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
TP73	7161	broad.mit.edu	37	1	3646064	3646064	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3646064delC	uc001akp.2	+						TP73_uc001akq.2_Intron|TP73_uc010nzj.1_3'UTR|TP73_uc001akr.2_Intron|TP73_uc009vlk.1_Intron|TP73_uc001aks.2_Intron|TP73_uc010nzk.1_Intron|TP73_uc010nzl.1_Intron	NM_005427	NP_005418			tumor protein p73 isoform a						cellular response to UV|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|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|protein tetramerization|response to gamma radiation|response to X-ray	chromatin|cytosol|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)														---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	5940064	5940065	+	Intron	DEL	CA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5940064_5940065delCA	uc001alq.1	-						NPHP4_uc001als.1_Intron|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron	NM_015102	NP_055917			nephroretinin						actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RPL22	6146	broad.mit.edu	37	1	6257785	6257785	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6257785delT	uc001amd.2	-	2	90	c.44delA	c.(43-45)AAGfs	p.K15fs	RPL22_uc001ame.2_Frame_Shift_Del_p.K15fs	NM_000983	NP_000974	P35268	RL22_HUMAN	ribosomal protein L22 proprotein	15					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	heparin binding|RNA binding|structural constituent of ribosome				0	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)				T	RUNX1	AML|CML								---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11227303	11227303	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11227303delA	uc001asd.2	-							NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
PLOD1	5351	broad.mit.edu	37	1	12033174	12033174	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12033174delA	uc001atm.2	+						PLOD1_uc010obb.1_Intron	NM_000302	NP_000293			lysyl hydroxylase 1 precursor						epidermis development|hydroxylysine biosynthetic process|protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein homodimerization activity			ovary(2)|breast(1)	3	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;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Minoxidil(DB00350)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	13882094	13882094	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13882094delA								PRAMEF17 (163030 upstream) : PDPN (28158 downstream)																																			---	---	---	---
PADI1	29943	broad.mit.edu	37	1	17555380	17555380	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17555380delG	uc001bah.1	+							NM_013358	NP_037490			peptidylarginine deiminase type I						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)													---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21191489	21191489	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21191489delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
USP48	84196	broad.mit.edu	37	1	22041775	22041775	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22041775delT	uc001bfb.2	-						USP48_uc001bfa.2_Intron|USP48_uc010odq.1_Intron|USP48_uc009vqc.2_Intron|USP48_uc001bfc.2_Intron	NM_032236	NP_115612			ubiquitin specific protease 48 isoform a						ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22569938	22569938	+	IGR	DEL	G	-	-	rs66593903		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22569938delG								WNT4 (99553 upstream) : ZBTB40 (208406 downstream)																																			---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23240246	23240246	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23240246delA	uc009vqj.1	+	17	3196	c.3051delA	c.(3049-3051)GGAfs	p.G1017fs	EPHB2_uc001bge.2_3'UTR|EPHB2_uc001bgf.2_3'UTR|EPHB2_uc010odu.1_3'UTR	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	1017	Cytoplasmic (Potential).				axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)										Hereditary_Prostate_Cancer				---	---	---	---
Unknown	0	broad.mit.edu	37	1	23571841	23571841	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23571841delA								HTR1D (50619 upstream) : HNRNPR (64436 downstream)																																			---	---	---	---
HNRNPR	10236	broad.mit.edu	37	1	23660245	23660245	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23660245delA	uc001bgr.3	-						HNRNPR_uc001bgp.3_Intron|HNRNPR_uc009vqk.2_Intron|HNRNPR_uc001bgs.3_Intron|HNRNPR_uc010odw.1_Intron|HNRNPR_uc010odx.1_Intron|HNRNPR_uc009vql.2_Intron	NM_005826	NP_005817			heterogeneous nuclear ribonucleoprotein R							catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26900923	26900923	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26900923delT	uc001bmr.1	+	22					RPS6KA1_uc010ofe.1_3'UTR|RPS6KA1_uc001bms.1_3'UTR|RPS6KA1_uc009vsl.1_3'UTR	NM_002953	NP_002944			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)														---	---	---	---
YTHDF2	51441	broad.mit.edu	37	1	29095518	29095518	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29095518delA	uc001brc.2	+	5					YTHDF2_uc001brd.2_3'UTR|YTHDF2_uc010ofx.1_3'UTR|YTHDF2_uc001bre.2_3'UTR	NM_016258	NP_057342			high glucose-regulated protein 8						humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SNRNP40	9410	broad.mit.edu	37	1	31736371	31736372	+	Intron	DEL	TG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31736371_31736372delTG	uc001bso.2	-						SNRNP40_uc009vtt.2_Intron|SNRNP40_uc010oge.1_Intron	NM_004814	NP_004805			WD repeat domain 57 (U5 snRNP specific)							catalytic step 2 spliceosome|cytoplasm|nucleoplasm|small nucleolar ribonucleoprotein complex|U5 snRNP	protein binding				0																		---	---	---	---
SNRNP40	9410	broad.mit.edu	37	1	31766006	31766006	+	Intron	DEL	A	-	-	rs112391814		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31766006delA	uc001bso.2	-						SNRNP40_uc010oge.1_Intron	NM_004814	NP_004805			WD repeat domain 57 (U5 snRNP specific)							catalytic step 2 spliceosome|cytoplasm|nucleoplasm|small nucleolar ribonucleoprotein complex|U5 snRNP	protein binding				0																		---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31791792	31791792	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31791792delA	uc001bsp.1	+						ZCCHC17_uc001bsq.1_Intron|ZCCHC17_uc010ogf.1_Intron|ZCCHC17_uc009vtu.1_Intron|ZCCHC17_uc001bsr.1_Intron|ZCCHC17_uc009vtv.1_Intron	NM_016505	NP_057589			zinc finger, CCHC domain containing 17							nucleolus	RNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)														---	---	---	---
KPNA6	23633	broad.mit.edu	37	1	32631599	32631599	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32631599delA	uc001bug.2	+						KPNA6_uc001buh.2_Intron|KPNA6_uc010ogx.1_Intron|KPNA6_uc010ogy.1_Intron|KPNA6_uc009vtz.2_Intron	NM_012316	NP_036448			karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
COL8A2	1296	broad.mit.edu	37	1	36564598	36564598	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36564598delG	uc001bzv.1	-	2	691	c.684delC	c.(682-684)CCCfs	p.P228fs	COL8A2_uc001bzw.1_Frame_Shift_Del_p.P163fs	NM_005202	NP_005193	P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2 precursor	228	Triple-helical region.				angiogenesis|cell-cell adhesion|extracellular matrix organization	basement membrane|collagen	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
NT5C1A	84618	broad.mit.edu	37	1	40131136	40131136	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40131136delG	uc001cdq.1	-							NM_032526	NP_115915			5'-nucleotidase, cytosolic IA						purine base metabolic process|purine nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
GPBP1L1	60313	broad.mit.edu	37	1	46095127	46095129	+	Intron	DEL	CCC	-	-	rs74074404		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46095127_46095129delCCC	uc001coq.2	-						GPBP1L1_uc001coo.2_Intron	NM_021639	NP_067652			GC-rich promoter binding protein 1-like 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51868224	51868224	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51868224delT	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
TXNDC12	51060	broad.mit.edu	37	1	52520571	52520572	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52520571_52520572delAA	uc001cti.2	-						BTF3L4_uc001ctk.2_5'Flank|BTF3L4_uc001ctl.2_5'Flank|BTF3L4_uc010onh.1_5'Flank	NM_015913	NP_056997			thioredoxin domain containing 12 precursor						activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(1)	1																		---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52744392	52744392	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52744392delT	uc001cto.2	+						ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
USP24	23358	broad.mit.edu	37	1	55563397	55563397	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55563397delA	uc001cyg.3	-							NM_015306	NP_056121			ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13																		---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59977913	59977913	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59977913delA	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
INADL	10207	broad.mit.edu	37	1	62267278	62267279	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62267278_62267279insT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
ALG6	29929	broad.mit.edu	37	1	63879927	63879928	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63879927_63879928delTT	uc010oow.1	+						ALG6_uc001daz.2_Intron|ALG6_uc009waj.2_Intron|ALG6_uc010oox.1_Intron	NM_013339	NP_037471			dolichyl pyrophosphate Man9GlcNAc2						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity				0																		---	---	---	---
LEPR	3953	broad.mit.edu	37	1	65915368	65915368	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65915368delT	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.2_Intron	NM_002303	NP_002294			leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)														---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67099769	67099769	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67099769delA	uc001dcr.2	+							NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
ZRANB2	9406	broad.mit.edu	37	1	71534883	71534883	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71534883delA	uc001dft.2	-						ZRANB2_uc001dfs.2_Intron|uc010oqr.1_5'Flank|MIR186_hsa-mir-186|MI0000483_5'Flank	NM_203350	NP_976225			zinc finger protein 265 isoform 1						mRNA processing|RNA splicing	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	74185634	74185637	+	IGR	DEL	AAAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74185634_74185637delAAAA								None (None upstream) : LRRIQ3 (306067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	78239446	78239446	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78239446delA								USP33 (13909 upstream) : FAM73A (5863 downstream)																																			---	---	---	---
FAM73A	374986	broad.mit.edu	37	1	78329478	78329478	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78329478delA	uc001dhx.2	+						FAM73A_uc010ork.1_Intron|FAM73A_uc010orl.1_Intron	NM_198549	NP_940951			hypothetical protein LOC374986							integral to membrane				ovary(1)	1				Colorectal(170;0.226)														---	---	---	---
FAM73A	374986	broad.mit.edu	37	1	78331963	78331964	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78331963_78331964insA	uc001dhx.2	+						FAM73A_uc010ork.1_Intron|FAM73A_uc010orl.1_Intron	NM_198549	NP_940951			hypothetical protein LOC374986							integral to membrane				ovary(1)	1				Colorectal(170;0.226)														---	---	---	---
IFI44	10561	broad.mit.edu	37	1	79121314	79121314	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79121314delT	uc001dip.3	+						IFI44_uc010orr.1_Intron|IFI44_uc010ors.1_Intron	NM_006417	NP_006408			interferon-induced, hepatitis C-associated						response to virus	cytoplasm				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82187279	82187279	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82187279delA	uc001dit.3	+						LPHN2_uc001dis.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82187977	82187977	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82187977delA	uc001dit.3	+						LPHN2_uc001dis.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
MCOLN3	55283	broad.mit.edu	37	1	85510738	85510739	+	Intron	INS	-	A	A	rs79389367	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85510738_85510739insA	uc001dkp.2	-						MCOLN3_uc001dkq.2_Intron|MCOLN3_uc001dkr.2_Intron|MCOLN3_uc001dks.3_Intron	NM_018298	NP_060768			mucolipin 3							integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86227122	86227123	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86227122_86227123insA	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
SEP15	9403	broad.mit.edu	37	1	87329389	87329389	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87329389delA	uc010osi.1	-						SEP15_uc010osj.1_Intron	NM_004261	NP_004252			15 kDa selenoprotein isoform 1 precursor						'de novo' posttranslational protein folding	endoplasmic reticulum lumen	selenium binding				0		Lung NSC(277;0.153)		all cancers(265;0.00744)|Epithelial(280;0.0333)														---	---	---	---
HS2ST1	9653	broad.mit.edu	37	1	87563396	87563396	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87563396delA	uc010osk.1	+						HS2ST1_uc001dmc.3_Intron|LOC339524_uc001dme.1_Intron	NM_012262	NP_036394			heparan sulfate 2-O-sulfotransferase 1 isoform							Golgi membrane|integral to membrane				central_nervous_system(1)	1		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)														---	---	---	---
BRDT	676	broad.mit.edu	37	1	92447354	92447354	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92447354delT	uc001dok.3	+						BRDT_uc001dol.3_Intron|BRDT_uc010osz.1_Intron|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Intron|BRDT_uc010otb.1_Intron|BRDT_uc001dom.3_Intron	NM_207189	NP_997072			testis-specific bromodomain protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
RPL5	6125	broad.mit.edu	37	1	93301569	93301569	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93301569delT	uc001doz.2	+						FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.2_Intron|RPL5_uc001dpb.2_Intron|RPL5_uc001dpd.2_5'Flank|SNORD21_uc001dpe.2_5'Flank	NM_000969	NP_000960			ribosomal protein L5						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)														---	---	---	---
FNBP1L	54874	broad.mit.edu	37	1	93995246	93995246	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93995246delA	uc001dpw.2	+	6	443	c.443delA	c.(442-444)GAAfs	p.E148fs	FNBP1L_uc001dpv.2_Frame_Shift_Del_p.E148fs|FNBP1L_uc010otk.1_5'UTR	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1	148	Induction of membrane tubulation (By similarity).|Potential.				endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)														---	---	---	---
SASS6	163786	broad.mit.edu	37	1	100572825	100572825	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100572825delA	uc001dsu.2	-						SASS6_uc009wdz.2_Intron	NM_194292	NP_919268			spindle assembly abnormal protein 6						centriole replication	centriole				upper_aerodigestive_tract(1)|ovary(1)	2		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	102251813	102251813	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102251813delT								S1PR1 (544737 upstream) : OLFM3 (16314 downstream)																																			---	---	---	---
SLC25A24	29957	broad.mit.edu	37	1	108728581	108728581	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108728581delA	uc001dvn.3	-						SLC25A24_uc001dvm.2_Intron	NM_013386	NP_037518			solute carrier family 25 member 24 isoform 1						transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding			ovary(1)	1		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)														---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113126864	113126864	+	Intron	DEL	A	-	-	rs76579294		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113126864delA	uc001ecd.2	-						ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Intron|ST7L_uc010owg.1_Intron|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Intron|ST7L_uc001ecf.2_Intron|ST7L_uc001ecg.2_Intron|ST7L_uc010owi.1_Intron|ST7L_uc001ech.2_Intron|ST7L_uc001eci.2_Intron|ST7L_uc009wgi.1_Intron|ST7L_uc010owj.1_Intron	NM_017744	NP_060214			suppression of tumorigenicity 7-like isoform 1						negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
DENND2C	163259	broad.mit.edu	37	1	115142747	115142747	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115142747delA	uc001efd.1	-						DENND2C_uc001eez.2_Intron|DENND2C_uc001efc.1_Intron	NM_198459	NP_940861			DENN/MADD domain containing 2C											skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115279333	115279334	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115279333_115279334delAA	uc001efk.2	-						CSDE1_uc001efi.2_Intron|CSDE1_uc001efj.2_Intron|CSDE1_uc001efl.2_Intron|CSDE1_uc001efm.2_Intron|CSDE1_uc009wgv.2_Intron|CSDE1_uc001efn.2_Intron	NM_001007553	NP_001007554			upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
TRIM45	80263	broad.mit.edu	37	1	117659023	117659023	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117659023delT	uc001egz.2	-						TRIM45_uc009whe.2_Intron|TRIM45_uc001eha.2_Intron	NM_025188	NP_079464			tripartite motif-containing 45 isoform 1							cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145581645	145581646	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145581645_145581646delTT	uc001emp.3	+						PIAS3_uc001eoc.1_Intron|PIAS3_uc001eod.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145645968	145645968	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145645968delA	uc001emp.3	+						RNF115_uc001eoj.2_Intron|RNF115_uc001eok.2_Intron|RNF115_uc009wiy.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
ANP32E	81611	broad.mit.edu	37	1	150199259	150199259	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150199259delT	uc001etw.2	-						ANP32E_uc010pbt.1_5'Flank|ANP32E_uc010pbu.1_Intron|ANP32E_uc010pbv.1_Intron|ANP32E_uc001etv.3_Intron|ANP32E_uc010pbw.1_Intron	NM_030920	NP_112182			acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasmic membrane-bounded vesicle|nucleus	phosphatase inhibitor activity				0	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
FAM63A	55793	broad.mit.edu	37	1	150972560	150972560	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150972560delT	uc001ewf.2	-						FAM63A_uc001ewc.2_Intron|FAM63A_uc010pcm.1_Intron|FAM63A_uc001ewd.2_Intron|FAM63A_uc001ewe.2_Intron|FAM63A_uc010pcn.1_Intron|FAM63A_uc001ewg.2_Intron	NM_018379	NP_001156731			hypothetical protein LOC55793 isoform 1								protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
POGZ	23126	broad.mit.edu	37	1	151402264	151402264	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151402264delA	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron|POGZ_uc001eyg.1_Intron	NM_015100	NP_055915			pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TUFT1	7286	broad.mit.edu	37	1	151530466	151530466	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151530466delA	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512			tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
CRNN	49860	broad.mit.edu	37	1	152384424	152384424	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152384424delT	uc001ezx.2	-							NM_016190	NP_057274			cornulin						cell-cell adhesion|response to heat	cytoplasm|membrane	calcium ion binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
