silent_p.L265L|SOCS5_uc002rvg.2_Silent_p.L296L	NM_014011	NP_054730	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	296					cell growth|cytokine-mediated signaling pathway|intracellular signal transduction|negative regulation of signal transduction|negative regulation of T-helper 2 cell differentiation|positive regulation of T-helper 1 cell differentiation|regulation of growth					ovary(1)|lung(1)|central_nervous_system(1)	3		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
FAM136A	84908	broad.mit.edu	37	2	70528022	70528022	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70528022G>A	uc002sgq.3	-	2	255	c.178C>T	c.(178-180)CCT>TCT	p.P60S	FAM136A_uc010fdp.2_RNA	NM_032822	NP_116211	Q96C01	F136A_HUMAN	hypothetical protein LOC84908	60						mitochondrion	protein binding				0																		---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102505275	102505275	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102505275C>T	uc002tbg.2	+	29	3569	c.3514C>T	c.(3514-3516)CAG>TAG	p.Q1172*	MAP4K4_uc002tbc.2_Nonsense_Mutation_p.Q1253*|MAP4K4_uc002tbd.2_Nonsense_Mutation_p.Q1145*|MAP4K4_uc002tbe.2_Nonsense_Mutation_p.Q1099*|MAP4K4_uc002tbf.2_Nonsense_Mutation_p.Q1206*|MAP4K4_uc010yvy.1_Nonsense_Mutation_p.Q1168*|MAP4K4_uc002tbh.2_Nonsense_Mutation_p.Q1098*|MAP4K4_uc002tbi.2_Nonsense_Mutation_p.Q975*|MAP4K4_uc010yvz.1_Nonsense_Mutation_p.Q1212*|MAP4K4_uc002tbk.2_Nonsense_Mutation_p.Q627*|MAP4K4_uc002tbl.2_Nonsense_Mutation_p.Q358*	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase	1172	CNH.|Mediates interaction with RAP2A.				intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
DLX1	1745	broad.mit.edu	37	2	172952721	172952721	+	Intron	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172952721G>A	uc002uhl.2	+						DLX1_uc002uhm.2_Intron	NM_178120	NP_835221			distal-less homeobox 1 isoform 1							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
DLX1	1745	broad.mit.edu	37	2	172952722	172952722	+	Intron	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172952722C>G	uc002uhl.2	+						DLX1_uc002uhm.2_Intron	NM_178120	NP_835221			distal-less homeobox 1 isoform 1							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198948557	198948557	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198948557A>T	uc010fsp.2	+	2	607	c.316A>T	c.(316-318)AGC>TGC	p.S106C	PLCL1_uc002uuv.3_Missense_Mutation_p.S27C	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	106	Interaction with PPP1C.				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198948558	198948558	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198948558G>T	uc010fsp.2	+	2	608	c.317G>T	c.(316-318)AGC>ATC	p.S106I	PLCL1_uc002uuv.3_Missense_Mutation_p.S27I	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	106	Interaction with PPP1C.				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207174357	207174357	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207174357G>T	uc002vbp.2	+	5	5355	c.5105G>T	c.(5104-5106)AGC>ATC	p.S1702I		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1702							nucleic acid binding|zinc ion binding			ovary(3)	3																		---	---	---	---
ARPC2	10109	broad.mit.edu	37	2	219114582	219114582	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219114582C>T	uc002vhd.2	+	10	928	c.816C>T	c.(814-816)GAC>GAT	p.D272D	ARPC2_uc002vhe.2_Silent_p.D272D|ARPC2_uc002vhf.2_Silent_p.D158D	NM_152862	NP_690601	O15144	ARPC2_HUMAN	actin related protein 2/3 complex subunit 2	272					cellular component movement	Arp2/3 protein complex|cell projection|Golgi apparatus	actin binding|structural constituent of cytoskeleton			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)														---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15753730	15753730	+	Splice_Site	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15753730C>G	uc003caj.1	-	11	1244	c.1101_splice	c.e11-1	p.K367_splice	ANKRD28_uc003cai.1_Splice_Site_p.K213_splice|ANKRD28_uc011avz.1_Splice_Site_p.K213_splice|ANKRD28_uc003cak.1_Splice_Site|ANKRD28_uc011awa.1_Splice_Site|ANKRD28_uc003cal.1_Splice_Site_p.K397_splice|ANKRD28_uc003cam.2_Splice_Site_p.K400_splice	NM_015199	NP_056014			ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
STAC	6769	broad.mit.edu	37	3	36422169	36422169	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36422169G>T	uc003cgh.1	+	1	73	c.34G>T	c.(34-36)GTG>TTG	p.V12L	STAC_uc010hgd.1_RNA|STAC_uc011aya.1_Missense_Mutation_p.V12L	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	12					intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37514835	37514835	+	Intron	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37514835C>G	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
CTNNB1	1499	broad.mit.edu	37	3	41266551	41266551	+	Silent	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41266551T>C	uc010hia.1	+	5	504	c.348T>C	c.(346-348)GCT>GCC	p.A116A	CTNNB1_uc003ckp.2_Silent_p.A116A|CTNNB1_uc003ckq.2_Silent_p.A116A|CTNNB1_uc003ckr.2_Silent_p.A116A|CTNNB1_uc011azf.1_Silent_p.A109A|CTNNB1_uc011azg.1_Silent_p.A44A|uc010hib.1_5'Flank	NM_001904	NP_001895	P35222	CTNB1_HUMAN	beta-catenin	116					adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding	p.A5_Q143del(7)|p.Q28_H134del(5)|p.W25_I140del(4)|p.T3_A126del(2)|p.V22_L139>V(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A20_Q143del(1)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S23_I140del(1)|p.A20_R151del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.D6_K133del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.D17_P128del(1)|p.H24_M131del(1)|p.A5_D144>D(1)|p.L7_I140del(1)|p.K19_Y142>V(1)|p.D17_A126del(1)|p.A20_L148del(1)|p.E9_I140del(1)|p.P16_K133del(1)|p.D6_I140del(1)|p.Q28_I140del(1)	CTNNB1/PLAG1(60)	liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1)	3166				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	Lithium(DB01356)		15	H|Mis|T	PLAG1	colorectal|cvarian| hepatoblastoma|others|pleomorphic salivary adenoma				Pilomatrixoma_Familial_Clustering_of				---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57893674	57893674	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57893674A>T	uc003dje.1	+	16	1719	c.1514A>T	c.(1513-1515)GAA>GTA	p.E505V	SLMAP_uc003djd.1_Missense_Mutation_p.E488V|SLMAP_uc003djf.1_Missense_Mutation_p.E467V|SLMAP_uc003djg.1_Missense_Mutation_p.E99V|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Missense_Mutation_p.E39V|SLMAP_uc003djh.2_Intron|SLMAP_uc003dji.1_Missense_Mutation_p.E39V|SLMAP_uc011bfb.1_Missense_Mutation_p.E39V|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	505	Cytoplasmic (Potential).|Potential.				muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)														---	---	---	---
FAM3D	131177	broad.mit.edu	37	3	58639429	58639429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58639429C>T	uc003dkq.2	-	3	390	c.93G>A	c.(91-93)ATG>ATA	p.M31I		NM_138805	NP_620160	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	31					negative regulation of insulin secretion	extracellular region	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)														---	---	---	---
BOC	91653	broad.mit.edu	37	3	112987223	112987223	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112987223C>G	uc003dzx.2	+	5	1075	c.454C>G	c.(454-456)CTG>GTG	p.L152V	BOC_uc010hqi.2_Missense_Mutation_p.L152V|BOC_uc003dzy.2_Missense_Mutation_p.L152V|BOC_uc003dzz.2_Missense_Mutation_p.L152V|BOC_uc003eab.2_5'Flank	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	152	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)															---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130284398	130284398	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130284398C>T	uc010htl.2	+	3	1253	c.1222C>T	c.(1222-1224)CGG>TGG	p.R408W		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	408	Nonhelical region.|VWFA 2.				axon guidance|cell adhesion	collagen		p.R408W(1)		ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
AMOTL2	51421	broad.mit.edu	37	3	134079212	134079212	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134079212G>A	uc003eqf.2	-	7	1910	c.1793C>T	c.(1792-1794)TCT>TTT	p.S598F	AMOTL2_uc003eqg.1_Missense_Mutation_p.S540F|AMOTL2_uc003eqh.1_Missense_Mutation_p.S538F|AMOTL2_uc003eqe.1_Missense_Mutation_p.S165F	NM_016201	NP_057285	Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	540	Potential.									large_intestine(1)	1																		---	---	---	---
CHST2	9435	broad.mit.edu	37	3	142841218	142841218	+	Silent	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142841218C>A	uc003evm.2	+	2	2449	c.1560C>A	c.(1558-1560)CTC>CTA	p.L520L		NM_004267	NP_004258	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O)	520	Lumenal (Potential).			L->A: Has weak or no effect.	inflammatory response|multicellular organismal development|N-acetylglucosamine metabolic process|sulfur compound metabolic process	integral to membrane|intrinsic to Golgi membrane|trans-Golgi network	N-acetylglucosamine 6-O-sulfotransferase activity			ovary(3)	3																		---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157921023	157921023	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157921023C>T	uc003fbt.2	+	4	594	c.483C>T	c.(481-483)AAC>AAT	p.N161N	RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Silent_p.N161N|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	161					nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
GABRB1	2560	broad.mit.edu	37	4	47163485	47163485	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47163485C>T	uc003gxh.2	+	4	834	c.460C>T	c.(460-462)CGA>TGA	p.R154*	GABRB1_uc011bze.1_Nonsense_Mutation_p.R84*	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	154	Extracellular (Probable).				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)													---	---	---	---
ABCG2	9429	broad.mit.edu	37	4	89039279	89039279	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89039279C>G	uc003hrg.2	-	7	1316	c.823G>C	c.(823-825)GGA>CGA	p.G275R	ABCG2_uc003hrh.2_Missense_Mutation_p.G275R|ABCG2_uc003hrf.2_Missense_Mutation_p.G145R	NM_004827	NP_004818	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G, member 2	275	ABC transporter.|Cytoplasmic (Potential).				cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)													---	---	---	---
ARSJ	79642	broad.mit.edu	37	4	114824822	114824822	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114824822T>C	uc003ibq.1	-	2	1296	c.408A>G	c.(406-408)ATA>ATG	p.I136M	ARSJ_uc010imu.1_Missense_Mutation_p.I136M|ARSJ_uc010imv.1_Translation_Start_Site	NM_024590	NP_078866	Q5FYB0	ARSJ_HUMAN	arylsulfatase J precursor	136						extracellular region	arylsulfatase activity|metal ion binding			ovary(1)	1		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)														---	---	---	---
IRX4	50805	broad.mit.edu	37	5	1880949	1880949	+	Splice_Site	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1880949C>T	uc003jcz.2	-	3	417	c.298_splice	c.e3-1	p.N100_splice	IRX4_uc011cmf.1_Splice_Site	NM_016358	NP_057442			iroquois homeobox 4						heart development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(108;0.242)														---	---	---	---
PRLR	5618	broad.mit.edu	37	5	35086349	35086349	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35086349C>A	uc003jjm.2	-	4	694	c.164G>T	c.(163-165)GGA>GTA	p.G55V	PRLR_uc003jjg.1_Missense_Mutation_p.G55V|PRLR_uc003jjh.1_Missense_Mutation_p.G55V|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Missense_Mutation_p.G55V|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_Intron|PRLR_uc010iuw.1_5'UTR	NM_000949	NP_000940	P16471	PRLR_HUMAN	prolactin receptor precursor	55	Fibronectin type-III 1.|Extracellular (Potential).				activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	36976155	36976155	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36976155T>A	uc003jkl.3	+	9	1645	c.1146T>A	c.(1144-1146)AAT>AAA	p.N382K	NIPBL_uc003jkk.3_Missense_Mutation_p.N382K|NIPBL_uc003jkm.1_Missense_Mutation_p.N261K	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	382					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
F2RL1	2150	broad.mit.edu	37	5	76129558	76129558	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76129558T>G	uc003keo.2	+	2	1301	c.1126T>G	c.(1126-1128)TCA>GCA	p.S376A		NM_005242	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1	376	Cytoplasmic (Potential).				blood coagulation|elevation of cytosolic calcium ion concentration|positive regulation of leukocyte chemotaxis|positive regulation of positive chemotaxis|regulation of blood coagulation	Golgi apparatus|integral to plasma membrane	receptor binding|thrombin receptor activity			central_nervous_system(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)														---	---	---	---
BHMT	635	broad.mit.edu	37	5	78421938	78421938	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78421938A>G	uc003kfu.3	+	6	800	c.695A>G	c.(694-696)AAG>AGG	p.K232R	BHMT_uc011cti.1_Missense_Mutation_p.K79R	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase	232	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)													---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79809578	79809578	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79809578G>C	uc003kgv.1	+	3	450	c.307G>C	c.(307-309)GAT>CAT	p.D103H	FAM151B_uc010jal.1_RNA	NM_205548	NP_991111	Q6UXP7	F151B_HUMAN	hypothetical protein LOC167555	103											0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90077349	90077349	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90077349C>T	uc003kju.2	+	65	13281	c.13185C>T	c.(13183-13185)AAC>AAT	p.N4395N	GPR98_uc003kjt.2_Silent_p.N2101N|GPR98_uc003kjw.2_Silent_p.N56N	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4395	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98239575	98239575	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98239575C>A	uc003knf.2	-	3	441	c.293G>T	c.(292-294)AGA>ATA	p.R98I		NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	98					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
PPIP5K2	23262	broad.mit.edu	37	5	102537312	102537312	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102537312A>T	uc003kod.3	+	31	4228	c.3709A>T	c.(3709-3711)AAA>TAA	p.K1237*	PPIP5K2_uc011cva.1_RNA|PPIP5K2_uc003koe.2_Nonsense_Mutation_p.K1216*|PPIP5K2_uc003kof.2_Nonsense_Mutation_p.K419*	NM_015216	NP_056031	O43314	VIP2_HUMAN	Histidine acid phosphatase domain containing 1	1237					inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2																		---	---	---	---
WDR36	134430	broad.mit.edu	37	5	110462553	110462553	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110462553T>A	uc003kpd.2	+	23	2945	c.2828T>A	c.(2827-2829)TTA>TAA	p.L943*	WDR36_uc010jbu.2_RNA	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	943					response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)|skin(1)	2		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130797632	130797632	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130797632C>T	uc003kvn.1	-	19	2836	c.2630G>A	c.(2629-2631)CGT>CAT	p.R877H	RAPGEF6_uc003kvp.1_Missense_Mutation_p.R927H|RAPGEF6_uc003kvo.1_Missense_Mutation_p.R882H|RAPGEF6_uc010jdi.1_Missense_Mutation_p.R877H|RAPGEF6_uc010jdj.1_Missense_Mutation_p.R877H|RAPGEF6_uc003kvq.2_Missense_Mutation_p.R594H|RAPGEF6_uc003kvr.2_Missense_Mutation_p.R877H|RAPGEF6_uc011cxe.1_RNA	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	877	Ras-GEF.				Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
NRG2	9542	broad.mit.edu	37	5	139231193	139231193	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139231193C>T	uc003lex.1	-	9	1993	c.1768G>A	c.(1768-1770)GAG>AAG	p.E590K	NRG2_uc003lev.1_Missense_Mutation_p.E598K|NRG2_uc003lew.1_Missense_Mutation_p.E592K|NRG2_uc003ley.1_Missense_Mutation_p.E584K	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1	590	Cytoplasmic (Potential).				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
LARS	51520	broad.mit.edu	37	5	145557164	145557164	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145557164C>A	uc003lnx.1	-	2	309	c.71G>T	c.(70-72)TGG>TTG	p.W24L	LARS_uc011dbq.1_Missense_Mutation_p.W24L|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Missense_Mutation_p.W24L	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	24					leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)													---	---	---	---