INTS3	65123	broad.mit.edu	37	1	153743305	153743305	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153743305delT	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron|INTS3_uc010peb.1_Intron|INTS3_uc001fcw.2_Intron|INTS3_uc010pec.1_Intron|INTS3_uc001fcy.2_Intron|INTS3_uc001fcx.2_Intron	NM_023015	NP_075391			integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155491509	155491510	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155491509_155491510insA	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron|ASH1L_uc009wqr.1_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	155571854	155571854	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155571854delT								LOC645676 (38122 upstream) : MSTO1 (8153 downstream)																																			---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155822905	155822905	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155822905delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
ROBLD3	28956	broad.mit.edu	37	1	156028210	156028210	+	3'UTR	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156028210delG	uc001fnb.3	+	4					ROBLD3_uc010pgy.1_3'UTR|RAB25_uc001fnc.2_5'Flank	NM_014017	NP_054736			roadblock domain-containing protein 3 isoform 1						cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade	lysosomal membrane|Ragulator complex					0																		---	---	---	---
HDGF	3068	broad.mit.edu	37	1	156713116	156713118	+	3'UTR	DEL	AGT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156713116_156713118delAGT	uc001fpy.3	-	6					MRPL24_uc001fpw.1_5'Flank|MRPL24_uc001fpx.1_5'Flank|HDGF_uc009wsd.2_3'UTR|HDGF_uc001fpz.3_3'UTR|HDGF_uc009wse.2_3'UTR|HDGF_uc010phr.1_3'UTR|HDGF_uc009wsf.2_3'UTR|HDGF_uc009wsg.2_Intron	NM_004494	NP_004485			hepatoma-derived growth factor isoform a						cell proliferation|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	DNA binding|growth factor activity|heparin binding|nucleotide binding			lung(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)														---	---	---	---
CCDC19	25790	broad.mit.edu	37	1	159856131	159856131	+	Intron	DEL	A	-	-	rs113465282		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159856131delA	uc001fui.2	-						CCDC19_uc009wtb.2_Intron|CCDC19_uc001fuj.2_Intron|CCDC19_uc001fuk.2_Intron|CCDC19_uc001ful.2_Intron|CCDC19_uc009wtc.1_Intron	NM_012337	NP_036469			nasopharyngeal epithelium specific protein 1							mitochondrion|soluble fraction				ovary(1)	1	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)															---	---	---	---
SLAMF1	6504	broad.mit.edu	37	1	160582201	160582202	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160582201_160582202delAA	uc001fwl.3	-						SLAMF1_uc010pjk.1_Intron|SLAMF1_uc010pjl.1_Intron|SLAMF1_uc010pjm.1_Intron	NM_003037	NP_003028			signaling lymphocytic activation molecule family						interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)															---	---	---	---
C1orf226	400793	broad.mit.edu	37	1	162351550	162351553	+	5'UTR	DEL	TCTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162351550_162351553delTCTT	uc001gby.2	+	1					C1orf226_uc010pkt.1_Intron	NM_001085375	NP_001078844			hypothetical protein LOC400793 isoform 2											ovary(1)	1																		---	---	---	---
UHMK1	127933	broad.mit.edu	37	1	162492171	162492171	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162492171delT	uc001gcc.1	+						UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Intron|uc001gcd.2_5'Flank	NM_175866	NP_787062			kinase interacting stathmin						cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	168841709	168841709	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168841709delT								MGC4473 (79589 upstream) : ATP1B1 (234238 downstream)																																			---	---	---	---
F5	2153	broad.mit.edu	37	1	169528244	169528244	+	Intron	DEL	A	-	-	rs139315961		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169528244delA	uc001ggg.1	-						F5_uc010plr.1_Intron	NM_000130	NP_000121			coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)													---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169790714	169790714	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169790714delT	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc010plu.1_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656			hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
FMO1	2326	broad.mit.edu	37	1	171252490	171252490	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171252490delA	uc009wvz.2	+						FMO1_uc010pme.1_Intron|FMO1_uc001ghl.2_Intron|FMO1_uc001ghm.2_Intron|FMO1_uc001ghn.2_Intron	NM_002021	NP_002012			flavin containing monooxygenase 1						NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum lumen|integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171452363	171452363	+	5'Flank	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171452363delA	uc010pmg.1	+						BAT2L2_uc001ghq.1_5'Flank|BAT2L2_uc001ghr.1_5'Flank	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
ACBD6	84320	broad.mit.edu	37	1	180382630	180382630	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180382630delT	uc001gog.2	-							NM_032360	NP_115736			acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1																		---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183502798	183502798	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183502798delT	uc001gqg.2	+						SMG7_uc010pob.1_Intron|SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Intron	NM_173156	NP_775179			SMG-7 homolog isoform 1						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
RGL1	23179	broad.mit.edu	37	1	183891293	183891295	+	Intron	DEL	AGG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183891293_183891295delAGG	uc001gqo.2	+						RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron|RGL1_uc010poi.1_Intron	NM_015149	NP_055964			ral guanine nucleotide dissociation						cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	protein binding|Ral guanyl-nucleotide exchange factor activity			breast(5)|ovary(4)|lung(2)	11																OREG0014047	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	188416136	188416139	+	IGR	DEL	TTCC	-	-	rs112749943		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188416136_188416139delTTCC								None (None upstream) : None (None downstream)																																			---	---	---	---
RGS21	431704	broad.mit.edu	37	1	192321501	192321502	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192321501_192321502insT	uc001gsh.2	+							NM_001039152	NP_001034241			regulator of G-protein signaling 21						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	196826695	196826696	+	IGR	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196826695_196826696insA								CFHR1 (25379 upstream) : CFHR4 (30516 downstream)																																			---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197480840	197480840	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197480840delA	uc010ppe.1	-						DENND1B_uc010ppf.1_Intron	NM_001142795	NP_001136267			DENN/MADD domain containing 1B isoform 1							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197514934	197514934	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197514934delT	uc010ppe.1	-						DENND1B_uc010ppf.1_Intron	NM_001142795	NP_001136267			DENN/MADD domain containing 1B isoform 1							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	199878367	199878367	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199878367delA								None (None upstream) : NR5A2 (118403 downstream)																																			---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200573140	200573140	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200573140delT	uc010ppk.1	-						KIF14_uc010ppj.1_Intron	NM_014875	NP_055690			kinesin family member 14						microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7																		---	---	---	---
DDX59	83479	broad.mit.edu	37	1	200632896	200632900	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200632896_200632900delAAAAA	uc009wzk.2	-						DDX59_uc010ppl.1_Intron	NM_001031725	NP_001026895			DEAD (Asp-Glu-Ala-Asp) box polypeptide 59							intracellular	ATP binding|ATP-dependent helicase activity|metal ion binding|RNA binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
IGFN1	91156	broad.mit.edu	37	1	201195812	201195812	+	Intron	DEL	A	-	-	rs34207437		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201195812delA	uc001gwc.2	+						IGFN1_uc001gwb.2_Intron	NM_178275	NP_840059			RecName: Full=Immunoglobulin-like and fibronectin type III domain-containing protein 1; AltName: Full=EEF1A2-binding protein 1; AltName: Full=KY-interacting protein 1;											ovary(2)|pancreas(1)	3																		---	---	---	---
SNRPE	6635	broad.mit.edu	37	1	203838991	203838991	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203838991delT	uc001hai.2	+						SNRPE_uc010pqn.1_Intron	NM_003094	NP_003085			small nuclear ribonucleoprotein polypeptide E						histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
MDM4	4194	broad.mit.edu	37	1	204498732	204498732	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204498732delG	uc001hba.2	+						MDM4_uc001hbd.1_Intron|MDM4_uc010pqw.1_Intron|MDM4_uc010pqx.1_Intron|MDM4_uc001hay.1_Intron|MDM4_uc001hbb.2_Intron|MDM4_uc010pqy.1_Intron|MDM4_uc001hbc.2_Intron|MDM4_uc009xbe.1_Intron	NM_002393	NP_002384			mouse double minute 4 homolog						apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)					A		GBM|bladder|retinoblastoma								---	---	---	---
RBBP5	5929	broad.mit.edu	37	1	205068005	205068005	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205068005delG	uc001hbu.1	-						RBBP5_uc010prd.1_Intron|RBBP5_uc001hbv.1_Intron|RBBP5_uc010pre.1_Intron	NM_005057	NP_005048			retinoblastoma binding protein 5						histone H3-K4 methylation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription, DNA-dependent	MLL1 complex|Set1C/COMPASS complex	methylated histone residue binding|transcription regulatory region DNA binding			lung(1)	1	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	211347241	211347241	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211347241delA								KCNH1 (39784 upstream) : RCOR3 (85467 downstream)																																			---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214560108	214560108	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214560108delT	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392			protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215901794	215901794	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215901794delA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216256672	216256672	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216256672delA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220324483	220324483	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220324483delA	uc010puk.1	-	35					RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_3'UTR|RAB3GAP2_uc001hmh.2_3'UTR	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
H3F3A	3020	broad.mit.edu	37	1	226252196	226252196	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226252196delA	uc001hpw.2	+						H3F3A_uc010pvl.1_Intron	NM_005324	NP_005315			H3 histone, family 3B						blood coagulation|nucleosome assembly	nucleoplasm|nucleosome	DNA binding				0	Breast(184;0.179)			GBM - Glioblastoma multiforme(131;0.203)												OREG0014293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227235587	227235587	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227235587delT	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqu.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227330816	227330816	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227330816delA	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
GALNT2	2590	broad.mit.edu	37	1	230382064	230382064	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230382064delA	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472			polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)																---	---	---	---
COG2	22796	broad.mit.edu	37	1	230828972	230828972	+	Intron	DEL	T	-	-	rs111313789		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230828972delT	uc001htw.2	+						COG2_uc001htx.2_Intron|COG2_uc010pwc.1_Intron	NM_007357	NP_031383			component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
LYST	1130	broad.mit.edu	37	1	235878728	235878729	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235878728_235878729delTT	uc001hxj.2	-						LYST_uc001hxi.2_Intron	NM_000081	NP_000072			lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											Chediak-Higashi_syndrome				---	---	---	---
NID1	4811	broad.mit.edu	37	1	236144007	236144007	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236144007delA	uc001hxo.2	-						NID1_uc009xgd.2_Intron|NID1_uc009xgc.2_Intron	NM_002508	NP_002499			nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)													---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236399233	236399233	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236399233delT	uc001hxt.2	-							NM_019891	NP_063944			endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	240072444	240072444	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240072444delA	uc001hyp.2	+	5	2472	c.1693delA	c.(1693-1695)AAAfs	p.K565fs		NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	565	Cytoplasmic (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242253557	242253557	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242253557delA	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242383097	242383097	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242383097delT	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245847716	245847716	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245847716delG	uc001ibf.1	+						KIF26B_uc001ibg.1_Intron|KIF26B_uc001ibh.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	248844550	248844550	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248844550delT								OR2T27 (30365 upstream) : OR14I1 (120 downstream)																																			---	---	---	---
TAF1B	9014	broad.mit.edu	37	2	9989571	9989571	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9989571delA	uc002qzz.2	+	3	287	c.187delA	c.(187-189)AAAfs	p.K63fs	TAF1B_uc010exc.2_Frame_Shift_Del_p.K63fs|TAF1B_uc002qzy.3_Frame_Shift_Del_p.K63fs|TAF1B_uc010yja.1_5'UTR|TAF1B_uc010exd.2_5'UTR	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B	63					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GRHL1	29841	broad.mit.edu	37	2	10092013	10092013	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10092013delG	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825			grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)														---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17959474	17959475	+	Intron	DEL	TA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17959474_17959475delTA	uc010exo.2	-						GEN1_uc002rct.2_Intron|GEN1_uc010yjs.1_Intron|GEN1_uc002rcu.2_Intron	NM_024624	NP_078900			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	25991779	25991779	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25991779delT	uc002rgs.2	-						ASXL2_uc002rgt.1_Intron	NM_018263	NP_060733			additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26363043	26363043	+	IGR	DEL	A	-	-	rs112696641		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26363043delA								RAB10 (2721 upstream) : HADHA (50462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36145053	36145053	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36145053delA								None (None upstream) : CRIM1 (438344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36526516	36526516	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36526516delT								None (None upstream) : CRIM1 (56881 downstream)																																			---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37277042	37277042	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37277042delT	uc002rpp.1	-							NM_019024	NP_061897			HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
C2orf56	55471	broad.mit.edu	37	2	37468695	37468695	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37468695delT	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron|C2orf56_uc010fah.2_5'Flank	NM_144736	NP_653337			hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)																---	---	---	---
THUMPD2	80745	broad.mit.edu	37	2	39964207	39964207	+	Intron	DEL	A	-	-	rs75145165		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39964207delA	uc002rru.2	-						THUMPD2_uc002rrv.2_Intron|THUMPD2_uc010ynt.1_Intron	NM_025264	NP_079540			THUMP domain containing 2								methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)																---	---	---	---
THADA	63892	broad.mit.edu	37	2	43624983	43624983	+	Intron	DEL	A	-	-	rs77307304		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43624983delA	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
THADA	63892	broad.mit.edu	37	2	43768234	43768234	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43768234delA	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44099563	44099563	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44099563delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882			ATP-binding cassette sub-family G member 8						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
CCDC104	112942	broad.mit.edu	37	2	55756167	55756167	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55756167delT	uc002ryy.2	+						CCDC104_uc002ryx.2_Intron	NM_080667	NP_542398			coiled-coil domain containing 104											ovary(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	58479808	58479808	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58479808delA								FANCL (11293 upstream) : None (None downstream)																																			---	---	---	---
USP34	9736	broad.mit.edu	37	2	61492720	61492720	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61492720delC	uc002sbe.2	-						USP34_uc002sbf.2_Intron	NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63053199	63053199	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63053199delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70392359	70392359	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70392359delA	uc002sgh.2	-							NM_017880	NP_060350			hypothetical protein LOC54980												0																		---	---	---	---
TIA1	7072	broad.mit.edu	37	2	70441335	70441335	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70441335delA	uc002sgj.3	-						TIA1_uc002sgk.3_Intron|TIA1_uc002sgl.3_Intron	NM_022173	NP_071505			TIA1 cytotoxic granule-associated RNA binding						apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0																		---	---	---	---
CCT7	10574	broad.mit.edu	37	2	73476418	73476419	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73476418_73476419delTT	uc002siz.2	+						CCT7_uc002sja.2_Intron|CCT7_uc010yrf.1_Intron|CCT7_uc010feu.2_Intron|CCT7_uc010yrg.1_Intron|CCT7_uc010yrh.1_Intron|CCT7_uc010yri.1_Intron	NM_006429	NP_006420			chaperonin containing TCP1, subunit 7 isoform a						'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86682418	86682418	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86682418delT	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903			jumonji domain containing 1A						androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86719331	86719333	+	3'UTR	DEL	TCT	-	-	rs139722069	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86719331_86719333delTCT	uc002sri.3	+	26					KDM3A_uc010ytj.1_3'UTR|KDM3A_uc010ytk.1_3'UTR	NM_018433	NP_060903			jumonji domain containing 1A						androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	90048090	90048091	+	Intron	DEL	CA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90048090_90048091delCA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
NCAPH	23397	broad.mit.edu	37	2	97020221	97020221	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97020221delT	uc002svz.1	+						NCAPH_uc010fhu.1_Intron|NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156			non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)																---	---	---	---
TXNDC9	10190	broad.mit.edu	37	2	99944255	99944256	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99944255_99944256delTT	uc002szz.2	-						TXNDC9_uc010yvp.1_Intron|TXNDC9_uc002taa.1_Intron	NM_005783	NP_005774			thioredoxin domain containing 9						cell redox homeostasis		protein binding				0																		---	---	---	---
TXNDC9	10190	broad.mit.edu	37	2	99949735	99949735	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99949735delA	uc002szz.2	-						TXNDC9_uc010yvp.1_Intron|TXNDC9_uc002taa.1_Intron	NM_005783	NP_005774			thioredoxin domain containing 9						cell redox homeostasis		protein binding				0																		---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101624787	101624787	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101624787delT	uc010fiv.2	-						RPL31_uc010yvu.1_Intron|RPL31_uc010yvv.1_Intron|RPL31_uc010fiu.1_Intron|TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896			TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116572705	116572705	+	Intron	DEL	T	-	-	rs79224686		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116572705delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
UGGT1	56886	broad.mit.edu	37	2	128874108	128874108	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128874108delT	uc002tps.2	+						UGGT1_uc010fme.1_Intron|UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505			UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
MGAT5	4249	broad.mit.edu	37	2	135012020	135012020	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135012020delT	uc002ttv.1	+	1	191	c.46delT	c.(46-48)TTTfs	p.F16fs		NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V	16	Helical; Signal-anchor for type II membrane protein; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)														---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141773219	141773219	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141773219delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148683686delA	uc002twg.2	+	11	1572	c.1303delA	c.(1303-1305)AAAfs	p.K435fs	ACVR2A_uc010zbn.1_Frame_Shift_Del_p.K327fs|ACVR2A_uc002twh.2_Frame_Shift_Del_p.K435fs	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	435	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149225889	149225889	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149225889delT	uc002twm.3	+						MBD5_uc010zbs.1_Intron|MBD5_uc010fns.2_Intron|MBD5_uc002twn.1_5'Flank	NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152302071	152302071	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152302071delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152830110	152830111	+	Intron	INS	-	G	G	rs139660380	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152830110_152830111insG	uc002tya.2	-						CACNB4_uc002txy.2_Intron|CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron|CACNB4_uc002tyb.2_Intron	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158406602	158406602	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158406602delT	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron|ACVR1C_uc010foe.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159912831	159912831	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159912831delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159954483	159954483	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159954483delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162868259	162868259	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162868259delA	uc002ubz.2	-						DPP4_uc010fpb.2_Intron	NM_001935	NP_001926			dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
FAP	2191	broad.mit.edu	37	2	163076484	163076484	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163076484delA	uc002ucd.2	-						FAP_uc010zct.1_Intron|FAP_uc010fpd.2_Intron|FAP_uc010fpe.1_Intron	NM_004460	NP_004451			fibroblast activation protein, alpha subunit						endothelial cell migration|negative regulation of extracellular matrix disassembly|proteolysis	cell junction|integral to membrane|invadopodium membrane|lamellipodium membrane	dipeptidyl-peptidase activity|metalloendopeptidase activity|protein homodimerization activity|serine-type endopeptidase activity			ovary(3)	3																		---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166771641	166771641	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166771641delA	uc002udk.2	-							NM_024753	NP_079029			tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
TTC30B	150737	broad.mit.edu	37	2	178415367	178415368	+	3'UTR	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178415367_178415368delTT	uc002uln.2	-	1					TTC30B_uc010zfc.1_3'UTR	NM_152517	NP_689730			tetratricopeptide repeat domain 30B						cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)															---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179156451	179156451	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179156451delC	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron|OSBPL6_uc002ulz.2_Intron	NM_032523	NP_115912			oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
GULP1	51454	broad.mit.edu	37	2	189434712	189434712	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189434712delA	uc010fru.2	+						GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron|GULP1_uc002uqh.1_5'Flank	NM_016315	NP_057399			GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)															---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200193649	200193649	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200193649delA	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																		---	---	---	---
NDUFB3	4709	broad.mit.edu	37	2	201943496	201943496	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201943496delT	uc002uwx.3	+							NM_002491	NP_002482			NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0					NADH(DB00157)													---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202446726	202446726	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202446726delA	uc002uye.2	-						ALS2CR11_uc002uyf.2_Intron|ALS2CR11_uc010fti.2_Intron	NM_152525	NP_689738			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ALS2CR8	79800	broad.mit.edu	37	2	203807442	203807442	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203807442delT	uc002uzo.2	+						ALS2CR8_uc002uzn.2_Intron|ALS2CR8_uc002uzm.2_Intron|ALS2CR8_uc010zhy.1_Intron|ALS2CR8_uc010zhz.1_Intron|ALS2CR8_uc010ftu.1_Intron|ALS2CR8_uc010zia.1_Intron|ALS2CR8_uc010zib.1_Intron|ALS2CR8_uc010zic.1_Intron|ALS2CR8_uc002uzp.2_Intron	NM_001104586	NP_001098056			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)	2																		---	---	---	---
CYP20A1	57404	broad.mit.edu	37	2	204137575	204137576	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204137575_204137576delTT	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	NM_177538	NP_803882			cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	206813725	206813725	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206813725delA								NRP2 (150869 upstream) : INO80D (44721 downstream)																																			---	---	---	---
PIKFYVE	200576	broad.mit.edu	37	2	209169732	209169732	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209169732delA	uc002vcz.2	+	12	1789	c.1631delA	c.(1630-1632)CAAfs	p.Q544fs	PIKFYVE_uc010fun.1_Frame_Shift_Del_p.Q225fs|PIKFYVE_uc002vcy.1_Intron|PIKFYVE_uc002vcv.2_Frame_Shift_Del_p.Q447fs|PIKFYVE_uc002vcw.2_Frame_Shift_Del_p.Q544fs|PIKFYVE_uc002vcx.2_Frame_Shift_Del_p.Q458fs	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	544					cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10																		---	---	---	---
MOGAT1	116255	broad.mit.edu	37	2	223562598	223562598	+	Intron	DEL	T	-	-	rs79429686		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223562598delT	uc010fws.1	+						MOGAT1_uc010fwt.1_Intron	NM_058165	NP_477513			monoacylglycerol O-acyltransferase 1						glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			breast(1)	1		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)														---	---	---	---
CCL20	6364	broad.mit.edu	37	2	228678439	228678439	+	5'Flank	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228678439delT	uc002vpl.2	+						CCL20_uc002vpm.2_5'Flank	NM_004591	NP_004582			chemokine (C-C motif) ligand 20 isoform 1						cell-cell signaling|chemotaxis|defense response to bacterium|immune response|inflammatory response|signal transduction	extracellular space	chemokine activity				0		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;7.3e-11)|all cancers(144;4.13e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)														---	---	---	---
CHRNG	1146	broad.mit.edu	37	2	233408190	233408191	+	Intron	INS	-	C	C	rs142201594		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233408190_233408191insC	uc002vsx.1	+						CHRNG_uc010fye.1_Intron	NM_005199	NP_005190			cholinergic receptor, nicotinic, gamma						muscle contraction	cell junction|postsynaptic membrane	acetylcholine receptor activity				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	237209275	237209278	+	IGR	DEL	TCCT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237209275_237209278delTCCT								ASB18 (36287 upstream) : IQCA1 (23516 downstream)																																			---	---	---	---
RAMP1	10267	broad.mit.edu	37	2	238786132	238786132	+	Intron	DEL	G	-	-	rs1210881	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238786132delG	uc002vxj.2	+							NM_005855	NP_005846			receptor activity-modifying protein 1 precursor						intracellular protein transport|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane	protein transporter activity				0		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)													---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5212424	5212424	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5212424delT	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654			ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)														---	---	---	---
VHL	7428	broad.mit.edu	37	3	10182937	10182937	+	5'Flank	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10182937delA	uc003bvc.2	+						VHL_uc003bvd.2_5'Flank	NM_000551	NP_000542			von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding			kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)			1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10427117	10427117	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10427117delA	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdo.2_Intron	NM_001001331	NP_001001331			plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
SYN2	6854	broad.mit.edu	37	3	12203172	12203173	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12203172_12203173insT	uc003bwm.2	+						SYN2_uc003bwl.1_Intron|SYN2_uc003bwn.2_5'UTR|TIMP4_uc003bwo.2_5'Flank	NM_133625	NP_598328			synapsin II isoform IIa						neurotransmitter secretion	synaptic vesicle	ATP binding|ligase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TMEM43	79188	broad.mit.edu	37	3	14173050	14173050	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14173050delT	uc003byk.2	+						TMEM43_uc003byl.1_Intron	NM_024334	NP_077310			transmembrane protein 43							endoplasmic reticulum|Golgi apparatus|integral to membrane|nuclear inner membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32549855	32549855	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32549855delA								CMTM6 (5452 upstream) : DYNC1LI1 (17614 downstream)																																			---	---	---	---
FBXL2	25827	broad.mit.edu	37	3	33425414	33425414	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33425414delT	uc003cfp.2	+						FBXL2_uc011axm.1_Intron|FBXL2_uc011axn.1_Intron|FBXL2_uc011axo.1_Intron|FBXL2_uc011axp.1_Intron|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|FBXL2_uc011axs.1_Intron	NM_012157	NP_036289			F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	36810381	36810381	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36810381delT								DCLK3 (29029 upstream) : TRANK1 (57930 downstream)																																			---	---	---	---
EPM2AIP1	9852	broad.mit.edu	37	3	37032586	37032586	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37032586delA	uc003cgk.2	-	1					MLH1_uc011aye.1_5'Flank|MLH1_uc003cgl.2_5'Flank|MLH1_uc011ayb.1_5'Flank|MLH1_uc010hge.2_5'Flank|MLH1_uc003cgn.3_5'Flank|MLH1_uc011ayc.1_5'Flank|MLH1_uc011ayd.1_5'Flank|MLH1_uc003cgo.2_5'Flank	NM_014805	NP_055620			EPM2A interacting protein 1							endoplasmic reticulum					0																		---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37370690	37370691	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37370690_37370691delTT	uc003cgv.2	+						GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Intron	NM_002078	NP_002069			golgi autoantigen, golgin subfamily a, 4						Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
SLC25A38	54977	broad.mit.edu	37	3	39437714	39437715	+	Intron	DEL	AT	-	-	rs73058289	by1000genomes;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39437714_39437715delAT	uc003cjo.2	+							NM_017875	NP_060345			solute carrier family 25, member 38						erythrocyte differentiation|heme biosynthetic process|transport	integral to membrane|mitochondrial inner membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44893098	44893098	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44893098delA	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
CCDC36	339834	broad.mit.edu	37	3	49278972	49278973	+	Intron	DEL	AC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49278972_49278973delAC	uc003cwk.2	+						CCDC36_uc003cwl.3_Intron|CCDC36_uc011bck.1_Intron	NM_178173	NP_835467			coiled-coil domain containing 36											ovary(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)														---	---	---	---
C3orf62	375341	broad.mit.edu	37	3	49308392	49308392	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49308392delA	uc003cwn.2	-	3					C3orf62_uc003cwm.2_3'UTR	NM_198562	NP_940964			hypothetical protein LOC375341												0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
USP4	7375	broad.mit.edu	37	3	49343050	49343050	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49343050delA	uc003cwq.2	-						USP4_uc003cwo.2_Intron|USP4_uc003cwp.2_Intron|USP4_uc003cwr.2_Intron	NM_003363	NP_003354			ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)														---	---	---	---
RBM5	10181	broad.mit.edu	37	3	50131007	50131007	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50131007delA	uc003cyg.2	+						RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron|RBM5_uc003cyf.2_Intron|RBM5_uc011bdj.1_Intron|RBM5_uc011bdk.1_Intron	NM_005778	NP_005769			RNA binding motif protein 5						apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
C3orf49	132200	broad.mit.edu	37	3	63821164	63821164	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63821164delA	uc003dls.3	+						THOC7_uc003dlt.3_Intron|THOC7_uc003dlu.3_Intron	NR_026866				RecName: Full=Putative uncharacterized protein C3orf49;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	87100193	87100193	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87100193delA								VGLL3 (59936 upstream) : CHMP2B (176220 downstream)																																			---	---	---	---
CGGBP1	8545	broad.mit.edu	37	3	88104473	88104473	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88104473delT	uc003dqs.2	-	4					CGGBP1_uc003dqt.2_3'UTR|CGGBP1_uc003dqu.2_3'UTR	NM_001008390	NP_001008391			CGG triplet repeat binding protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding				0		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)														---	---	---	---
MINA	84864	broad.mit.edu	37	3	97669754	97669754	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97669754delA	uc003drz.1	-						MINA_uc003dry.1_5'Flank|MINA_uc003dsa.1_Intron|MINA_uc003dsb.1_Intron|MINA_uc003dsc.1_Intron|MINA_uc010hpa.1_Intron	NM_001042533	NP_001035998			MYC induced nuclear antigen isoform a						ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1																		---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100330092	100330093	+	Intron	INS	-	TTCT	TTCT	rs143346795	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100330092_100330093insTTCT	uc003duc.2	+							NM_032787	NP_116176			G protein-coupled receptor 128 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100471886	100471886	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100471886delT	uc003dun.2	-						ABI3BP_uc003duj.2_Intron|ABI3BP_uc003duk.2_Intron|ABI3BP_uc003dul.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_Intron	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108133346	108133346	+	Intron	DEL	T	-	-	rs79578015		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108133346delT	uc003dxa.1	-							NM_014981	NP_055796			myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108147078	108147078	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108147078delA	uc003dxa.1	-							NM_014981	NP_055796			myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
ZDHHC23	254887	broad.mit.edu	37	3	113675094	113675094	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113675094delA	uc003eau.2	+						ZDHHC23_uc003eav.2_Intron|ZDHHC23_uc003eaw.1_5'Flank	NM_173570	NP_775841			zinc finger, DHHC domain containing 23							integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
HCLS1	3059	broad.mit.edu	37	3	121377299	121377299	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121377299delT	uc003eeh.3	-						HCLS1_uc011bjj.1_Intron|HCLS1_uc011bjk.1_Intron|HCLS1_uc011bjl.1_Intron	NM_005335	NP_005326			hematopoietic cell-specific Lyn substrate 1						erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|response to hormone stimulus	mitochondrion|nucleus|plasma membrane	DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(114;0.0912)														---	---	---	---
IQCB1	9657	broad.mit.edu	37	3	121518237	121518237	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121518237delA	uc010hre.1	-						IQCB1_uc003eek.2_Intron|IQCB1_uc010hrf.1_Intron	NM_001023570	NP_001018864			IQ motif containing B1 isoform a						cilium assembly|maintenance of organ identity|photoreceptor cell maintenance	centrosome|photoreceptor connecting cilium	calmodulin binding				0				GBM - Glioblastoma multiforme(114;0.0983)														---	---	---	---