ADAMTS2	9509	broad.mit.edu	37	5	178770929	178770929	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178770929G>A	uc003mjw.2	-	2	373	c.373C>T	c.(373-375)CGG>TGG	p.R125W	ADAMTS2_uc011dgm.1_Missense_Mutation_p.R125W	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	125					collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)														---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10621657	10621657	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10621657C>G	uc010joo.2	+	4	1550	c.999C>G	c.(997-999)GAC>GAG	p.D333E	GCNT2_uc010jol.2_Missense_Mutation_p.D47E|GCNT2_uc010jom.2_RNA|GCNT2_uc010jop.2_RNA|GCNT2_uc003mza.2_RNA|GCNT2_uc003mzc.3_Missense_Mutation_p.D332E|GCNT2_uc003mzd.2_Missense_Mutation_p.D331E|GCNT2_uc003mze.2_Missense_Mutation_p.D333E	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,	333	Lumenal (Potential).					Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)														---	---	---	---
NUP153	9972	broad.mit.edu	37	6	17637500	17637500	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17637500G>A	uc003ncd.1	-	16	2548	c.2348C>T	c.(2347-2349)ACC>ATC	p.T783I	NUP153_uc011dje.1_Missense_Mutation_p.T814I|NUP153_uc010jpl.1_Missense_Mutation_p.T741I	NM_005124	NP_005115	P49790	NU153_HUMAN	nucleoporin 153kDa	783					carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(4)|ovary(2)|breast(2)|skin(1)	9	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)															---	---	---	---
HIST1H2AC	8334	broad.mit.edu	37	6	26124625	26124625	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26124625G>A	uc003ngm.2	+	1	253	c.165G>A	c.(163-165)GTG>GTA	p.V55V	HIST1H2BC_uc003ngk.3_5'Flank|HIST1H2BC_uc003ngl.2_5'Flank|HIST1H2AC_uc003ngn.2_RNA|HIST1H2AC_uc003ngo.2_RNA|HIST1H2AC_uc003ngp.2_Silent_p.V55V	NM_003512	NP_003503	Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	55					nucleosome assembly	nucleosome|nucleus	DNA binding				0																		---	---	---	---
OR2B2	81697	broad.mit.edu	37	6	27880064	27880064	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27880064A>T	uc011dkw.1	-	1	34	c.34T>A	c.(34-36)TTC>ATC	p.F12I		NM_033057	NP_149046	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B,	12	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
C6orf27	80737	broad.mit.edu	37	6	31742299	31742299	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31742299G>T	uc011dog.1	-	5	953	c.715C>A	c.(715-717)CCT>ACT	p.P239T	C6orf27_uc003nxd.2_5'UTR|C6orf27_uc011doh.1_RNA	NM_025258	NP_079534	Q9Y334	G7C_HUMAN	G7c protein precursor	239						extracellular region				ovary(3)	3																		---	---	---	---
KIFC1	3833	broad.mit.edu	37	6	33372693	33372693	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33372693A>G	uc003oef.3	+	7	1271	c.821A>G	c.(820-822)CAG>CGG	p.Q274R	KIFC1_uc011drf.1_Missense_Mutation_p.Q266R	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1	274	Potential.				blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0																		---	---	---	---
TTBK1	84630	broad.mit.edu	37	6	43251905	43251905	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43251905C>A	uc003ouq.1	+	14	3706	c.3427C>A	c.(3427-3429)CCC>ACC	p.P1143T		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1143						cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)															---	---	---	---
CD109	135228	broad.mit.edu	37	6	74520793	74520793	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74520793G>A	uc003php.2	+	28	4050	c.3625G>A	c.(3625-3627)GTG>ATG	p.V1209M	CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Missense_Mutation_p.V1209M|CD109_uc010kba.2_Missense_Mutation_p.V1132M	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor	1209						anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
PHACTR2	9749	broad.mit.edu	37	6	144074962	144074962	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144074962G>A	uc003qjq.3	+	4	464	c.334G>A	c.(334-336)GAG>AAG	p.E112K	PHACTR2_uc010khh.2_Missense_Mutation_p.E112K|PHACTR2_uc010khi.2_Missense_Mutation_p.E123K|PHACTR2_uc003qjr.3_Missense_Mutation_p.E123K	NM_014721	NP_055536	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2 isoform 3	112							actin binding|protein phosphatase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152642453	152642453	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152642453A>C	uc010kiw.2	-	84	16758	c.16156T>G	c.(16156-16158)TTA>GTA	p.L5386V	SYNE1_uc010kiv.2_5'Flank|SYNE1_uc003qos.3_5'Flank|SYNE1_uc003qot.3_Missense_Mutation_p.L5315V|SYNE1_uc003qou.3_Missense_Mutation_p.L5386V|SYNE1_uc010kiz.2_Missense_Mutation_p.L1141V	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5386	Potential.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
MMD2	221938	broad.mit.edu	37	7	4949577	4949577	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4949577T>C	uc003sno.3	-	6	740	c.544A>G	c.(544-546)AAG>GAG	p.K182E	MMD2_uc003snl.1_RNA|MMD2_uc003snn.3_Missense_Mutation_p.K158E|MMD2_uc010ksq.2_Missense_Mutation_p.K158E	NM_001100600	NP_001094070	Q8IY49	PAQRA_HUMAN	monocyte to macrophage	182	Cytoplasmic (Potential).					integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)														---	---	---	---
DGKB	1607	broad.mit.edu	37	7	14775719	14775719	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14775719T>G	uc003ssz.2	-	4	456	c.269A>C	c.(268-270)AAG>ACG	p.K90T	DGKB_uc011jxt.1_Missense_Mutation_p.K83T|DGKB_uc003sta.2_Missense_Mutation_p.K90T|DGKB_uc011jxu.1_Missense_Mutation_p.K90T|DGKB_uc011jxv.1_Missense_Mutation_p.K90T	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1	90					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	38398218	38398218	+	Intron	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38398218T>C	uc003tgp.1	+						uc003tgr.2_Silent_p.P83P					Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																														---	---	---	---
URGCP	55665	broad.mit.edu	37	7	43916920	43916920	+	Silent	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43916920C>G	uc003tiw.2	-	6	2199	c.2142G>C	c.(2140-2142)GGG>GGC	p.G714G	URGCP_uc003tiu.2_Silent_p.G671G|URGCP_uc003tiv.2_Silent_p.G639G|URGCP_uc003tix.2_Silent_p.G705G|URGCP_uc003tiy.2_Silent_p.G671G|URGCP_uc003tiz.2_Silent_p.G671G|URGCP_uc011kbj.1_Silent_p.G671G	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	714					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72891508	72891508	+	Silent	SNP	T	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72891508T>A	uc003tyc.2	-	7	2628	c.2283A>T	c.(2281-2283)TCA>TCT	p.S761S		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	761					ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
GPC2	221914	broad.mit.edu	37	7	99773523	99773523	+	Intron	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99773523G>A	uc003utv.2	-						GPC2_uc010lgr.2_Intron|GPC2_uc003utw.1_Intron|STAG3_uc010lgs.1_5'Flank|STAG3_uc003utx.1_5'Flank|STAG3_uc011kjk.1_5'Flank	NM_152742	NP_689955			glypican 2 precursor							anchored to membrane|endoplasmic reticulum|extracellular space|plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)|pancreas(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
FEZF1	389549	broad.mit.edu	37	7	121943235	121943235	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121943235G>C	uc003vkd.2	-	2	1006	c.932C>G	c.(931-933)ACG>AGG	p.T311R	FEZF1_uc003vkc.2_Missense_Mutation_p.T261R|uc010lko.1_5'Flank|uc003vkf.1_5'Flank	NM_001024613	NP_001019784	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1 isoform 1	311					cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3																		---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126086318	126086318	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126086318G>T	uc003vlr.2	-	9	2850	c.2539C>A	c.(2539-2541)CAG>AAG	p.Q847K	GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Missense_Mutation_p.Q847K|GRM8_uc010lkz.1_RNA	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	847	Cytoplasmic (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
MGAM	8972	broad.mit.edu	37	7	141759688	141759688	+	Silent	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141759688T>C	uc003vwy.2	+	33	4035	c.3981T>C	c.(3979-3981)CCT>CCC	p.P1327P		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	1327	Glucoamylase.|Lumenal (Potential).				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)													---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	147844629	147844629	+	Silent	SNP	A	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147844629A>G	uc003weu.1	+	17	3117	c.2601A>G	c.(2599-2601)GTA>GTG	p.V867V		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	867	Laminin G-like 3.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151859545	151859545	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151859545T>C	uc003wla.2	-	43	11336	c.11117A>G	c.(11116-11118)AAG>AGG	p.K3706R	MLL3_uc003wkz.2_Missense_Mutation_p.K2767R|MLL3_uc003wky.2_Missense_Mutation_p.K1215R	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3706					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)				N		medulloblastoma								---	---	---	---
ANK1	286	broad.mit.edu	37	8	41554006	41554006	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41554006C>T	uc003xok.2	-	26	2919	c.2835G>A	c.(2833-2835)GCG>GCA	p.A945A	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Silent_p.A261A|ANK1_uc003xoi.2_Silent_p.A945A|ANK1_uc003xoj.2_Silent_p.A945A|ANK1_uc003xol.2_Silent_p.A945A|ANK1_uc003xom.2_Silent_p.A986A	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	945	ZU5.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77618385	77618385	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77618385C>T	uc003yav.2	+	2	2449	c.2062C>T	c.(2062-2064)CGG>TGG	p.R688W	ZFHX4_uc003yat.1_Missense_Mutation_p.R688W|ZFHX4_uc003yau.1_Missense_Mutation_p.R688W|ZFHX4_uc003yaw.1_Missense_Mutation_p.R688W	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	688						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)												HNSCC(33;0.089)			---	---	---	---
PTDSS1	9791	broad.mit.edu	37	8	97321806	97321806	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97321806C>T	uc003yht.1	+	9	1131	c.1029C>T	c.(1027-1029)ACC>ACT	p.T343T	PTDSS1_uc003yhu.1_Silent_p.T197T	NM_014754	NP_055569	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	343					phosphatidylserine biosynthetic process	integral to membrane	transferase activity			ovary(1)	1	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)													---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110467013	110467013	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110467013G>A	uc003yne.2	+	45	6910	c.6806G>A	c.(6805-6807)CGA>CAA	p.R2269Q		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2269	Extracellular (Potential).|G8 1.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	286547	286547	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:286547G>A	uc003zgf.2	+	3	355	c.243G>A	c.(241-243)CAG>CAA	p.Q81Q	DOCK8_uc011lls.1_Silent_p.Q81Q|DOCK8_uc010mgu.2_5'UTR|DOCK8_uc010mgv.2_Silent_p.Q13Q|DOCK8_uc010mgt.2_Silent_p.Q13Q|DOCK8_uc003zgg.2_Silent_p.Q13Q|DOCK8_uc003zgh.2_RNA	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	81					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)														---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8518422	8518422	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8518422G>A	uc003zkk.2	-	20	1680	c.969C>T	c.(967-969)CCC>CCT	p.P323P	PTPRD_uc003zkp.2_Silent_p.P323P|PTPRD_uc003zkq.2_Silent_p.P323P|PTPRD_uc003zkr.2_Silent_p.P317P|PTPRD_uc003zks.2_Silent_p.P313P|PTPRD_uc003zkl.2_Silent_p.P323P|PTPRD_uc003zkm.2_Silent_p.P310P|PTPRD_uc003zkn.2_Silent_p.P323P|PTPRD_uc003zko.2_Silent_p.P320P	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	323	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)			---	---	---	---
FAM108B1	51104	broad.mit.edu	37	9	74485012	74485012	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74485012C>T	uc004aim.1	-	3	1236	c.634G>A	c.(634-636)GAT>AAT	p.D212N	FAM108B1_uc004ail.2_Missense_Mutation_p.D212N	NM_001025780	NP_001020951	Q5VST6	F108B_HUMAN	family with sequence similarity 108, member B1	212						extracellular region	hydrolase activity				0																		---	---	---	---
UBQLN1	29979	broad.mit.edu	37	9	86279967	86279967	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86279967C>A	uc004amv.2	-	9	2000	c.1426G>T	c.(1426-1428)GAA>TAA	p.E476*	UBQLN1_uc004amw.2_Nonsense_Mutation_p.E448*	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1	476					apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0																		---	---	---	---
FAM22G	441457	broad.mit.edu	37	9	99699543	99699543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99699543C>T	uc004awq.1	+	5	1895	c.1180C>T	c.(1180-1182)CAC>TAC	p.H394Y	HIATL2_uc004awr.1_Intron	NM_001045477	NP_001038942	Q5VZR2	FA22G_HUMAN	hypothetical protein LOC441457	394										skin(1)	1		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
RNF20	56254	broad.mit.edu	37	9	104324258	104324258	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104324258G>A	uc004bbn.2	+	19	2806	c.2716G>A	c.(2716-2718)GAT>AAT	p.D906N		NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20	906					histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)														---	---	---	---
PSMD5	5711	broad.mit.edu	37	9	123605197	123605197	+	5'UTR	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123605197C>A	uc004bko.2	-	1					PSMD5_uc011lye.1_5'UTR|LOC253039_uc004bkq.2_5'Flank|LOC253039_uc004bkp.2_5'Flank	NM_005047	NP_005038			proteasome 26S non-ATPase subunit 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding				0																		---	---	---	---
OR1K1	392392	broad.mit.edu	37	9	125562861	125562861	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125562861C>A	uc011lze.1	+	1	460	c.460C>A	c.(460-462)CAC>AAC	p.H154N		NM_080859	NP_543135	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K,	154	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
MRPS2	51116	broad.mit.edu	37	9	138395625	138395625	+	Silent	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138395625G>C	uc004cfv.3	+	4	611	c.537G>C	c.(535-537)GCG>GCC	p.A179A	MRPS2_uc004cfw.3_Silent_p.A89A|MRPS2_uc004cfx.3_Silent_p.A94A|MRPS2_uc010nat.2_Silent_p.A160A|uc004cfy.2_Intron	NM_016034	NP_057118	Q9Y399	RT02_HUMAN	mitochondrial ribosomal protein S2	179					translation	mitochondrion|small ribosomal subunit	structural constituent of ribosome				0				OV - Ovarian serous cystadenocarcinoma(145;1.46e-53)|Epithelial(140;2.04e-47)|all cancers(34;1.23e-42)														---	---	---	---
AKR1C1	1645	broad.mit.edu	37	10	5014928	5014928	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5014928G>C	uc001iho.2	+	12	1674	c.833G>C	c.(832-834)AGA>ACA	p.R278T	AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C1_uc001ihq.2_Missense_Mutation_p.R278T	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	278	NADP (By similarity).				bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)													---	---	---	---
PPYR1	5540	broad.mit.edu	37	10	47087175	47087175	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47087175C>T	uc001jee.2	+	3	811	c.392C>T	c.(391-393)TCG>TTG	p.S131L	ANXA8_uc001jed.3_Intron|PPYR1_uc009xna.2_Missense_Mutation_p.S131L	NM_005972	NP_005963	P50391	NPY4R_HUMAN	pancreatic polypeptide receptor 1	131	Helical; Name=3; (Potential).				blood circulation|digestion|feeding behavior	integral to plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78771724	78771724	+	Splice_Site	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78771724C>T	uc001jxn.2	-	18	2269	c.2092_splice	c.e18+1	p.P698_splice	KCNMA1_uc001jxj.2_Splice_Site_p.L702_splice|KCNMA1_uc001jxk.1_Splice_Site_p.R313_splice|KCNMA1_uc009xrt.1_Splice_Site_p.L518_splice|KCNMA1_uc001jxl.1_Splice_Site_p.L352_splice|KCNMA1_uc001jxo.2_Splice_Site_p.L698_splice|KCNMA1_uc001jxm.2_Splice_Site_p.L698_splice|KCNMA1_uc001jxq.2_Splice_Site_p.L698_splice	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
CYP26A1	1592	broad.mit.edu	37	10	94834977	94834977	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94834977G>A	uc001kil.2	+	4	822	c.777G>A	c.(775-777)CGG>CGA	p.R259R	CYP26A1_uc001kik.1_Silent_p.R190R|CYP26A1_uc001kim.1_Silent_p.R157R	NM_000783	NP_000774	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A,	259					negative regulation of retinoic acid receptor signaling pathway|retinoic acid catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|oxygen binding|retinoic acid 4-hydroxylase activity|retinoic acid binding			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		Colorectal(252;0.122)																---	---	---	---