NEK11	79858	broad.mit.edu	37	3	130799250	130799251	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130799250_130799251insT	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc003enw.1_Intron|NEK11_uc011blm.1_Intron|NEK11_uc010hto.1_5'Flank	NM_024800	NP_079076			NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6																		---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131963189	131963189	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131963189delA	uc003eom.2	-							NM_130808	NP_570720			copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
PLS1	5357	broad.mit.edu	37	3	142413165	142413165	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142413165delT	uc010huv.2	+						PLS1_uc003euz.2_Intron|PLS1_uc003eva.2_Intron	NM_001145319	NP_001138791			plastin 1							cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(1)	1																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143515797	143515797	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143515797delA	uc003evn.2	-						SLC9A9_uc011bnk.1_Intron	NM_173653	NP_775924			solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3																		---	---	---	---
CP	1356	broad.mit.edu	37	3	148899609	148899609	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148899609delT	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003eww.3_5'Flank|CP_uc003ewx.3_Intron|CP_uc003ewz.2_Intron	NM_000096	NP_000087			ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)													---	---	---	---
C3orf79	152118	broad.mit.edu	37	3	153203781	153203781	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153203781delT	uc003ezt.2	+							NM_001101337	NP_001094807			chromosome 3 open reading frame 79												0																		---	---	---	---
DHX36	170506	broad.mit.edu	37	3	154010602	154010602	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154010602delT	uc003ezy.3	-						DHX36_uc010hvq.2_Intron|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916			DEAH (Asp-Glu-Ala-His) box polypeptide 36							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
TIPARP	25976	broad.mit.edu	37	3	156423064	156423065	+	3'UTR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156423064_156423065insT	uc003fav.2	+	6					TIPARP_uc003faw.2_3'UTR	NM_015508	NP_056323			TCDD-inducible poly(ADP-ribose) polymerase								NAD+ ADP-ribosyltransferase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|breast(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
MFSD1	64747	broad.mit.edu	37	3	158544891	158544891	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158544891delT	uc003fcl.1	+						MFSD1_uc003fcm.1_Intron|MFSD1_uc003fcn.1_Intron|MFSD1_uc011bow.1_Intron|MFSD1_uc011box.1_Intron	NM_022736	NP_073573			major facilitator superfamily domain containing						transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	160093679	160093679	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160093679delA	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_Intron|IFT80_uc003fdd.1_Intron|IFT80_uc003fde.1_Intron	NM_020800	NP_065851			WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
SMC4	10051	broad.mit.edu	37	3	160141141	160141147	+	Intron	DEL	TTTTTTG	-	-	rs4679884		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160141141_160141147delTTTTTTG	uc003fdh.2	+						IFT80_uc003fda.2_Intron|SMC4_uc010hwc.1_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|SMC4_uc003fdl.2_Intron	NM_001002800	NP_001002800			SMC4 structural maintenance of chromosomes						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169801681	169801682	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169801681_169801682insT	uc003fgi.2	+						GPR160_uc010hwq.2_Intron	NM_014373	NP_055188			G protein-coupled receptor 160							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
SLC2A2	6514	broad.mit.edu	37	3	170736123	170736123	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170736123delT	uc003fhe.1	-						SLC2A2_uc003fhf.1_Intron|SLC2A2_uc011bpu.1_Intron	NM_000340	NP_000331			solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)															---	---	---	---
ACTL6A	86	broad.mit.edu	37	3	179305643	179305643	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179305643delA	uc003fjw.2	+						ACTL6A_uc003fjx.2_Intron|ACTL6A_uc003fjy.2_Intron	NM_004301	NP_004292			actin-like 6A isoform 1						chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179439084	179439084	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179439084delA	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179479203	179479203	+	Intron	DEL	T	-	-	rs74695249		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179479203delT	uc003fkh.2	+							NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183436187	183436187	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183436187delT	uc003fly.2	+							NM_018023	NP_060493			YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184742112	184742112	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184742112delT	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118			vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
MAP3K13	9175	broad.mit.edu	37	3	185181253	185181253	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185181253delA	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron|MAP3K13_uc011bru.1_Intron|MAP3K13_uc003fpi.2_Intron|MAP3K13_uc010hyg.2_Intron	NM_004721	NP_004712			mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)															---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185978142	185978143	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185978142_185978143insA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
DGKG	1608	broad.mit.edu	37	3	186015279	186015279	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186015279delA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193360958	193360958	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193360958delA	uc003ftm.2	+						OPA1_uc003ftg.2_Intron|OPA1_uc003fth.2_Intron|OPA1_uc003fti.2_Intron|OPA1_uc003ftj.2_Intron|OPA1_uc003ftk.2_Intron|OPA1_uc003ftl.2_Intron|OPA1_uc003ftn.2_Intron	NM_015560	NP_056375			optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)														---	---	---	---
PCYT1A	5130	broad.mit.edu	37	3	195975231	195975231	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195975231delT	uc003fwg.2	-						PCYT1A_uc003fwh.2_Intron	NM_005017	NP_005008			choline phosphate cytidylyltransferase 1 alpha							cytosol|soluble fraction	choline-phosphate cytidylyltransferase activity				0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)													---	---	---	---
WDR53	348793	broad.mit.edu	37	3	196281881	196281882	+	Intron	INS	-	AGGTAGAATTA	AGGTAGAATTA	rs147559216	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196281881_196281882insAGGTAGAATTA	uc003fwt.2	-							NM_182627	NP_872433			WD repeat domain 53											breast(1)|skin(1)	2	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)														---	---	---	---
MFI2	4241	broad.mit.edu	37	3	196746721	196746721	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196746721delA	uc003fxk.3	-						MFI2_uc003fxl.3_Intron|MFI2_uc011bua.1_Intron	NM_005929	NP_005920			melanoma-associated antigen p97 isoform 1						cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)														---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1919853	1919853	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1919853delT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.1_Intron|WHSC1_uc003geh.1_Intron	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
TBC1D14	57533	broad.mit.edu	37	4	6998263	6998265	+	Intron	DEL	AAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6998263_6998265delAAA	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron|TBC1D14_uc010idh.2_Intron|TBC1D14_uc011bwh.1_5'Flank	NM_001113361	NP_001106832			TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
SH3TC1	54436	broad.mit.edu	37	4	8242814	8242814	+	3'UTR	DEL	T	-	-	rs67520179		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8242814delT	uc003gkv.3	+	18					SH3TC1_uc003gkw.3_3'UTR|SH3TC1_uc003gkx.3_RNA|SH3TC1_uc003gky.2_RNA	NM_018986	NP_061859			SH3 domain and tetratricopeptide repeats 1								binding			large_intestine(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	9053504	9053504	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9053504delA								LOC650293 (101378 upstream) : USP17 (306605 downstream)																																			---	---	---	---
WDR1	9948	broad.mit.edu	37	4	10099543	10099548	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10099543_10099548delAAAAAA	uc003gmf.2	-						WDR1_uc003gmg.2_Intron	NM_017491	NP_059830			WD repeat-containing protein 1 isoform 1						platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)														---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13582681	13582681	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13582681delA	uc003gmz.1	-							NM_148894	NP_683692			biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
CPEB2	132864	broad.mit.edu	37	4	15059946	15059946	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15059946delT	uc003gni.1	+						CPEB2_uc003gnj.1_Intron|CPEB2_uc003gnk.1_Intron|CPEB2_uc003gnl.1_Intron|CPEB2_uc003gnm.1_Intron|CPEB2_uc003gnn.1_Intron	NM_182485	NP_872291			cytoplasmic polyadenylation element binding						regulation of translation	cytoplasm	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
PROM1	8842	broad.mit.edu	37	4	16014803	16014803	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16014803delT	uc003goo.2	-						PROM1_uc003gor.2_Intron|PROM1_uc003gos.2_Intron|PROM1_uc003got.2_Intron|PROM1_uc003gou.2_Intron|PROM1_uc003gop.2_Intron|PROM1_uc003goq.3_Intron|PROM1_uc010iec.1_Intron	NM_006017	NP_006008			prominin 1 isoform 1						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7																		---	---	---	---
TAPT1	202018	broad.mit.edu	37	4	16189981	16189982	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16189981_16189982delAA	uc010ied.1	-						TAPT1_uc011bxd.1_Intron|TAPT1_uc011bxe.1_Intron	NM_153365	NP_699196			transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0																		---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20535489	20535490	+	Intron	DEL	AC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20535489_20535490delAC	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778			slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	25043001	25043001	+	IGR	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25043001delG								LGI2 (10587 upstream) : SEPSECS (78627 downstream)																																			---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25392745	25392745	+	Intron	DEL	A	-	-	rs74723419		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25392745delA	uc003gro.2	+						ANAPC4_uc003grp.2_Intron|ANAPC4_uc010iet.1_Intron|ANAPC4_uc010ieu.1_Intron	NM_013367	NP_037499			anaphase-promoting complex subunit 4						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|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 K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)																---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27019137	27019137	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27019137delT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
RFC1	5981	broad.mit.edu	37	4	39313233	39313233	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39313233delA	uc003gty.1	-						RFC1_uc003gtx.1_Intron	NM_002913	NP_002904			replication factor C large subunit						DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|telomere maintenance via telomerase|transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39974662	39974662	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39974662delT	uc003guv.3	-						PDS5A_uc010ifo.2_Intron|PDS5A_uc003guw.3_Intron	NM_001100399	NP_001093869			PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0																		---	---	---	---
GABRB1	2560	broad.mit.edu	37	4	47428212	47428212	+	3'UTR	DEL	A	-	-	rs111359296		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47428212delA	uc003gxh.2	+	9					GABRB1_uc011bze.1_3'UTR	NM_000812	NP_000803			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48514377	48514377	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48514377delA	uc003gyh.1	-						FRYL_uc003gyf.1_Intron|FRYL_uc003gyg.1_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625211	48625213	+	Intron	DEL	AAC	-	-	rs776579	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625211_48625213delAAC	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	53429797	53429798	+	IGR	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53429797_53429798insA								SPATA18 (466340 upstream) : USP46 (27331 downstream)																																			---	---	---	---
SRD5A3	79644	broad.mit.edu	37	4	56217825	56217825	+	Intron	DEL	A	-	-	rs34820507		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56217825delA	uc003hau.2	+							NM_024592	NP_078868			steroid 5 alpha-reductase 3						androgen biosynthetic process|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|polyprenol catabolic process	endoplasmic reticulum membrane|integral to membrane	3-oxo-5-alpha-steroid 4-dehydrogenase activity|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0	all_cancers(7;0.0308)|all_lung(4;0.00195)|Lung NSC(11;0.00431)|all_epithelial(27;0.0425)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.0179)															---	---	---	---
CSN2	1447	broad.mit.edu	37	4	70826811	70826811	+	5'Flank	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70826811delA	uc003hes.3	-						CSN2_uc003het.3_5'Flank	NM_001891	NP_001882			casein beta precursor						calcium ion transport	extracellular region	calcium ion binding|enzyme inhibitor activity|transporter activity				0																		---	---	---	---
DCK	1633	broad.mit.edu	37	4	71892332	71892332	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71892332delT	uc003hfx.2	+						DCK_uc011cbb.1_Intron	NM_000788	NP_000779			deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)													---	---	---	---
PARM1	25849	broad.mit.edu	37	4	75959192	75959192	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75959192delA	uc003hih.1	+							NM_015393	NP_056208			prostatic androgen-repressed message-1						positive regulation of telomerase activity	early endosome|endosome membrane|Golgi membrane|integral to membrane|late endosome|plasma membrane				ovary(1)	1																		---	---	---	---
SDAD1	55153	broad.mit.edu	37	4	76891521	76891521	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76891521delT	uc003hje.3	-	10	943	c.824delA	c.(823-825)AAGfs	p.K275fs	SDAD1_uc003hjf.3_Frame_Shift_Del_p.K178fs|SDAD1_uc011cbr.1_Frame_Shift_Del_p.K238fs	NM_018115	NP_060585	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	275	Potential.				protein transport|ribosomal large subunit biogenesis	nucleolus	protein binding			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
CCNI	10983	broad.mit.edu	37	4	77969240	77969240	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77969240delT	uc003hkm.2	-	7					CCNI_uc011ccb.1_3'UTR	NM_006835	NP_006826			cyclin I						spermatogenesis					ovary(1)	1																		---	---	---	---
PRKG2	5593	broad.mit.edu	37	4	82013427	82013427	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82013427delA	uc003hmh.2	-						PRKG2_uc011ccf.1_Intron|PRKG2_uc011ccg.1_Intron|PRKG2_uc011cch.1_Intron	NM_006259	NP_006250			protein kinase, cGMP-dependent, type II						platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7																		---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83796063	83796064	+	Intron	DEL	AC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83796063_83796064delAC	uc003hnf.2	-						SEC31A_uc003hne.2_5'Flank|SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron|SEC31A_uc003hnn.1_Intron|SEC31A_uc003hno.2_Intron	NM_001077207	NP_001070675			SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
MRPS18C	51023	broad.mit.edu	37	4	84380859	84380859	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84380859delT	uc003hor.3	+						MRPS18C_uc011ccu.1_Intron	NM_016067	NP_057151			mitochondrial ribosomal protein S18C precursor						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome				0		Hepatocellular(203;0.114)																---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87080754	87080754	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87080754delA	uc003hpq.2	-						MAPK10_uc010ikg.2_Intron|MAPK10_uc003hpr.2_Intron|MAPK10_uc003hps.2_Intron|MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpu.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc010ikh.1_Intron|uc003hpw.2_Intron	NM_138982	NP_620448			mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
SMARCAD1	56916	broad.mit.edu	37	4	95206100	95206100	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95206100delT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron|SMARCAD1_uc011cdw.1_Intron	NM_020159	NP_064544			SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)														---	---	---	---
SMARCAD1	56916	broad.mit.edu	37	4	95210566	95210567	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95210566_95210567insT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron|SMARCAD1_uc011cdw.1_Intron	NM_020159	NP_064544			SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)														---	---	---	---
RAP1GDS1	5910	broad.mit.edu	37	4	99342309	99342309	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99342309delT	uc003htx.3	+						RAP1GDS1_uc003htw.3_Intron|RAP1GDS1_uc003htv.3_Intron|RAP1GDS1_uc003htz.3_Intron|RAP1GDS1_uc003hty.3_Intron|RAP1GDS1_uc003hua.3_Intron	NM_001100427	NP_001093897			RAP1, GTP-GDP dissociation stimulator 1 isoform								binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)				T	NUP98	T-ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	4	103705941	103705946	+	IGR	DEL	CCTCCT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103705941_103705946delCCTCCT								MANBA (23790 upstream) : UBE2D3 (9601 downstream)																																			---	---	---	---
PAPSS1	9061	broad.mit.edu	37	4	108608337	108608337	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108608337delA	uc003hyk.2	-						PAPSS1_uc011cfh.1_Intron	NM_005443	NP_005434			3'-phosphoadenosine 5'-phosphosulfate synthase						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)														---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123234945	123234945	+	Intron	DEL	A	-	-	rs72925991	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123234945delA	uc003ieh.2	+						KIAA1109_uc003iel.1_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123264519	123264519	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123264519delT	uc003ieh.2	+						KIAA1109_uc003iem.2_Intron|KIAA1109_uc003ien.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
ADAD1	132612	broad.mit.edu	37	4	123342283	123342283	+	Intron	DEL	A	-	-	rs35017745		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123342283delA	uc003ieo.2	+						ADAD1_uc003iep.2_Intron|ADAD1_uc003ieq.2_Intron	NM_139243	NP_640336			adenosine deaminase domain containing 1						multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	123533754	123533754	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123533754delT								IL2 (156104 upstream) : IL21 (29 downstream)																																			---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126398215	126398215	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126398215delA	uc003ifj.3	+						FAT4_uc011cgp.1_Intron|FAT4_uc003ifi.1_Intron	NM_024582	NP_078858			FAT tumor suppressor homolog 4 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