FAM178A	55719	broad.mit.edu	37	10	102703877	102703877	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102703877G>A	uc001krt.3	+	12	3291	c.2749G>A	c.(2749-2751)GTG>ATG	p.V917M	FAM178A_uc001krs.2_Missense_Mutation_p.V917M	NM_018121	NP_060591	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 1	917											0																		---	---	---	---
OR4C13	283092	broad.mit.edu	37	11	49974747	49974747	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49974747G>C	uc010rhz.1	+	1	773	c.773G>C	c.(772-774)AGA>ACA	p.R258T		NM_001001955	NP_001001955	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C,	258	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(1)	4																		---	---	---	---
PATL1	219988	broad.mit.edu	37	11	59406668	59406668	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59406668G>T	uc001noe.3	-	18	2287	c.2144C>A	c.(2143-2145)ACG>AAG	p.T715K		NM_152716	NP_689929	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog	715	Region C.				cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
NRXN2	9379	broad.mit.edu	37	11	64453188	64453188	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64453188A>T	uc001oar.2	-	7	1521	c.1082T>A	c.(1081-1083)GTG>GAG	p.V361E	NRXN2_uc001oas.2_Missense_Mutation_p.V337E|NRXN2_uc001oaq.2_Missense_Mutation_p.V35E	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10																		---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107965631	107965631	+	Silent	SNP	T	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107965631T>C	uc001pjv.2	+	15	2327	c.1660T>C	c.(1660-1662)TTG>CTG	p.L554L	CUL5_uc001pju.2_RNA	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing	554					cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
DLAT	1737	broad.mit.edu	37	11	111896309	111896309	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111896309C>T	uc001pmo.2	+	1	772	c.113C>T	c.(112-114)TCT>TTT	p.S38F	DLAT_uc009yyk.1_Missense_Mutation_p.S38F|DLAT_uc010rwr.1_Missense_Mutation_p.S38F	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor	38					glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)													---	---	---	---
ITGB7	3695	broad.mit.edu	37	12	53587133	53587133	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53587133C>T	uc009zmv.2	-	11	1588	c.1517G>A	c.(1516-1518)CGC>CAC	p.R506H	ITGB7_uc001scc.2_Missense_Mutation_p.R506H|ITGB7_uc010snz.1_Intron	NM_000889	NP_000880	P26010	ITB7_HUMAN	integrin, beta 7 precursor	506	Cysteine-rich tandem repeats.|Extracellular (Potential).|I.				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|regulation of immune response	integrin complex	identical protein binding|metal ion binding|receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|breast(1)	8																		---	---	---	---
PCBP2	5094	broad.mit.edu	37	12	53861060	53861060	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53861060G>C	uc001sdl.3	+	11	1132	c.782G>C	c.(781-783)GGC>GCC	p.G261A	PCBP2_uc001sdc.3_Missense_Mutation_p.G261A|PCBP2_uc001sdb.3_Missense_Mutation_p.G257A|PCBP2_uc001sde.3_Missense_Mutation_p.G257A|PCBP2_uc001sdi.3_Missense_Mutation_p.G230A|PCBP2_uc001sdd.3_Missense_Mutation_p.G226A|PCBP2_uc001sdf.3_Missense_Mutation_p.G226A|PCBP2_uc009zna.2_Missense_Mutation_p.G218A|PCBP2_uc010soi.1_Missense_Mutation_p.G11A|PCBP2_uc001sdj.3_Missense_Mutation_p.G11A|PCBP2_uc010soj.1_Missense_Mutation_p.G11A|PCBP2_uc001sdk.3_Missense_Mutation_p.G46A|PCBP2_uc010soh.1_Missense_Mutation_p.G257A	NM_001128911	NP_001122383	Q15366	PCBP2_HUMAN	poly(rC) binding protein 2 isoform d	261					innate immune response|negative regulation of defense response to virus|negative regulation of type I interferon production|nuclear mRNA splicing, via spliceosome|proteasomal ubiquitin-dependent protein catabolic process|response to virus	cytosol|nucleoplasm|ribonucleoprotein complex	DNA binding|RNA binding|ubiquitin protein ligase binding				0																		---	---	---	---
TPH2	121278	broad.mit.edu	37	12	72388269	72388269	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72388269A>C	uc009zrw.1	+	8	1133	c.992A>C	c.(991-993)AAG>ACG	p.K331T	TPH2_uc001swy.2_Missense_Mutation_p.K241T	NM_173353	NP_775489	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	331					aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)|skin(1)	4					L-Tryptophan(DB00150)													---	---	---	---
E2F7	144455	broad.mit.edu	37	12	77444344	77444344	+	Intron	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77444344G>C	uc001sym.3	-						E2F7_uc001syn.2_Intron	NM_203394	NP_976328			E2F transcription factor 7						cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104153051	104153051	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104153051G>A	uc001tjw.2	+	65	7434	c.7248G>A	c.(7246-7248)CCG>CCA	p.P2416P	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	2416	Extracellular (Potential).|FAS1 7.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121879985	121879985	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121879985G>C	uc001uat.2	-	19	3363	c.3259C>G	c.(3259-3261)CGG>GGG	p.R1087G	KDM2B_uc001uaq.2_Missense_Mutation_p.R527G|KDM2B_uc010szy.1_Missense_Mutation_p.R527G|KDM2B_uc001uar.2_Missense_Mutation_p.R678G|KDM2B_uc001uas.2_Missense_Mutation_p.R1018G|KDM2B_uc001uau.2_Intron|KDM2B_uc001uao.2_Missense_Mutation_p.R335G|KDM2B_uc010szx.1_Missense_Mutation_p.R335G|KDM2B_uc001uap.2_RNA	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	1087	F-box.				embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
ANKLE2	23141	broad.mit.edu	37	12	133313601	133313601	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133313601T>A	uc001ukx.2	-	8	1538	c.1471A>T	c.(1471-1473)ATC>TTC	p.I491F	ANKLE2_uc009zyw.1_5'Flank|ANKLE2_uc001uky.3_Missense_Mutation_p.I429F	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	491						cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20637013	20637013	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20637013G>A	uc001umr.2	+	19	3237	c.2939G>A	c.(2938-2940)GGT>GAT	p.G980D	ZMYM2_uc001ums.2_Missense_Mutation_p.G980D|ZMYM2_uc001umt.2_Missense_Mutation_p.G980D|ZMYM2_uc001umv.2_Missense_Mutation_p.G360D|ZMYM2_uc001umw.2_Missense_Mutation_p.G433D	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	980					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
DZIP1	22873	broad.mit.edu	37	13	96251648	96251648	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96251648G>C	uc001vmk.2	-	15	2360	c.1508C>G	c.(1507-1509)CCA>CGA	p.P503R	DZIP1_uc001vmj.2_5'UTR|DZIP1_uc001vml.2_Missense_Mutation_p.P484R	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2	503					germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)															---	---	---	---
RTN1	6252	broad.mit.edu	37	14	60212479	60212479	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60212479G>A	uc001xen.1	-	2	1171	c.962C>T	c.(961-963)TCG>TTG	p.S321L		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	321					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)														---	---	---	---
SIX4	51804	broad.mit.edu	37	14	61190681	61190681	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61190681C>T	uc001xfc.2	-	1	112	c.112G>A	c.(112-114)GGC>AGC	p.G38S	SIX4_uc010app.1_Missense_Mutation_p.G30S	NM_017420	NP_059116	Q9UIU6	SIX4_HUMAN	sine oculis homeobox homolog 4	38	Ala-rich.					nucleus				breast(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0275)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71524358	71524358	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71524358C>T	uc001xmo.2	+	26	5215	c.4769C>T	c.(4768-4770)TCT>TTT	p.S1590F	PCNX_uc010are.1_Missense_Mutation_p.S1479F|PCNX_uc010arf.1_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	1590						integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