PLK4	10733	broad.mit.edu	37	4	128807987	128807987	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128807987delA	uc003ifo.2	+						PLK4_uc011cgs.1_Intron|PLK4_uc011cgt.1_Intron	NM_014264	NP_055079			polo-like kinase 4						G2/M transition of mitotic cell cycle|positive regulation of centriole replication|trophoblast giant cell differentiation	centriole|cleavage furrow|cytosol|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0																		---	---	---	---
SCLT1	132320	broad.mit.edu	37	4	129864050	129864050	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129864050delA	uc003igp.2	-						SCLT1_uc003ign.2_Intron|SCLT1_uc003igo.2_Intron|SCLT1_uc003igq.2_Intron|SCLT1_uc010iob.1_Intron	NM_144643	NP_653244			sodium channel associated protein 1							centrosome				ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	133259021	133259022	+	IGR	INS	-	A	A	rs146147061	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133259021_133259022insA								None (None upstream) : PCDH10 (811448 downstream)																																			---	---	---	---
ELF2	1998	broad.mit.edu	37	4	139983329	139983329	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139983329delT	uc003ihp.1	-						ELF2_uc003ihm.1_Intron|ELF2_uc003ihn.1_Intron|ELF2_uc003iho.1_Intron|ELF2_uc011chc.1_5'UTR	NM_201999	NP_973728			E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
ELMOD2	255520	broad.mit.edu	37	4	141448706	141448706	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141448706delA	uc003iik.2	+							NM_153702	NP_714913			ELMO/CED-12 domain containing 2						phagocytosis|regulation of defense response to virus|response to virus	cytoskeleton	GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	142950187	142950187	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142950187delT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
SMAD1	4086	broad.mit.edu	37	4	146478879	146478882	+	Intron	DEL	CTTA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146478879_146478882delCTTA	uc003ikc.2	+						SMAD1_uc003ikd.2_Intron|SMAD1_uc010iov.2_Intron|SMAD1_uc011cic.1_Intron	NM_005900	NP_005891			Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)															OREG0016348	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151642666	151642667	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151642666_151642667delTT	uc010ipj.2	-						LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
PRSS48	345062	broad.mit.edu	37	4	152204057	152204057	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152204057delA	uc011cif.1	+						PRSS48_uc011cig.1_Intron	NM_183375	NP_899231			epidermis-specific serine protease-like protein						proteolysis	extracellular region	serine-type endopeptidase activity			large_intestine(1)	1																		---	---	---	---
PPID	5481	broad.mit.edu	37	4	159638482	159638482	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159638482delT	uc003iqc.2	-							NM_005038	NP_005029			peptidylprolyl isomerase D						protein folding	cytoplasm|intermediate filament cytoskeleton	cyclosporin A binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0159)														---	---	---	---
C4orf43	55319	broad.mit.edu	37	4	164428219	164428219	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164428219delA	uc003iqq.3	+	2	319	c.38delA	c.(37-39)GAAfs	p.E13fs		NM_018352	NP_060822	Q96EY4	CD043_HUMAN	hypothetical protein LOC55319	13											0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	165865192	165865192	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165865192delA								MARCH1 (559990 upstream) : TRIM61 (10408 downstream)																																			---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169589217	169589217	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169589217delT	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
NEK1	4750	broad.mit.edu	37	4	170428203	170428203	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170428203delT	uc003isb.1	-	21	2400	c.1908delA	c.(1906-1908)AAAfs	p.K636fs	NEK1_uc003isc.1_Frame_Shift_Del_p.K592fs|NEK1_uc003isd.1_Frame_Shift_Del_p.K664fs|NEK1_uc003ise.1_Frame_Shift_Del_p.K620fs|NEK1_uc003isf.1_Frame_Shift_Del_p.K567fs	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	636					cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173930550	173930551	+	Intron	DEL	TG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173930550_173930551delTG	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176622970	176622970	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176622970delT	uc003iuf.2	-						GPM6A_uc011ckj.1_Intron|GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron	NM_201591	NP_963885			glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184174897	184174897	+	Intron	DEL	T	-	-	rs111846382		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184174897delT	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron	NM_024949	NP_079225			WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)														---	---	---	---
IRF2	3660	broad.mit.edu	37	4	185339758	185339758	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185339758delT	uc003iwf.3	-	4	492	c.292delA	c.(292-294)AGCfs	p.S98fs		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	98	IRF tryptophan pentad repeat.				blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)														---	---	---	---
IRX2	153572	broad.mit.edu	37	5	2749792	2749793	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2749792_2749793delTT	uc003jda.2	-	2	600_601	c.358_359delAA	c.(358-360)AACfs	p.N120fs	C5orf38_uc003jdc.2_5'Flank|C5orf38_uc011cmg.1_5'Flank|C5orf38_uc011cmh.1_5'Flank|C5orf38_uc011cmi.1_5'Flank|C5orf38_uc011cmj.1_5'Flank|IRX2_uc003jdb.2_Frame_Shift_Del_p.N120fs	NM_001134222	NP_001127694	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	120	Homeobox; TALE-type.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1				GBM - Glioblastoma multiforme(108;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	3278904	3278905	+	IGR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3278904_3278905insT								C5orf38 (523392 upstream) : IRX1 (317263 downstream)																																			---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5457380	5457380	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5457380delT	uc003jdm.3	+							NM_015325	NP_056140			hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NSUN2	54888	broad.mit.edu	37	5	6610179	6610180	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6610179_6610180delTT	uc003jdu.2	-						NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225			NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1																		---	---	---	---
NSUN2	54888	broad.mit.edu	37	5	6623158	6623160	+	Intron	DEL	AAA	-	-	rs111573762		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6623158_6623160delAAA	uc003jdu.2	-						NSUN2_uc003jdt.2_5'Flank|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225			NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1																		---	---	---	---
SRD5A1	6715	broad.mit.edu	37	5	6633704	6633704	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6633704delG	uc003jdw.2	+	1	205	c.15delG	c.(13-15)ACGfs	p.T5fs	NSUN2_uc003jdu.2_5'Flank|NSUN2_uc011cmk.1_5'Flank|NSUN2_uc003jdv.2_5'Flank|SRD5A1_uc011cml.1_RNA|SRD5A1_uc011cmm.1_Frame_Shift_Del_p.R14fs	NM_001047	NP_001038	P18405	S5A1_HUMAN	steroid-5-alpha-reductase 1	5					androgen biosynthetic process|cell differentiation|sex determination|sex differentiation	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|electron carrier activity				0					Dutasteride(DB01126)|Finasteride(DB01216)													---	---	---	---
MTRR	4552	broad.mit.edu	37	5	7885676	7885676	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7885676delT	uc003jed.2	+						MTRR_uc010itn.1_Intron|MTRR_uc003jee.3_Intron|MTRR_uc003jef.3_Intron|MTRR_uc003jeg.3_Intron|MTRR_uc010ito.2_Intron	NM_024010	NP_076915			methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)													---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13727544	13727544	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13727544delT	uc003jfd.2	-						DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	5	17333068	17333068	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17333068delT								BASP1 (56133 upstream) : None (None downstream)																																			---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31508944	31508945	+	Intron	DEL	TC	-	-	rs146890140	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31508944_31508945delTC	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron|RNASEN_uc003jhi.2_Intron|RNASEN_uc010iui.1_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32242341	32242341	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32242341delT	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536			myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
SUB1	10923	broad.mit.edu	37	5	32601324	32601324	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32601324delT	uc003jhs.2	+	5					SUB1_uc003jht.2_RNA	NM_006713	NP_006704			activated RNA polymerase II transcription						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus|transcription factor complex	protein binding|single-stranded DNA binding|transcription coactivator activity				0																		---	---	---	---
PRLR	5618	broad.mit.edu	37	5	35086663	35086664	+	Intron	DEL	GT	-	-	rs73767508	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35086663_35086664delGT	uc003jjm.2	-						PRLR_uc003jjg.1_Intron|PRLR_uc003jjh.1_Intron|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Intron|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_Intron|PRLR_uc010iuw.1_5'Flank	NM_000949	NP_000940			prolactin receptor precursor						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)													---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38959432	38959432	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38959432delA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron	NM_152756	NP_689969			rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)																	---	---	---	---
FYB	2533	broad.mit.edu	37	5	39203039	39203040	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39203039_39203040insC	uc003jls.2	-	1	90_91	c.23_24insG	c.(22-24)GGCfs	p.G8fs	FYB_uc003jlt.2_Frame_Shift_Ins_p.G8fs|FYB_uc003jlu.2_Frame_Shift_Ins_p.G8fs|FYB_uc011cpl.1_Frame_Shift_Ins_p.G18fs	NM_199335	NP_955367	O15117	FYB_HUMAN	FYN binding protein (FYB-120/130) isoform 2	8					cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
C7	730	broad.mit.edu	37	5	40945509	40945509	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40945509delT	uc003jmh.2	+						C7_uc011cpn.1_Intron	NM_000587	NP_000578			complement component 7 precursor						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)																---	---	---	---
OXCT1	5019	broad.mit.edu	37	5	41731886	41731886	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41731886delA	uc003jmn.2	-						OXCT1_uc011cpo.1_Intron|OXCT1_uc011cpp.1_Intron	NM_000436	NP_000427			3-oxoacid CoA transferase 1 precursor						cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)													---	---	---	---
ZNF131	7690	broad.mit.edu	37	5	43123288	43123288	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43123288delT	uc011cpw.1	+						ZNF131_uc010ivl.1_Intron|ZNF131_uc003jnj.3_Intron|ZNF131_uc003jnk.2_Intron|ZNF131_uc003jnn.3_Intron|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron|ZNF131_uc003jnm.2_Intron	NM_003432	NP_003423			zinc finger protein 131							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43278153	43278155	+	Intron	DEL	TTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43278153_43278155delTTT	uc003jno.2	+							NM_153361	NP_699192			serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9																		---	---	---	---
C5orf34	375444	broad.mit.edu	37	5	43508596	43508596	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43508596delA	uc003jnz.1	-						C5orf34_uc011cpx.1_Intron	NM_198566	NP_940968			hypothetical protein LOC375444											breast(1)	1	Lung NSC(6;2.07e-05)																	---	---	---	---
GPBP1	65056	broad.mit.edu	37	5	56557233	56557233	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56557233delA	uc003jrh.3	+						GPBP1_uc010iwg.2_Intron|GPBP1_uc003jri.3_Intron|GPBP1_uc003jrj.3_Intron|GPBP1_uc003jrk.3_Intron|GPBP1_uc003jrl.3_Intron	NM_022913	NP_075064			GC-rich promoter binding protein 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)														---	---	---	---
PLK2	10769	broad.mit.edu	37	5	57754160	57754160	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57754160delA	uc003jrn.2	-						PLK2_uc011cql.1_Frame_Shift_Del_p.Y133fs	NM_006622	NP_006613			polo-like kinase 2						positive regulation of I-kappaB kinase/NF-kappaB cascade		ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)														---	---	---	---
CDK7	1022	broad.mit.edu	37	5	68555513	68555513	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68555513delA	uc003jvs.3	+						CDK7_uc003jvt.3_Intron|CDK7_uc003jvu.3_Intron	NM_001799	NP_001790			cyclin-dependent kinase 7						androgen receptor signaling pathway|cell division|cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex|mitochondrion	androgen receptor binding|ATP binding|cyclin-dependent protein kinase activity|DNA-dependent ATPase activity|protein C-terminus binding|RNA polymerase II carboxy-terminal domain kinase activity|transcription coactivator activity			lung(1)	1		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)									NER					---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69717512	69717512	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69717512delG	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron|GTF2H2B_uc003jza.3_Intron|GTF2H2B_uc003jzd.1_5'Flank	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
GCNT4	51301	broad.mit.edu	37	5	74324312	74324313	+	3'UTR	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74324312_74324313insA	uc003kdn.2	-	1						NM_016591	NP_057675			core 2 beta-1,6-N-acetylglucosaminyltransferase						protein O-linked glycosylation	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)														---	---	---	---
JMY	133746	broad.mit.edu	37	5	78610473	78610473	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78610473delC	uc003kfx.3	+	9	2978	c.2458delC	c.(2458-2460)CCCfs	p.P820fs	JMY_uc003kfw.1_Frame_Shift_Del_p.P466fs	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein	820	Pro-rich.				'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)														---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79809324	79809324	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79809324delT	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111			hypothetical protein LOC167555												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)														---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94826831	94826831	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94826831delA	uc003klb.2	-							NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94859256	94859256	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94859256delA	uc003klb.2	-						TTC37_uc010jbf.1_Intron	NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112884829	112884829	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112884829delT	uc003kqn.2	+						YTHDC2_uc010jce.1_Intron|YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739			YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)														---	---	---	---
SNCAIP	9627	broad.mit.edu	37	5	121787400	121787400	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121787400delA	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|uc003ktb.1_Intron|SNCAIP_uc003ktc.1_Intron	NM_005460	NP_005451			synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)														---	---	---	---
SNX2	6643	broad.mit.edu	37	5	122165208	122165208	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122165208delT	uc003kte.2	+						SNX2_uc011cwn.1_Intron	NM_003100	NP_003091			sorting nexin 2						cell communication|endocytosis|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding|protein transporter activity			kidney(1)	1		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)														---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122930883	122930883	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122930883delT	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Intron	NM_004384	NP_004375			casein kinase 1, gamma 3 isoform 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)														---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132272730	132272730	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132272730delA	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron|AFF4_uc003kyf.3_Intron	NM_014423	NP_055238			ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134153425	134153425	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134153425delT	uc003kzw.2	+							NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
CATSPER3	347732	broad.mit.edu	37	5	134331762	134331762	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134331762delG	uc003lag.2	+							NM_178019	NP_821138			cation channel, sperm associated 3						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
PKD2L2	27039	broad.mit.edu	37	5	137241780	137241780	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137241780delA	uc003lby.2	+						PKD2L2_uc010jep.1_Intron|PKD2L2_uc003lbw.1_Intron|PKD2L2_uc003lbx.2_Intron|PKD2L2_uc011cyi.1_Intron	NM_014386	NP_055201			polycystic kidney disease 2-like 2							integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
PKD2L2	27039	broad.mit.edu	37	5	137243584	137243584	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137243584delT	uc003lby.2	+	7	1185	c.1129delT	c.(1129-1131)TTTfs	p.F377fs	PKD2L2_uc003lbw.1_Frame_Shift_Del_p.F377fs|PKD2L2_uc003lbx.2_Frame_Shift_Del_p.F377fs|PKD2L2_uc011cyi.1_5'UTR	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	377	Helical; (Potential).					integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
DNAJC18	202052	broad.mit.edu	37	5	138760860	138760860	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138760860delT	uc003len.2	-						DNAJC18_uc010jff.2_Intron	NM_152686	NP_689899			DnaJ (Hsp40) homolog, subfamily C, member 18						protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)|kidney(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142273722	142273722	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142273722delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
RBM27	54439	broad.mit.edu	37	5	145665677	145665677	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145665677delA	uc003lnz.3	+	21						NM_018989	NP_061862			RNA binding motif protein 27						mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147902626	147902626	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147902626delA	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron	NM_000870	NP_000861			serotonin 5-HT4 receptor isoform b						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