TDP1	55775	broad.mit.edu	37	14	90509472	90509472	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90509472G>A	uc001xxy.2	+	17	2111	c.1812G>A	c.(1810-1812)ATG>ATA	p.M604I	TDP1_uc010atm.2_RNA|TDP1_uc001xxz.2_Missense_Mutation_p.M604I|TDP1_uc010atn.2_3'UTR|TDP1_uc001xya.2_Missense_Mutation_p.M365I|TDP1_uc001xyb.2_RNA|TDP1_uc010ato.2_Missense_Mutation_p.C568Y	NM_018319	NP_060789	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	604					cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)									Repair_of_DNA-protein_crosslinks					---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27572153	27572153	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27572153C>T	uc001zbg.1	+	4	634	c.468C>T	c.(466-468)GAC>GAT	p.D156D	GABRG3_uc001zbf.2_Silent_p.D156D	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma	156	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
FSIP1	161835	broad.mit.edu	37	15	40056058	40056058	+	Missense_Mutation	SNP	A	T	T	rs138828157	by1000genomes	TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40056058A>T	uc001zki.2	-	5	741	c.523T>A	c.(523-525)TTT>ATT	p.F175I		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	175										ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)														---	---	---	---
IVD	3712	broad.mit.edu	37	15	40699917	40699917	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40699917G>A	uc001zls.3	+	2	568	c.234G>A	c.(232-234)AAG>AAA	p.K78K	IVD_uc001zlq.2_Intron	NM_002225	NP_002216	P26440	IVD_HUMAN	isovaleryl Coenzyme A dehydrogenase isoform 1	75					leucine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|isovaleryl-CoA dehydrogenase activity			ovary(1)	1		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43281074	43281074	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43281074C>T	uc001zqq.2	-	35	4006	c.3940G>A	c.(3940-3942)GAT>AAT	p.D1314N		NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin	1314					cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
LYSMD2	256586	broad.mit.edu	37	15	52017075	52017075	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52017075C>T	uc002abi.2	-	2	1018	c.517G>A	c.(517-519)GAA>AAA	p.E173K	LYSMD2_uc002abj.2_Missense_Mutation_p.E82K	NM_153374	NP_699205	Q8IV50	LYSM2_HUMAN	LysM, putative peptidoglycan-binding, domain	173					cell wall macromolecule catabolic process						0				all cancers(107;0.00258)														---	---	---	---
MYO5A	4644	broad.mit.edu	37	15	52718164	52718164	+	Silent	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52718164G>T	uc002aby.2	-	4	562	c.318C>A	c.(316-318)GTC>GTA	p.V106V	MYO5A_uc002abx.3_Silent_p.V106V|MYO5A_uc010uge.1_5'UTR	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	106	Myosin head-like.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)														---	---	---	---
ADAMTS7	11173	broad.mit.edu	37	15	79068555	79068555	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79068555C>T	uc002bej.3	-	11	1892	c.1681G>A	c.(1681-1683)GCC>ACC	p.A561T	ADAMTS7_uc010und.1_Intron|ADAMTS7_uc002bek.1_Missense_Mutation_p.A561T	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	561	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
KCTD5	54442	broad.mit.edu	37	16	2732593	2732593	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2732593G>T	uc002crd.2	+	1	99	c.44G>T	c.(43-45)GGC>GTC	p.G15V		NM_018992	NP_061865	Q9NXV2	KCTD5_HUMAN	potassium channel tetramerisation domain	15					interspecies interaction between organisms	cytosol|nucleus|voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity				0																		---	---	---	---
RPAIN	84268	broad.mit.edu	37	17	5323593	5323593	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5323593G>A	uc002gbq.2	+	1	633	c.63G>A	c.(61-63)TGG>TGA	p.W21*	NUP88_uc002gbo.1_5'Flank|NUP88_uc010vsx.1_5'Flank|NUP88_uc010cle.1_5'Flank|NUP88_uc010vsy.1_5'Flank|RPAIN_uc010vsz.1_Nonsense_Mutation_p.W21*|RPAIN_uc002gbp.1_Missense_Mutation_p.E75K|RPAIN_uc010vta.1_Nonsense_Mutation_p.W21*|RPAIN_uc010vtb.1_Nonsense_Mutation_p.W21*|RPAIN_uc002gbs.2_Missense_Mutation_p.E75K|RPAIN_uc002gbt.2_Nonsense_Mutation_p.W21*|RPAIN_uc002gbu.2_Missense_Mutation_p.E75K|RPAIN_uc002gbv.2_RNA|RPAIN_uc002gbr.2_RNA|RPAIN_uc002gbw.2_Nonsense_Mutation_p.W21*	NM_001033002	NP_001028174	Q86UA6	RIP_HUMAN	RPA interacting protein isoform b	21					DNA recombination|DNA repair|DNA-dependent DNA replication|protein import into nucleus|response to UV	cytoplasm|cytoplasm|nucleolus|PML body|PML body	metal ion binding|protein complex binding				0																		---	---	---	---
TP53	7157	broad.mit.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	T	T	rs11540652		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577538C>T	uc002gim.2	-	7	937	c.743G>A	c.(742-744)CGG>CAG	p.R248Q	TP53_uc002gig.1_Missense_Mutation_p.R248Q|TP53_uc002gih.2_Missense_Mutation_p.R248Q|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116Q|TP53_uc010cng.1_Missense_Mutation_p.R116Q|TP53_uc002gii.1_Missense_Mutation_p.R116Q|TP53_uc010cnh.1_Missense_Mutation_p.R248Q|TP53_uc010cni.1_Missense_Mutation_p.R248Q|TP53_uc002gij.2_Missense_Mutation_p.R248Q|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R155Q|TP53_uc002gio.2_Missense_Mutation_p.R116Q	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	248	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (in a sporadic cancer; 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.R248Q(523)|p.R248W(443)|p.R248L(63)|p.R248P(12)|p.R248G(11)|p.R248R(10)|p.0?(7)|p.R155Q(4)|p.N247_R248delNR(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(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)		R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIN87_STOMACH)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NIHOVCAR3_OVARY)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(HCC70_BREAST)|R248Q(KYSE150_OESOPHAGUS)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PC14_LUNG)	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)			---	---	---	---
WDR16	146845	broad.mit.edu	37	17	9503508	9503508	+	Intron	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9503508G>T	uc002gly.2	+						WDR16_uc002glz.2_Intron|WDR16_uc010coc.2_Intron	NM_145054	NP_659491			WD40-repeat protein upregulated in HCC isoform							cytoplasm|intracellular membrane-bounded organelle	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
SREBF1	6720	broad.mit.edu	37	17	17718174	17718174	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17718174G>A	uc002gru.1	-	14	2771	c.2577C>T	c.(2575-2577)ATC>ATT	p.I859I	SREBF1_uc002gro.3_5'Flank|SREBF1_uc002grp.1_Silent_p.I478I|SREBF1_uc002grq.1_Silent_p.I378I|SREBF1_uc002grr.1_Silent_p.I605I|SREBF1_uc002grs.1_Silent_p.I835I|SREBF1_uc002grt.1_Silent_p.I889I|MIR33B_hsa-mir-33b|MI0003646_5'Flank	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription	859	Cytoplasmic (Potential).				cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1																		---	---	---	---
ALDH3A1	218	broad.mit.edu	37	17	19644420	19644420	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19644420T>G	uc010cqu.2	-	5	1123	c.793A>C	c.(793-795)AAG>CAG	p.K265Q	ALDH3A1_uc010vzd.1_Missense_Mutation_p.K265Q|ALDH3A1_uc002gwj.2_Missense_Mutation_p.K265Q|ALDH3A1_uc010cqv.2_Missense_Mutation_p.K265Q|ALDH3A1_uc002gwk.2_Missense_Mutation_p.K382Q|ALDH3A1_uc002gwl.1_Missense_Mutation_p.K192Q	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1	265					cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)													---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21319343	21319343	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21319343C>T	uc002gyv.1	+	3	1394	c.689C>T	c.(688-690)GCG>GTG	p.A230V		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	230	Cytoplasmic (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)										Prostate(3;0.18)			---	---	---	---
SLFN12	55106	broad.mit.edu	37	17	33738495	33738495	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33738495G>A	uc002hji.3	-	4	1976	c.1599C>T	c.(1597-1599)GCC>GCT	p.A533A	SLFN12_uc002hjj.3_Silent_p.A533A|SLFN12_uc010cts.2_Silent_p.A533A	NM_018042	NP_060512	Q8IYM2	SLN12_HUMAN	schlafen family member 12	533							ATP binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
SOX9	6662	broad.mit.edu	37	17	70119839	70119839	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70119839G>A	uc002jiw.2	+	3	1213	c.841G>A	c.(841-843)GAC>AAC	p.D281N	uc002jiv.2_5'Flank	NM_000346	NP_000337	P48436	SOX9_HUMAN	transcription factor SOX9	281					cAMP-mediated signaling|negative regulation of transcription, DNA-dependent|positive regulation of branching involved in ureteric bud morphogenesis|protein complex assembly|renal vesicle induction	nucleus|protein complex	core promoter sequence-specific DNA binding|enhancer binding|protein kinase A catalytic subunit binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription				0		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)															---	---	---	---
TBC1D16	125058	broad.mit.edu	37	17	77984139	77984139	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77984139C>A	uc002jxj.2	-	3	715	c.599G>T	c.(598-600)CGG>CTG	p.R200L		NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	200						intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78280179	78280179	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78280179C>G	uc002jyf.2	+	12	2481	c.2338C>G	c.(2338-2340)CAC>GAC	p.H780D	uc002jyg.1_Missense_Mutation_p.H511D	NM_020954	NP_066005			hypothetical protein LOC57714																														---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21114441	21114441	+	Missense_Mutation	SNP	G	A	A	rs113371321		TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21114441G>A	uc002kum.3	-	23	3834	c.3560C>T	c.(3559-3561)GCG>GTG	p.A1187V	NPC1_uc010dlu.1_5'Flank|NPC1_uc010xaz.1_Missense_Mutation_p.A920V	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	1187					autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
DSG4	147409	broad.mit.edu	37	18	28993403	28993403	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28993403G>C	uc002kwq.2	+	16	3103	c.2968G>C	c.(2968-2970)GTG>CTG	p.V990L	DSG4_uc002kwr.2_Missense_Mutation_p.V1009L	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 2 preproprotein	990	Cytoplasmic (Potential).				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)															---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67365760	67365760	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67365760T>A	uc002lkl.2	+	5	720	c.530T>A	c.(529-531)GTG>GAG	p.V177E		NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6	177	IRS-type PTB.						insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2226569	2226569	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2226569C>T	uc002lvb.3	+	27	4085	c.4049C>T	c.(4048-4050)CCG>CTG	p.P1350L	DOT1L_uc002lvc.1_Missense_Mutation_p.P644L	NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase	1350						nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		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)														---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33424576	33424576	+	Splice_Site	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33424576C>G	uc002nty.2	-	8	757	c.668_splice	c.e8-1	p.D223_splice	CCDC123_uc002ntx.2_Splice_Site|CCDC123_uc010edg.2_Splice_Site|CCDC123_uc002ntz.1_Splice_Site_p.D223_splice|CCDC123_uc002nua.2_Splice_Site_p.D223_splice	NM_032816	NP_116205			coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)																	---	---	---	---
ATP4A	495	broad.mit.edu	37	19	36042408	36042408	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36042408G>A	uc002oal.1	-	19	2855	c.2826C>T	c.(2824-2826)ATC>ATT	p.I942I	ATP4A_uc010eee.1_Silent_p.I100I	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A	942	Helical; (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding			ovary(1)	1	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)													---	---	---	---
ALKBH6	84964	broad.mit.edu	37	19	36505131	36505131	+	5'Flank	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36505131G>C	uc002oct.2	-						ALKBH6_uc002ocv.1_Missense_Mutation_p.A2G|ALKBH6_uc002ocx.1_5'UTR|ALKBH6_uc002ocw.1_Missense_Mutation_p.A2G|ALKBH6_uc010eeo.1_5'UTR|ALKBH6_uc010eep.1_Missense_Mutation_p.A2G|uc002ocy.2_5'Flank	NM_032878	NP_116267			alkB, alkylation repair homolog 6 isoform 2							cytoplasm|nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0	all_lung(56;1.35e-06)|Lung NSC(56;2.15e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
SAMD4B	55095	broad.mit.edu	37	19	39868254	39868254	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39868254G>C	uc002olb.2	+	10	2269	c.1234G>C	c.(1234-1236)GAT>CAT	p.D412H	SAMD4B_uc002ola.2_Missense_Mutation_p.D412H	NM_018028	NP_060498	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	412							protein binding				0	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)															---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43680179	43680179	+	Silent	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43680179A>T	uc002ovu.2	-	3	683	c.552T>A	c.(550-552)GGT>GGA	p.G184G	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovx.2_Silent_p.G184G|PSG5_uc002ovv.2_Silent_p.G277G|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	184	Ig-like C2-type 1.				female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
ZNF283	284349	broad.mit.edu	37	19	44352280	44352280	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44352280C>T	uc002oxr.3	+	7	1795	c.1527C>T	c.(1525-1527)CAC>CAT	p.H509H	ZNF283_uc002oxp.3_Silent_p.H370H	NM_181845	NP_862828	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	509					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)																---	---	---	---
APOC1	341	broad.mit.edu	37	19	45419535	45419535	+	Silent	SNP	G	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45419535G>T	uc002pac.1	+	4	399	c.147G>T	c.(145-147)CGG>CGT	p.R49R	APOC1_uc002pad.1_Silent_p.R49R|APOC1_uc002pae.1_Silent_p.R49R|APOC1_uc002paf.1_RNA	NM_001645	NP_001636	P02654	APOC1_HUMAN	apolipoprotein C-I precursor	49					cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of fatty acid biosynthetic process|negative regulation of lipoprotein lipase activity|negative regulation of phosphatidylcholine catabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of cholesterol esterification|very-low-density lipoprotein particle assembly|very-low-density lipoprotein particle clearance	chylomicron|endoplasmic reticulum|high-density lipoprotein particle|very-low-density lipoprotein particle	fatty acid binding|phosphatidylcholine binding|phosphatidylcholine-sterol O-acyltransferase activator activity|phospholipase inhibitor activity				0	Lung NSC(12;0.0018)|all_lung(12;0.00481)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)														---	---	---	---
CARD8	22900	broad.mit.edu	37	19	48725048	48725048	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48725048G>A	uc002pie.3	-	7	1095	c.782C>T	c.(781-783)CCC>CTC	p.P261L	CARD8_uc002pii.3_Missense_Mutation_p.P367L|CARD8_uc002pid.1_5'Flank|CARD8_uc010xzi.1_Missense_Mutation_p.P262L|CARD8_uc010els.2_Intron|CARD8_uc010xzj.1_Missense_Mutation_p.P367L|CARD8_uc010xzk.1_Missense_Mutation_p.P286L|CARD8_uc002pif.3_Missense_Mutation_p.P261L|CARD8_uc002pig.3_Missense_Mutation_p.P92L|CARD8_uc002pih.3_Missense_Mutation_p.P317L|CARD8_uc010xzl.1_Missense_Mutation_p.P317L|CARD8_uc010xzm.1_Missense_Mutation_p.P367L	NM_014959	NP_055774	Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	261					negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)														---	---	---	---
TBC1D17	79735	broad.mit.edu	37	19	50387960	50387960	+	Silent	SNP	C	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50387960C>G	uc002pqo.2	+	13	1541	c.1389C>G	c.(1387-1389)CTC>CTG	p.L463L	TBC1D17_uc010ybg.1_Silent_p.L430L|TBC1D17_uc002pqp.2_Silent_p.L114L|TBC1D17_uc002pqq.1_RNA|TBC1D17_uc002pqr.2_Silent_p.L114L|TBC1D17_uc002pqs.2_RNA	NM_024682	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	463	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)														---	---	---	---
SHANK1	50944	broad.mit.edu	37	19	51192466	51192466	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51192466G>A	uc002psx.1	-	15	2054	c.2035C>T	c.(2035-2037)CGG>TGG	p.R679W	SHANK1_uc002psw.1_Missense_Mutation_p.R63W	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	679	PDZ.				cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)														---	---	---	---
KLK13	26085	broad.mit.edu	37	19	51563768	51563768	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51563768A>T	uc002pvn.2	-	2	204	c.161T>A	c.(160-162)CTA>CAA	p.L54Q	KLK13_uc002pvl.2_RNA|KLK13_uc002pvm.2_RNA|KLK13_uc002pvo.2_RNA|KLK13_uc002pvp.2_RNA|KLK13_uc010eon.2_Missense_Mutation_p.L54Q|KLK13_uc002pvq.2_RNA|KLK13_uc010eoo.2_Intron|KLK13_uc002pvr.2_Missense_Mutation_p.L54Q	NM_015596	NP_056411	Q9UKR3	KLK13_HUMAN	kallikrein 13 precursor	54	Peptidase S1.				proteolysis		protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)														---	---	---	---