DCTN4	51164	broad.mit.edu	37	5	150111159	150111159	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150111159delA	uc003lsv.2	-						DCTN4_uc003lsu.2_Intron|DCTN4_uc010jhi.2_Intron|DCTN4_uc010jhj.2_Intron|DCTN4_uc011dck.1_Intron	NM_016221	NP_057305			dynactin 4 (p62) isoform b							centrosome|nucleus	protein N-terminus binding			central_nervous_system(1)	1		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153674366	153674366	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153674366delT	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron	NM_198321	NP_938080			GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)															---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153718077	153718077	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153718077delT	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.2_Intron	NM_198321	NP_938080			GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155771422	155771422	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155771422delT	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	156021886	156021887	+	Intron	DEL	TC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156021886_156021887delTC	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ADAM19	8728	broad.mit.edu	37	5	156847642	156847645	+	Intron	DEL	AAAA	-	-	rs150233893		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156847642_156847645delAAAA	uc003lww.1	-											SubName: Full=cDNA FLJ34145 fis, clone FCBBF3011867, highly similar to ADAM 19 (EC 3.4.24.-);						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167379581	167379581	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167379581delT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
FAM153A	285596	broad.mit.edu	37	5	177167589	177167589	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177167589delT	uc010jkp.1	-						FAM153A_uc011dgd.1_Intron|FAM153A_uc003mib.1_Intron|FAM153A_uc003mic.2_Intron	NM_173663	NP_775934			hypothetical protein LOC285596											skin(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177695605	177695605	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177695605delG	uc003mje.2	-						COL23A1_uc010jkt.2_Intron	NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
HNRNPH1	3187	broad.mit.edu	37	5	179044122	179044122	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179044122delA	uc003mkf.3	-						HNRNPH1_uc011dgn.1_Intron|HNRNPH1_uc003mkg.3_Intron|HNRNPH1_uc003mke.3_Intron|HNRNPH1_uc003mkh.3_Intron	NM_005520	NP_005511			heterogeneous nuclear ribonucleoprotein H1						regulation of RNA splicing	actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|poly(U) RNA binding|protein binding				0																		---	---	---	---
IRF4	3662	broad.mit.edu	37	6	398749	398750	+	Intron	DEL	CA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:398749_398750delCA	uc003msz.3	+						IRF4_uc010jne.1_Intron|IRF4_uc003mta.3_Intron|IRF4_uc003mtb.3_Intron|IRF4_uc003mtc.1_Intron	NM_002460	NP_002451			interferon regulatory factor 4						interferon-gamma-mediated signaling pathway|positive regulation of interleukin-10 biosynthetic process|positive regulation of interleukin-13 biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of transcription, DNA-dependent|regulation of T-helper cell differentiation|T cell activation|type I interferon-mediated signaling pathway	cytoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(1)	1		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)				T	IGH@	MM 								---	---	---	---
DSP	1832	broad.mit.edu	37	6	7562607	7562608	+	Intron	DEL	TT	-	-	rs147191716		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7562607_7562608delTT	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
SYCP2L	221711	broad.mit.edu	37	6	10906052	10906052	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10906052delA	uc003mzo.2	+						SYCP2L_uc011din.1_Intron|SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364			synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	12165337	12165337	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12165337delT								HIVEP1 (106 upstream) : EDN1 (125192 downstream)																																			---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15246694	15246695	+	5'UTR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15246694_15246695insT	uc003nbj.2	+	1					JARID2_uc011diu.1_Intron|JARID2_uc011div.1_5'Flank	NM_004973	NP_004964			jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
KDM1B	221656	broad.mit.edu	37	6	18222307	18222307	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18222307delA	uc003nco.1	+	15					KDM1B_uc003ncn.1_3'UTR|KDM1B_uc003ncp.1_3'UTR|KDM1B_uc003ncq.1_Frame_Shift_Del_p.K203fs	NM_153042	NP_694587			amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1																		---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	21108618	21108619	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21108618_21108619insT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc003ndf.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
SLC17A3	10786	broad.mit.edu	37	6	25845376	25845377	+	3'UTR	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25845376_25845377insA	uc003nfi.3	-	12					SLC17A3_uc003nfk.3_3'UTR	NM_006632	NP_006623			solute carrier family 17 (sodium phosphate),						glucose-6-phosphate transport|urate metabolic process	apical plasma membrane|brush border membrane|endoplasmic reticulum membrane|integral to plasma membrane|perinuclear region of cytoplasm	drug transmembrane transporter activity|efflux transmembrane transporter activity|organic anion transmembrane transporter activity|sodium:phosphate symporter activity|toxin transporter activity|urate transmembrane transporter activity|voltage-gated anion channel activity				0																		---	---	---	---
HIST1H2BJ	8970	broad.mit.edu	37	6	27099962	27099962	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27099962delA	uc003niu.1	-						HIST1H2AG_uc003niw.2_5'Flank					Homo sapiens histone cluster 1, H2bj, mRNA (cDNA clone IMAGE:4048288), with apparent retained intron.						defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding				0																		---	---	---	---
OR5V1	81696	broad.mit.edu	37	6	29323702	29323702	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29323702delT	uc011dlo.1	-	1	353	c.271delA	c.(271-273)AGCfs	p.S91fs		NM_030876	NP_110503	Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V,	91	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|kidney(1)	4																		---	---	---	---
HLA-E	3133	broad.mit.edu	37	6	30459582	30459582	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30459582delT	uc003nqg.2	+						HLA-E_uc011dmg.1_Intron|HLA-E_uc011dmh.1_Intron	NM_005516	NP_005507			major histocompatibility complex, class I, E						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5																		---	---	---	---
VARS2	57176	broad.mit.edu	37	6	30893244	30893244	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30893244delC	uc003nsc.1	+						VARS2_uc011dmx.1_Intron|VARS2_uc011dmy.1_Intron|VARS2_uc011dmz.1_Intron|VARS2_uc011dna.1_Intron|VARS2_uc011dnb.1_Intron|VARS2_uc011dnc.1_Intron|VARS2_uc011dnd.1_Intron|VARS2_uc010jsg.1_Intron|VARS2_uc010jsh.1_Intron	NM_020442	NP_065175			valyl-tRNA synthetase 2, mitochondrial						valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31602641	31602641	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31602641delC	uc003nvb.3	+	21	5296	c.5047delC	c.(5047-5049)CCCfs	p.P1683fs	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Frame_Shift_Del_p.P1683fs	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1683	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0																		---	---	---	---
LSM2	57819	broad.mit.edu	37	6	31765402	31765402	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31765402delA	uc003nxg.2	-	5					VARS_uc003nxe.2_5'Flank|VARS_uc011doi.1_5'Flank	NM_021177	NP_067000			LSM2 homolog, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytosol|nucleoplasm	U6 snRNA binding				0																		---	---	---	---
EHMT2	10919	broad.mit.edu	37	6	31860026	31860026	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31860026delA	uc003nxz.1	-						EHMT2_uc003nxy.1_Intron|EHMT2_uc011don.1_Intron|EHMT2_uc003nya.1_Intron	NM_006709	NP_006700			euchromatic histone-lysine N-methyltransferase 2						DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1																		---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32497712	32497713	+	Intron	INS	-	A	A	rs146725750	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32497712_32497713insA	uc003obj.2	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB5_uc003obk.3_Intron	NM_002125	NP_002116			major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
SCUBE3	222663	broad.mit.edu	37	6	35207392	35207393	+	Intron	INS	-	AG	AG			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35207392_35207393insAG	uc003okf.1	+						SCUBE3_uc003okg.1_Intron|SCUBE3_uc003okh.1_Intron	NM_152753	NP_689966			signal peptide, CUB domain, EGF-like 3						protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1																		---	---	---	---
FANCE	2178	broad.mit.edu	37	6	35424297	35424300	+	Intron	DEL	TTTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35424297_35424300delTTTT	uc003oko.1	+						FANCE_uc010jvw.1_Intron	NM_021922	NP_068741			Fanconi anemia, complementation group E						DNA repair	nucleoplasm	protein binding			ovary(1)|lung(1)|skin(1)	3								N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
C6orf126	389383	broad.mit.edu	37	6	35745414	35745414	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35745414delA	uc010jvz.1	+						C6orf126_uc003olc.1_Intron	NM_207409	NP_997292			hypothetical protein LOC389383 precursor						digestion|lipid catabolic process	extracellular region	enzyme activator activity				0																		---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38565663	38565664	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38565663_38565664insA	uc003ooa.3	-						BTBD9_uc003ony.3_5'Flank|BTBD9_uc010jwv.2_5'Flank|BTBD9_uc010jww.2_5'Flank|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125			BTB (POZ) domain containing 9 isoform a						cell adhesion						0																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38867746	38867747	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38867746_38867747delAA	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
C6orf153	88745	broad.mit.edu	37	6	42994802	42994802	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42994802delA	uc003otp.1	+							NM_033112	NP_149103			hypothetical protein LOC88745						ribosomal small subunit biogenesis|rRNA processing	nucleolus					0			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
CRIP3	401262	broad.mit.edu	37	6	43275190	43275190	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43275190delA	uc010jyn.1	-						CRIP3_uc003ouu.1_Intron	NM_206922	NP_996805			cysteine-rich protein 3							cytoplasm	zinc ion binding			skin(1)	1			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)															---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44371468	44371468	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44371468delT	uc003oxl.2	+							NM_001253	NP_001244			CDC5-like						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
CYP39A1	51302	broad.mit.edu	37	6	46619887	46619887	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46619887delA	uc003oyf.1	-						CYP39A1_uc011dwa.1_Intron|CYP39A1_uc010jzd.1_Intron|SLC25A27_uc011dwb.1_5'Flank|SLC25A27_uc003oyg.2_5'Flank|SLC25A27_uc003oyh.2_5'Flank|SLC25A27_uc011dwc.1_5'Flank	NM_016593	NP_057677			cytochrome P450, family 39, subfamily A,						bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1																		---	---	---	---
CENPQ	55166	broad.mit.edu	37	6	49456585	49456586	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49456585_49456586delTT	uc003ozh.1	+							NM_018132	NP_060602			centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)																	---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49701364	49701364	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49701364delT	uc003ozs.2	-							NM_006061	NP_006052			cysteine-rich secretory protein 3 precursor						innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	50864684	50864687	+	IGR	DEL	CTTC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50864684_50864687delCTTC								TFAP2B (49359 upstream) : PKHD1 (615458 downstream)																																			---	---	---	---
EFHC1	114327	broad.mit.edu	37	6	52318750	52318750	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52318750delT	uc003pap.3	+						EFHC1_uc011dwv.1_Intron|EFHC1_uc011dww.1_Intron	NM_018100	NP_060570			EF-hand domain (C-terminal) containing 1							axoneme|neuronal cell body	calcium ion binding|protein C-terminus binding			ovary(2)|skin(1)	3	Lung NSC(77;0.109)																	---	---	---	---
DST	667	broad.mit.edu	37	6	56434717	56434717	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56434717delT	uc003pdf.2	-	48	7486	c.7458delA	c.(7456-7458)AAAfs	p.K2486fs	DST_uc003pcz.3_Frame_Shift_Del_p.K2308fs|DST_uc011dxj.1_Frame_Shift_Del_p.K2337fs|DST_uc011dxk.1_Frame_Shift_Del_p.K2348fs|DST_uc003pcy.3_Frame_Shift_Del_p.K1982fs	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	4394					cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
GUSBL2	375513	broad.mit.edu	37	6	58285234	58285234	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58285234delT	uc011dxq.1	-						GUSBL2_uc011dxp.1_Intron|GUSBL2_uc003peb.3_Intron|GUSBL2_uc003pec.3_Intron|GUSBL2_uc003ped.3_Intron|GUSBL2_uc003pee.3_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348869; Flags: Fragment;												0																		---	---	---	---
BAI3	577	broad.mit.edu	37	6	69785876	69785876	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69785876delT	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695			brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70500156	70500156	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70500156delA	uc003pfa.2	-						LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838			liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																		---	---	---	---
FAM135A	57579	broad.mit.edu	37	6	71248202	71248202	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71248202delA	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_Intron	NM_001162529	NP_001156001			hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1																		---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71508370	71508370	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71508370delA	uc003pfr.2	+	6	754	c.506delA	c.(505-507)GAAfs	p.E169fs	SMAP1_uc011dxy.1_RNA|SMAP1_uc003pfs.2_Frame_Shift_Del_p.E142fs|SMAP1_uc010kao.2_Frame_Shift_Del_p.E142fs|SMAP1_uc010kap.2_Frame_Shift_Del_p.E159fs	NM_001044305	NP_001037770	Q8IYB5	SMAP1_HUMAN	stromal membrane-associated GTPase-activating	169					regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75840613	75840614	+	Frame_Shift_Del	DEL	AC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75840613_75840614delAC	uc003phs.2	-	36	6187_6188	c.6021_6022delGT	c.(6019-6024)CTGTACfs	p.L2007fs	COL12A1_uc003pht.2_Frame_Shift_Del_p.L843fs	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2007_2008	Fibronectin type-III 15.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
TMEM30A	55754	broad.mit.edu	37	6	75965692	75965692	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75965692delT	uc003phw.2	-	7					TMEM30A_uc003phx.2_3'UTR	NM_018247	NP_060717			transmembrane protein 30A isoform 1							integral to membrane					0																		---	---	---	---
FILIP1	27145	broad.mit.edu	37	6	76072773	76072773	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76072773delT	uc003pia.2	-						FILIP1_uc003phy.1_Intron|FILIP1_uc003phz.2_5'Flank|FILIP1_uc010kbe.2_Intron	NM_015687	NP_056502			filamin A interacting protein 1											skin(3)|ovary(1)	4																		---	---	---	---
HTR1B	3351	broad.mit.edu	37	6	78172873	78172873	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78172873delG	uc003pil.1	-	1	248	c.248delC	c.(247-249)CCGfs	p.P83fs		NM_000863	NP_000854	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B	83	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cAMP biosynthetic process|synaptic transmission	integral to plasma membrane	protein binding|serotonin receptor activity				0		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Dexfenfluramine(DB01191)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Naratriptan(DB00952)|Pindolol(DB00960)|Propranolol(DB00571)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Venlafaxine(DB00285)|Zolmitriptan(DB00315)													---	---	---	---
ELOVL4	6785	broad.mit.edu	37	6	80634580	80634580	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80634580delA	uc003pja.3	-						ELOVL4_uc011dyt.1_Intron	NM_022726	NP_073563			elongation of very long chain fatty acids-like						fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	G-protein coupled photoreceptor activity|protein binding|transferase activity, transferring acyl groups other than amino-acyl groups			ovary(1)|skin(1)	2		all_cancers(76;1.83e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.011)		BRCA - Breast invasive adenocarcinoma(397;0.0168)	Alpha-Linolenic Acid(DB00132)													---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	80880979	80880979	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80880979delA	uc003pjd.2	+						BCKDHB_uc003pje.2_Intron	NM_000056	NP_000047			branched chain keto acid dehydrogenase E1 beta						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|carboxy-lyase activity|protein binding				0		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)														---	---	---	---
IBTK	25998	broad.mit.edu	37	6	82914730	82914730	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82914730delA	uc003pjl.1	-						IBTK_uc011dyu.1_5'UTR|IBTK_uc011dyv.1_Intron|IBTK_uc011dyw.1_Intron|IBTK_uc010kbi.1_Intron|IBTK_uc003pjm.2_Intron	NM_015525	NP_056340			inhibitor of Bruton's tyrosine kinase						negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88311390	88311390	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88311390delA	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513			origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89601639	89601639	+	Intron	DEL	A	-	-	rs138933610		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89601639delA	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791			RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)														---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89650996	89650996	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89650996delT	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791			RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90374456	90374456	+	Intron	DEL	A	-	-	rs3818133	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90374456delA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MAP3K7	6885	broad.mit.edu	37	6	91226170	91226170	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91226170delA	uc003pnz.1	-	17					MAP3K7_uc003pny.1_3'UTR|MAP3K7_uc003poa.1_3'UTR|MAP3K7_uc003pob.1_3'UTR|MAP3K7_uc003poc.1_3'UTR	NM_145331	NP_663304			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)	6		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97054121	97054121	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97054121delT	uc003pos.1	+						FHL5_uc003pot.1_Intron	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
FBXL4	26235	broad.mit.edu	37	6	99353272	99353272	+	Intron	DEL	A	-	-	rs6935315	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99353272delA	uc003ppf.1	-						FBXL4_uc003ppg.1_Intron|FBXL4_uc003pph.1_Intron|FBXL4_uc010kcp.2_Intron	NM_012160	NP_036292			F-box and leucine-rich repeat protein 4						ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex				skin(2)	2		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)														---	---	---	---
USP45	85015	broad.mit.edu	37	6	99883880	99883880	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99883880delT	uc003ppx.2	-						USP45_uc003ppv.2_Intron|USP45_uc003ppw.2_Intron	NM_001080481	NP_001073950			ubiquitin specific peptidase 45						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|breast(1)	2		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)														---	---	---	---
PREP	5550	broad.mit.edu	37	6	105725779	105725779	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105725779delA	uc003prc.2	-	15						NM_002726	NP_002717			prolyl endopeptidase						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)													---	---	---	---
SCML4	256380	broad.mit.edu	37	6	108123862	108123867	+	Intron	DEL	CCTCTC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108123862_108123867delCCTCTC	uc010kdf.2	-						SCML4_uc003prz.3_Intron|SCML4_uc011eam.1_Intron	NM_198081	NP_932347			sex comb on midleg-like 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)														---	---	---	---
SEC63	11231	broad.mit.edu	37	6	108197689	108197690	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108197689_108197690delAA	uc003psc.3	-						SEC63_uc003psb.3_Intron	NM_007214	NP_009145			SEC63-like protein						protein folding|protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|receptor activity|unfolded protein binding			ovary(1)|skin(1)	2		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)														---	---	---	---
SNX3	8724	broad.mit.edu	37	6	108533549	108533549	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108533549delT	uc003psh.2	-						SNX3_uc003psi.2_Intron|SNX3_uc010kdi.2_Intron	NM_003795	NP_003786			sorting nexin 3 isoform a						cell communication|endocytosis|protein transport	early endosome|endosome membrane	phosphatidylinositol-3-phosphate binding|protein phosphatase binding				0		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108687358	108687358	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108687358delA	uc003psj.2	+							NM_145315	NP_660358			lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
RPF2	84154	broad.mit.edu	37	6	111306053	111306053	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111306053delA	uc003pun.2	+						RPF2_uc003puo.2_Intron	NM_032194	NP_115570			brix domain containing 1							nucleolus	protein binding			ovary(2)	2																		---	---	---	---
FYN	2534	broad.mit.edu	37	6	112025372	112025372	+	Intron	DEL	T	-	-	rs67511839		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112025372delT	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron|FYN_uc003pvh.2_Intron|FYN_uc010kdy.1_5'Flank	NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
MCM9	254394	broad.mit.edu	37	6	119245307	119245307	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119245307delA	uc003pyh.2	-							NM_153255	NP_694987			minichromosome maintenance complex component 9						DNA replication		ATP binding|DNA binding|nucleoside-triphosphatase activity			ovary(1)	1		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)														---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121563198	121563198	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121563198delA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron|C6orf170_uc003pyp.1_Intron	NM_152730	NP_689943			hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)														---	---	---	---
FABP7	2173	broad.mit.edu	37	6	123101679	123101679	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123101679delT	uc003pzf.2	+						FABP7_uc003pzd.2_Intron|FABP7_uc003pze.1_3'UTR	NM_001446	NP_001437			fatty acid binding protein 7, brain						negative regulation of cell proliferation	cytoplasm	lipid binding|transporter activity				0				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|gamma-Homolinolenic acid(DB00154)|Icosapent(DB00159)													---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123702474	123702475	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123702474_123702475delAA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010kem.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
TPD52L1	7164	broad.mit.edu	37	6	125493304	125493311	+	Intron	DEL	TTTCTTTC	-	-	rs34678154		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125493304_125493311delTTTCTTTC	uc003pzu.1	+						TPD52L1_uc003pzv.1_Intron|TPD52L1_uc003pzw.1_Intron|TPD52L1_uc003pzx.1_Intron|TPD52L1_uc003pzy.1_Intron	NM_003287	NP_003278			tumor protein D52-like 1 isoform 1						DNA fragmentation involved in apoptotic nuclear change|G2/M transition of mitotic cell cycle|induction of apoptosis|positive regulation of JNK cascade|positive regulation of MAP kinase activity	perinuclear region of cytoplasm	caspase activator activity|protein heterodimerization activity|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)														---	---	---	---
NCOA7	135112	broad.mit.edu	37	6	126215915	126215915	+	Intron	DEL	T	-	-	rs111496290		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126215915delT	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron	NM_181782	NP_861447			nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)														---	---	---	---
NCOA7	135112	broad.mit.edu	37	6	126244008	126244009	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126244008_126244009insT	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron|NCOA7_uc003qak.2_Intron	NM_181782	NP_861447			nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128291226	128291226	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128291226delA	uc003qbk.2	-	30					PTPRK_uc003qbj.2_3'UTR|PTPRK_uc010kfc.2_3'UTR|PTPRK_uc011ebu.1_3'UTR	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128718505	128718505	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128718505delT	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron|PTPRK_uc003qbm.3_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130373910	130373911	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130373910_130373911insT	uc003qbt.2	+						L3MBTL3_uc003qbu.2_Intron	NM_032438	NP_115814			l(3)mbt-like 3 isoform a						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)														---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131481276	131481276	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131481276delA	uc003qck.2	+	3	262	c.229delA	c.(229-231)AAAfs	p.K77fs	AKAP7_uc011ebz.1_Frame_Shift_Del_p.K55fs	NM_016377	NP_057461	O43687	AKA7A_HUMAN	A-kinase anchor protein 7 isoform gamma	Error:Variant_position_missing_in_O43687_after_alignment					intracellular signal transduction|ion transport	apical plasma membrane|intracellular|lateral plasma membrane	protein kinase A binding			ovary(2)	2	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)														---	---	---	---
ENPP3	5169	broad.mit.edu	37	6	132061607	132061607	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132061607delT	uc003qcu.3	+						ENPP3_uc010kfq.2_Intron|ENPP3_uc003qcv.2_Intron	NM_005021	NP_005012			ectonucleotide pyrophosphatase/phosphodiesterase						immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133804345	133804345	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133804345delT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron|uc003qef.1_Intron	NM_004100	NP_004091			eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)														---	---	---	---
SLC2A12	154091	broad.mit.edu	37	6	134312046	134312046	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134312046delT	uc003qem.1	-	5						NM_145176	NP_660159			solute carrier family 2 (facilitated glucose							endomembrane system|integral to membrane|perinuclear region of cytoplasm|plasma membrane	D-glucose transmembrane transporter activity			ovary(1)	1	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)														---	---	---	---
FAM54A	113115	broad.mit.edu	37	6	136554647	136554647	+	Intron	DEL	A	-	-	rs2274141	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136554647delA	uc010kgp.1	-						FAM54A_uc003qgt.1_Intron|FAM54A_uc003qgu.1_Intron	NM_001099286	NP_001092756			DUF729 domain containing 1											skin(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00228)|OV - Ovarian serous cystadenocarcinoma(155;0.00504)														---	---	---	---
REPS1	85021	broad.mit.edu	37	6	139247466	139247466	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139247466delA	uc003qii.2	-						REPS1_uc003qig.3_Intron|REPS1_uc011edr.1_Intron|REPS1_uc003qij.2_Intron|REPS1_uc003qik.2_Intron	NM_031922	NP_114128			RALBP1 associated Eps domain containing 1							coated pit|plasma membrane	calcium ion binding|SH3 domain binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144744924	144744925	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144744924_144744925insT	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144806371	144806372	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144806371_144806372insT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	145167776	145167776	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145167776delA	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149862317	149862319	+	Intron	DEL	TTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149862317_149862319delTTT	uc003qmo.1	-						PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Intron	NM_139126	NP_624311			peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
C6orf72	116254	broad.mit.edu	37	6	149901277	149901277	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149901277delA	uc003qmq.1	+						C6orf72_uc010kie.1_Intron	NM_138785	NP_620140			hypothetical protein LOC116254 precursor							integral to membrane					0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.66e-12)|GBM - Glioblastoma multiforme(68;0.171)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152599580	152599580	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152599580delT	uc010kiw.2	-						SYNE1_uc010kiv.2_Intron|SYNE1_uc003qos.3_Intron|SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kiy.1_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						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)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152725563	152725563	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152725563delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						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)			---	---	---	---
RGS17	26575	broad.mit.edu	37	6	153344475	153344476	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153344475_153344476insA	uc003qpm.2	-							NM_012419	NP_036551			regulator of G-protein signalling 17						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			pancreas(1)	1		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)										Lung_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	6	154259550	154259550	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154259550delT								RGS17 (807161 upstream) : OPRM1 (72086 downstream)																																			---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158551549	158551549	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158551549delA	uc003qrc.2	-						SERAC1_uc003qrb.2_Intron	NM_032861	NP_116250			serine active site containing 1						GPI anchor metabolic process|intracellular protein transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	binding|hydrolase activity, acting on ester bonds				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	167342834	167342834	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167342834delA								RPS6KA2 (67063 upstream) : RNASET2 (174 downstream)																																			---	---	---	---
RNASET2	8635	broad.mit.edu	37	6	167369430	167369430	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167369430delG	uc003qve.2	-						RNASET2_uc003qvh.2_Intron|RNASET2_uc003qvf.2_Intron|RNASET2_uc003qvg.2_Intron|RNASET2_uc003qvi.1_Intron	NM_003730	NP_003721			ribonuclease T2 precursor						RNA catabolic process	extracellular region	ribonuclease T2 activity|RNA binding				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)														---	---	---	---
TCP10	6953	broad.mit.edu	37	6	167786551	167786551	+	Intron	DEL	T	-	-	rs146852129		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167786551delT	uc003qvu.2	-							NM_004610	NP_004601			t-complex 10							cytosol				breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)														---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168276400	168276400	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168276400delA	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
KIF25	3834	broad.mit.edu	37	6	168430556	168430556	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168430556delA	uc003qwk.1	+						KIF25_uc003qwl.1_Intron	NM_030615	NP_085118			kinesin family member 25 isoform 1						microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)														---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	168910885	168910885	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168910885delT	uc003qws.1	+						SMOC2_uc003qwr.1_Intron	NM_022138	NP_071421			SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)														---	---	---	---
WDR27	253769	broad.mit.edu	37	6	170070554	170070554	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170070554delA	uc003qwx.2	-						WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron|WDR27_uc011egw.1_Intron|WDR27_uc010kkx.2_3'UTR					RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)														---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170118766	170118766	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170118766delA	uc011egy.1	-						PHF10_uc011egz.1_Intron|PHF10_uc011eha.1_5'Flank	NM_018288	NP_060758			PHD finger protein 10 isoform a						nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	npBAF complex	zinc ion binding			urinary_tract(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)														---	---	---	---
PRKAR1B	5575	broad.mit.edu	37	7	646959	646960	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:646959_646960delTT	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726			protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)														---	---	---	---
C7orf50	84310	broad.mit.edu	37	7	1167118	1167118	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1167118delA	uc003sju.2	-						C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726			hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)														---	---	---	---
PMS2	5395	broad.mit.edu	37	7	6036896	6036896	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6036896delA	uc003spl.2	-						PMS2_uc003spj.2_Intron|PMS2_uc003spk.2_Intron|PMS2_uc011jwl.1_Intron|PMS2_uc010ktg.2_Intron|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Intron	NM_000535	NP_000526			PMS2 postmeiotic segregation increased 2 isoform						mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)				Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
USP42	84132	broad.mit.edu	37	7	6156259	6156259	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6156259delT	uc011jwo.1	+						USP42_uc011jwn.1_Intron|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron|USP42_uc011jwr.1_5'Flank	NM_032172	NP_115548			ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
RAC1	5879	broad.mit.edu	37	7	6439959	6439959	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6439959delT	uc003spx.2	+						RAC1_uc003spw.2_Intron	NM_006908	NP_008839			ras-related C3 botulinum toxin substrate 1						actin filament polymerization|apoptosis|axon guidance|cell motility|cell-matrix adhesion|induction of apoptosis by extracellular signals|inflammatory response|lamellipodium assembly|localization within membrane|negative regulation of interleukin-23 production|negative regulation of receptor-mediated endocytosis|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of lamellipodium assembly|positive regulation of Rho protein signal transduction|regulation of cell migration|regulation of defense response to virus by virus|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|ruffle organization|small GTPase mediated signal transduction|T cell costimulation|viral reproduction	cytosol|melanosome|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity|thioesterase binding			lung(2)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.104)	Pravastatin(DB00175)|Simvastatin(DB00641)													---	---	---	---
BZW2	28969	broad.mit.edu	37	7	16745815	16745815	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16745815delA	uc003stl.2	+	12					BZW2_uc003stm.2_3'UTR|BZW2_uc003stj.2_3'UTR|BZW2_uc003stk.2_3'UTR|BZW2_uc003stp.2_3'UTR|BZW2_uc010kua.2_3'UTR	NM_001159767	NP_001153239			basic leucine zipper and W2 domains 2						cell differentiation|nervous system development|RNA metabolic process		protein binding			ovary(2)	2	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)														---	---	---	---
ABCB5	340273	broad.mit.edu	37	7	20739337	20739337	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20739337delA	uc003suw.3	+						ABCB5_uc010kuh.2_Intron	NM_178559	NP_848654			ATP-binding cassette, sub-family B, member 5						regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6																		---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23436136	23436136	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23436136delA	uc003swg.2	-							NM_006547	NP_006538			insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation|translation	cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			ovary(2)	2																		---	---	---	---
C7orf46	340277	broad.mit.edu	37	7	23737684	23737684	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23737684delT	uc003swo.3	+						C7orf46_uc003swq.3_Intron|C7orf46_uc003swr.3_Intron|C7orf46_uc003swp.3_Intron|C7orf46_uc010kup.2_Intron	NM_199136	NP_954587			hypothetical protein LOC340277 isoform 1												0																		---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29152222	29152222	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29152222delT	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601			serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30113605	30113606	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30113605_30113606delAA	uc003tam.1	+						PLEKHA8_uc003tao.2_Intron|PLEKHA8_uc003tap.1_Intron|PLEKHA8_uc003tan.2_Intron	NM_032639	NP_116028			pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4																		---	---	---	---
GARS	2617	broad.mit.edu	37	7	30662267	30662267	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30662267delT	uc003tbm.2	+							NM_002047	NP_002038			glycyl-tRNA synthetase						cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33192289	33192289	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33192289delT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kan.1_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BMPER	168667	broad.mit.edu	37	7	34118338	34118338	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34118338delT	uc011kap.1	+							NM_133468	NP_597725			BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	34977470	34977470	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34977470delA	uc003tem.3	-						DPY19L1_uc003tel.1_Intron	NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