MIR522	574495	broad.mit.edu	37	19	54254517	54254517	+	RNA	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54254517G>A	hsa-mir-522|MI0003177	+			c.53G>A			MIR519A1_hsa-mir-519a-1|MI0003178_5'Flank|MIR527_hsa-mir-527|MI0003179_5'Flank																	0																		---	---	---	---
ZSCAN5A	79149	broad.mit.edu	37	19	56734056	56734056	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56734056G>C	uc002qmq.2	-	4	809	c.643C>G	c.(643-645)CTG>GTG	p.L215V	ZSCAN5A_uc010ygi.1_Missense_Mutation_p.L98V|ZSCAN5A_uc002qmr.2_Missense_Mutation_p.L215V|ZSCAN5A_uc002qms.1_Missense_Mutation_p.L215V	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	215					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ZNF264	9422	broad.mit.edu	37	19	57723882	57723882	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57723882C>T	uc002qob.2	+	4	1830	c.1417C>T	c.(1417-1419)CAC>TAC	p.H473Y		NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264	473	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)														---	---	---	---
TRIM28	10155	broad.mit.edu	37	19	59060446	59060446	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59060446A>T	uc002qtg.1	+	12	1790	c.1501A>T	c.(1501-1503)AGC>TGC	p.S501C	TRIM28_uc010eut.1_Missense_Mutation_p.S419C|TRIM28_uc002qth.1_Missense_Mutation_p.S116C	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	tripartite motif-containing 28 protein	501	HP1 box.			S->A: No effect on interaction with PPP1CA nor on sumoylation levels. Decreased sumoylation levels; when associated with D-440 and D-824.	epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)														---	---	---	---
HSPA12B	116835	broad.mit.edu	37	20	3729958	3729958	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3729958G>A	uc002wjd.2	+	9	1033	c.930G>A	c.(928-930)ATG>ATA	p.M310I	HSPA12B_uc010zqi.1_Missense_Mutation_p.M309I|HSPA12B_uc002wje.2_Missense_Mutation_p.M223I|HSPA12B_uc010zqj.1_Missense_Mutation_p.M144I	NM_052970	NP_443202	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	310							ATP binding				0																		---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51872378	51872378	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51872378A>G	uc002xwo.2	+	2	3337	c.2381A>G	c.(2380-2382)GAC>GGC	p.D794G		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	794					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)															---	---	---	---
ADRM1	11047	broad.mit.edu	37	20	60881358	60881358	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60881358G>A	uc002ycn.2	+	4	516	c.436G>A	c.(436-438)GAA>AAA	p.E146K	ADRM1_uc011aai.1_Missense_Mutation_p.E146K|ADRM1_uc002yco.2_Missense_Mutation_p.E146K|ADRM1_uc002ycp.1_RNA	NM_007002	NP_008933	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1 precursor	146	Gly-rich.				proteasome assembly|transcription elongation from RNA polymerase II promoter	cytoplasm|integral to plasma membrane|membrane fraction|nucleus|proteasome complex	endopeptidase activator activity|protease binding|proteasome binding				0	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)															---	---	---	---
KRTAP13-4	284827	broad.mit.edu	37	21	31802803	31802803	+	Silent	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31802803C>A	uc011acw.1	+	1	210	c.210C>A	c.(208-210)ACC>ACA	p.T70T		NM_181600	NP_853631	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	70	3.|4 X 10 AA approximate repeats.					intermediate filament					0																		---	---	---	---
KRTAP20-2	337976	broad.mit.edu	37	21	32007675	32007675	+	Silent	SNP	C	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32007675C>A	uc011adg.1	+	1	93	c.93C>A	c.(91-93)GGC>GGA	p.G31G		NM_181616	NP_853647	Q3LI61	KR202_HUMAN	keratin associated protein 20-2	31						intermediate filament				central_nervous_system(1)	1																		---	---	---	---
C21orf29	54084	broad.mit.edu	37	21	45929225	45929225	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45929225C>T	uc002zfe.1	-	10	1677	c.1611G>A	c.(1609-1611)AGG>AGA	p.R537R	C21orf29_uc010gpv.1_Silent_p.R469R	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29 precursor	537	EAR 5.				cell adhesion	extracellular region	structural molecule activity				0																		---	---	---	---
PATZ1	23598	broad.mit.edu	37	22	31741159	31741159	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31741159G>A	uc003akq.2	-	1	1091	c.430C>T	c.(430-432)CTG>TTG	p.L144L	PATZ1_uc003akp.2_Silent_p.L144L|PATZ1_uc003akr.2_Silent_p.L144L|PATZ1_uc003aks.2_Silent_p.L144L|uc003akt.2_5'Flank	NM_014323	NP_055138	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	144					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/PATZ1(2)	soft_tissue(2)	2																		---	---	---	---
P2RY8	286530	broad.mit.edu	37	X	1584824	1584824	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1584824C>T	uc004cpz.2	-	2	876	c.628G>A	c.(628-630)GTG>ATG	p.V210M		NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8	210	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		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)						T	CRLF2	B-ALL|Downs associated ALL								---	---	---	---
DMD	1756	broad.mit.edu	37	X	31676164	31676164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31676164C>T	uc004dda.1	-	54	8214	c.7970G>A	c.(7969-7971)AGA>AAA	p.R2657K	DMD_uc004dcr.1_Missense_Mutation_p.R197K|DMD_uc004dcs.1_Missense_Mutation_p.R197K|DMD_uc004dct.1_Missense_Mutation_p.R197K|DMD_uc004dcu.1_Missense_Mutation_p.R197K|DMD_uc004dcv.1_Missense_Mutation_p.R197K|DMD_uc004dcw.2_Missense_Mutation_p.R1313K|DMD_uc004dcx.2_Missense_Mutation_p.R1316K|DMD_uc004dcz.2_Missense_Mutation_p.R2534K|DMD_uc004dcy.1_Missense_Mutation_p.R2653K|DMD_uc004ddb.1_Missense_Mutation_p.R2649K	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2657	Spectrin 18.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
RP2	6102	broad.mit.edu	37	X	46736939	46736939	+	Splice_Site	SNP	G	C	C			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46736939G>C	uc004dgw.3	+	4	1073	c.884_splice	c.e4-1	p.G295_splice		NM_006915	NP_008846			XRP2 protein						cell morphogenesis|CTP biosynthetic process|GTP biosynthetic process|protein folding|UTP biosynthetic process|visual perception	cytoplasm|plasma membrane	ATP binding|GTP binding|GTPase activator activity|nucleoside diphosphate kinase activity|unfolded protein binding				0																		---	---	---	---
ACRC	93953	broad.mit.edu	37	X	70823745	70823745	+	Silent	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70823745C>T	uc004eae.2	+	8	1119	c.618C>T	c.(616-618)GAC>GAT	p.D206D	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	206	Asp/Ser-rich.					nucleus				ovary(3)	3	Renal(35;0.156)																	---	---	---	---
RGAG4	340526	broad.mit.edu	37	X	71350454	71350454	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71350454C>T	uc010nlh.1	-	1	1298	c.937G>A	c.(937-939)GTT>ATT	p.V313I	NHSL2_uc011mqa.1_Intron|RGAG4_uc004eaj.1_RNA	NM_001024455	NP_001019626	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	313										ovary(2)|skin(1)	3	Renal(35;0.156)																	---	---	---	---
ELF4	2000	broad.mit.edu	37	X	129205140	129205140	+	Silent	SNP	G	A	A			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129205140G>A	uc004evd.3	-	7	1069	c.684C>T	c.(682-684)TAC>TAT	p.Y228Y	ELF4_uc004eve.3_Silent_p.Y228Y	NM_001421	NP_001412	Q99607	ELF4_HUMAN	E74-like factor 4	228	ETS.				natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter	PML body	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1								T	ERG	AML								---	---	---	---
MAGEA10	4109	broad.mit.edu	37	X	151303021	151303021	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4288-01	TCGA-BR-4288-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151303021T>G	uc004ffk.2	-	5	1480	c.1072A>C	c.(1072-1074)AGT>CGT	p.S358R	MAGEA10_uc004ffl.2_Missense_Mutation_p.S358R	NM_001011543	NP_001011543	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	358											0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