ANLN	54443	broad.mit.edu	37	7	36466411	36466411	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36466411delT	uc003tff.2	+						ANLN_uc011kaz.1_Intron|ANLN_uc003tfg.2_Intron|ANLN_uc010kxe.2_Intron	NM_018685	NP_061155			anillin, actin binding protein						cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3																		---	---	---	---
AMPH	273	broad.mit.edu	37	7	38543103	38543103	+	Intron	DEL	T	-	-	rs10225047		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38543103delT	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626			amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39125421	39125421	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39125421delT	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183			POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44260400	44260400	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44260400delC	uc003tkq.2	-						CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron|CAMK2B_uc003tkn.2_Intron	NM_001220	NP_001211			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
C7orf69	80099	broad.mit.edu	37	7	47859242	47859242	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47859242delA	uc003tnz.3	+	3					PKD1L1_uc003tny.1_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Intron	NM_025031	NP_079307			hypothetical protein LOC80099 precursor							extracellular region					0																		---	---	---	---
SUMF2	25870	broad.mit.edu	37	7	56144741	56144741	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56144741delT	uc003trv.2	+						PSPH_uc003trj.2_Intron|SUMF2_uc011kcv.1_Intron|SUMF2_uc011kcw.1_Intron|SUMF2_uc011kcx.1_Intron|SUMF2_uc003trt.2_Intron|SUMF2_uc011kcy.1_Intron|SUMF2_uc011kcz.1_Intron|SUMF2_uc003tru.2_Intron|SUMF2_uc011kda.1_Intron|SUMF2_uc003trx.2_Intron	NM_001130069	NP_001123541			sulfatase modifying factor 2 isoform e							endoplasmic reticulum lumen	metal ion binding			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56474339	56474340	+	IGR	INS	-	AAGG	AAGG			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56474339_56474340insAAGG								PSPH (290249 upstream) : DKFZp434L192 (89576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65222951	65222951	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65222951delT	uc003tud.1	-						CCT6P1_uc003tug.2_Intron|CCT6P1_uc003tuh.2_Intron|CCT6P1_uc003tui.2_Intron|uc003tuk.1_5'Flank					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	68106578	68106590	+	IGR	DEL	AAAAAAAAAAAAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68106578_68106590delAAAAAAAAAAAAA								None (None upstream) : AUTS2 (957315 downstream)																																			---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71902643	71902644	+	Intron	INS	-	TTTC	TTTC	rs10653402		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71902643_71902644insTTTC	uc003twc.3	-							NM_001017440	NP_001017440			calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73663895	73663895	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73663895delA	uc003uaj.2	-						RFC2_uc011kfa.1_Intron|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Intron	NM_181471	NP_852136			replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	74040337	74040337	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74040337delT								GTF2IRD1 (23419 upstream) : GTF2I (31693 downstream)																																			---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74105135	74105135	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74105135delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75068666	75068666	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75068666delT	uc010lde.1	-						POM121C_uc003udk.3_Intron					Homo sapiens POM121-2 mRNA for nuclear pore membrane protein 121-2, partial cds.						mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0																		---	---	---	---
PTPN12	5782	broad.mit.edu	37	7	77213057	77213057	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77213057delA	uc003ugh.2	+						PTPN12_uc011kgp.1_Intron|PTPN12_uc011kgq.1_Intron|PTPN12_uc010ldq.1_Intron|PTPN12_uc010ldr.1_Intron	NM_002835	NP_002826			protein tyrosine phosphatase, non-receptor type							soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79818381	79818381	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79818381delT	uc003uhb.1	+						GNAI1_uc011kgt.1_Intron	NM_002069	NP_002060			guanine nucleotide binding protein (G protein),						cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	82286831	82286831	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82286831delA								CACNA2D1 (213800 upstream) : PCLO (96490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	84506130	84506130	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84506130delA								SEMA3A (681913 upstream) : SEMA3D (118744 downstream)																																			---	---	---	---
DMTF1	9988	broad.mit.edu	37	7	86823978	86823978	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86823978delT	uc003uih.2	+						DMTF1_uc003uii.2_Intron|DMTF1_uc003uij.2_Intron|DMTF1_uc011khb.1_Intron|DMTF1_uc003uik.2_Intron|DMTF1_uc003uil.2_Intron|DMTF1_uc003uin.2_Intron	NM_001142327	NP_001135799			cyclin D binding myb-like transcription factor 1						cell cycle	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(14;0.0058)																	---	---	---	---
SLC25A13	10165	broad.mit.edu	37	7	95775777	95775777	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95775777delA	uc003uof.3	-						SLC25A13_uc003uog.3_Intron|SLC25A13_uc011kik.1_Intron	NM_014251	NP_055066			solute carrier family 25, member 13 isoform 2						ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)													---	---	---	---
TECPR1	25851	broad.mit.edu	37	7	97870693	97870693	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97870693delA	uc003upg.2	-						TECPR1_uc003uph.1_Intron	NM_015395	NP_056210			tectonin beta-propeller repeat containing 1							integral to membrane	protein binding			pancreas(1)	1																OREG0018181	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ARPC1A	10552	broad.mit.edu	37	7	98946355	98946355	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98946355delT	uc003upx.1	+						ARPC1A_uc010lfu.1_Intron|ARPC1A_uc003upy.1_Intron|ARPC1A_uc011kit.1_Intron	NM_006409	NP_006400			actin related protein 2/3 complex subunit 1A						actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
CYP3A4	1576	broad.mit.edu	37	7	99355990	99355990	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99355990delA	uc003urv.1	-						CYP3A4_uc003urw.1_Intron|CYP3A4_uc011kiz.1_Intron|CYP3A4_uc011kja.1_Intron|CYP3A4_uc011kjb.1_Intron	NM_017460	NP_059488			cytochrome P450, family 3, subfamily A,						alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process	cell surface|endoplasmic reticulum membrane|integral to membrane|microsome	albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity			central_nervous_system(3)|ovary(1)	4	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)													---	---	---	---
CYP3A43	64816	broad.mit.edu	37	7	99463417	99463417	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99463417delT	uc003urx.1	+						CYP3A43_uc003ury.1_Intron|CYP3A43_uc003urz.1_Intron|CYP3A43_uc003usa.1_Intron|CYP3A43_uc010lgi.1_Intron|CYP3A43_uc003usb.1_Intron	NM_057095	NP_476436			cytochrome P450, family 3, subfamily A,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Cetirizine(DB00341)|Doxycycline(DB00254)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	99581179	99581179	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99581179delC	uc003usi.2	+											RecName: Full=Putative zinc-alpha-2-glycoprotein-like 2; Flags: Precursor;																														---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99710906	99710906	+	Intron	DEL	A	-	-	rs75828513		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99710906delA	uc003uti.2	-						TAF6_uc003utg.2_Intron|TAF6_uc003uth.2_Intron|TAF6_uc003utk.2_Intron|TAF6_uc011kji.1_Intron|TAF6_uc003utj.2_Intron|TAF6_uc003utl.2_Intron|TAF6_uc003utm.2_Intron|TAF6_uc003utn.1_Intron	NM_139315	NP_647476			TBP-associated factor 6 isoform alpha						negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
TFR2	7036	broad.mit.edu	37	7	100229247	100229248	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100229247_100229248delAA	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218			transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
POLR2J	5439	broad.mit.edu	37	7	102114989	102114990	+	Intron	INS	-	C	C	rs145000593		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102114989_102114990insC	uc003uzp.1	-							NM_006234	NP_006225			DNA directed RNA polymerase II polypeptide J						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|LRR domain binding|protein dimerization activity			pancreas(1)	1																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129395139	129395139	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129395139delT	uc003voz.2	+	11					NRF1_uc003vpa.2_3'UTR|NRF1_uc011kpa.1_3'UTR|NRF1_uc003vpb.2_3'UTR	NM_005011	NP_005002			nuclear respiratory factor 1						generation of precursor metabolites and energy|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1																		---	---	---	---
TMEM209	84928	broad.mit.edu	37	7	129823958	129823958	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129823958delT	uc003vpn.2	-						TMEM209_uc010lmc.1_Intron	NM_032842	NP_116231			transmembrane protein 209							integral to membrane				ovary(2)|large_intestine(1)	3	Melanoma(18;0.0435)																	---	---	---	---
TMEM209	84928	broad.mit.edu	37	7	129842518	129842518	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129842518delT	uc003vpn.2	-						TMEM209_uc010lmc.1_Intron|TMEM209_uc003vpo.2_Intron	NM_032842	NP_116231			transmembrane protein 209							integral to membrane				ovary(2)|large_intestine(1)	3	Melanoma(18;0.0435)																	---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130148870	130148870	+	Intron	DEL	A	-	-	rs77402405		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130148870delA	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
LRGUK	136332	broad.mit.edu	37	7	133848045	133848045	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133848045delT	uc003vrm.1	+							NM_144648	NP_653249			leucine-rich repeats and guanylate kinase domain								ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5																		---	---	---	---
CALD1	800	broad.mit.edu	37	7	134576497	134576507	+	Intron	DEL	AAAAAAAAAAA	-	-	rs33997290		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134576497_134576507delAAAAAAAAAAA	uc003vrz.2	+						CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_Intron|CALD1_uc003vsc.2_Intron|CALD1_uc003vsd.2_Intron	NM_033138	NP_149129			caldesmon 1 isoform 1						cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0																		---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135047371	135047371	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135047371delT	uc011kpy.1	-	11					CNOT4_uc003vss.2_3'UTR|CNOT4_uc011kpz.1_3'UTR|CNOT4_uc003vst.2_3'UTR	NM_001008225	NP_001008226			CCR4-NOT transcription complex, subunit 4						nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
LUZP6	767558	broad.mit.edu	37	7	135614510	135614510	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135614510delT	uc003vte.3	-	4					LUZP6_uc010lmv.2_RNA	NM_145808	NP_665807			myotrophin												0																		---	---	---	---
CREB3L2	64764	broad.mit.edu	37	7	137586255	137586255	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137586255delA	uc003vtw.2	-						CREB3L2_uc003vtx.1_Intron|CREB3L2_uc003vtv.2_Intron	NM_194071	NP_919047			cAMP responsive element binding protein 3-like						chondrocyte differentiation|positive regulation of transcription, DNA-dependent|response to endoplasmic reticulum stress|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	cAMP response element binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L2(158)	soft_tissue(158)|upper_aerodigestive_tract(1)|ovary(1)	160								T	FUS	fibromyxoid sarcoma								---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138265557	138265557	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138265557delT	uc003vuc.2	+						TRIM24_uc003vub.2_Intron	NM_015905	NP_056989			transcriptional intermediary factor 1 alpha						cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8																		---	---	---	---
BRAF	673	broad.mit.edu	37	7	140476994	140476995	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140476994_140476995delTT	uc003vwc.3	-							NM_004333	NP_004324			B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				---	---	---	---
AGK	55750	broad.mit.edu	37	7	141352440	141352440	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141352440delT	uc003vwi.2	+							NM_018238	NP_060708			acylglycerol kinase precursor						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)																	---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144532719	144532719	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144532719delA	uc003weq.2	-						TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890			thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
ZNF786	136051	broad.mit.edu	37	7	148771740	148771741	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148771740_148771741delAA	uc003wfh.2	-						ZNF786_uc011kuk.1_Intron|ZNF786_uc003wfi.2_Intron	NM_152411	NP_689624			zinc finger protein 786						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)															---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151902167	151902167	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151902167delT	uc003wla.2	-						MLL3_uc003wkz.2_Intron	NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152100799	152100800	+	Intron	DEL	AT	-	-	rs2982753		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152100799_152100800delAT	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						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								---	---	---	---
Unknown	0	broad.mit.edu	37	7	155907140	155907140	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155907140delA								SHH (302173 upstream) : C7orf4 (426045 downstream)																																			---	---	---	---
FBXO25	26260	broad.mit.edu	37	8	363407	363407	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:363407delT	uc003wox.2	+						FBXO25_uc003woy.2_Intron|FBXO25_uc003woz.2_Intron	NM_183421	NP_904357			F-box only protein 25 isoform 1							nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	5221165	5221166	+	IGR	INS	-	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5221165_5221166insG								CSMD1 (368837 upstream) : None (None downstream)																																			---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9610303	9610303	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9610303delA	uc003wss.2	+						TNKS_uc011kww.1_Intron	NM_003747	NP_003738			tankyrase, TRF1-interacting ankyrin-related						mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)														---	---	---	---
ZDHHC2	51201	broad.mit.edu	37	8	17067432	17067432	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17067432delT	uc003wxe.2	+							NM_016353	NP_057437			zinc finger, DHHC-type containing 2							integral to membrane	acyltransferase activity|zinc ion binding				0				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)														---	---	---	---
PCM1	5108	broad.mit.edu	37	8	17871605	17871610	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17871605_17871610delAAAAAA	uc003wyi.3	+						PCM1_uc011kyh.1_Intron|PCM1_uc003wyj.3_Intron|PCM1_uc011kyi.1_Intron|PCM1_uc011kyj.1_Intron|PCM1_uc003wyk.3_Intron|PCM1_uc011kyk.1_Intron	NM_006197	NP_006188			pericentriolar material 1						centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)				T	RET|JAK2	papillary thyroid|CML|MPD								---	---	---	---
Unknown	0	broad.mit.edu	37	8	20231288	20231290	+	IGR	DEL	AGG	-	-	rs150136657		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20231288_20231290delAGG								LZTS1 (118485 upstream) : None (None downstream)																																			---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21550684	21550684	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21550684delT	uc003wzu.1	-	9					GFRA2_uc003wzv.1_3'UTR|GFRA2_uc003wzw.1_3'UTR	NM_001495	NP_001486			GDNF family receptor alpha 2 isoform a							anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity				0				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)														---	---	---	---
XPO7	23039	broad.mit.edu	37	8	21849583	21849583	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21849583delT	uc003xaa.3	+						XPO7_uc010lti.2_Intron|XPO7_uc010ltk.2_Intron	NM_015024	NP_055839			exportin 7 isoform b						mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)														---	---	---	---
FGF17	8822	broad.mit.edu	37	8	21900286	21900288	+	5'Flank	DEL	CTC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21900286_21900288delCTC	uc003xag.2	+						FGF17_uc003xah.2_5'Flank|FGF17_uc003xai.2_5'Flank	NM_003867	NP_003858			fibroblast growth factor 17 precursor						cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|nervous system development	extracellular space	growth factor activity|type 1 fibroblast growth factor receptor binding|type 2 fibroblast growth factor receptor binding				0				Colorectal(74;8.48e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0618)														---	---	---	---
EPB49	2039	broad.mit.edu	37	8	21926552	21926552	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21926552delC	uc011kyt.1	+	5	504	c.275delC	c.(274-276)TCCfs	p.S92fs	EPB49_uc010ltl.2_Frame_Shift_Del_p.S92fs|EPB49_uc011kys.1_Intron|EPB49_uc010ltn.2_Frame_Shift_Del_p.S67fs|EPB49_uc011kyu.1_Frame_Shift_Del_p.S92fs|EPB49_uc011kyv.1_Frame_Shift_Del_p.S92fs|EPB49_uc010ltq.2_Frame_Shift_Del_p.S92fs	NM_001114136	NP_001107608	Q08495	DEMA_HUMAN	erythrocyte membrane protein band 4.9 isoform 1	92					actin filament bundle assembly|actin filament capping	actin cytoskeleton|nucleus	actin binding			central_nervous_system(1)	1				Colorectal(74;9.05e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0631)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22471510	22471510	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22471510delA	uc003xch.2	+						KIAA1967_uc003xci.2_Intron|KIAA1967_uc003xcj.1_Intron	NM_199205	NP_954675			p30 DBC protein						apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22477167	22477169	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22477167_22477169delAGA	uc003xch.2	+	21	2881_2883	c.2744_2746delAGA	c.(2743-2748)GAGAAG>GAG	p.K916del	KIAA1967_uc003xci.2_In_Frame_Del_p.K916del|KIAA1967_uc003xcj.1_3'UTR	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	916					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
KCTD9	54793	broad.mit.edu	37	8	25287255	25287255	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25287255delT	uc003xeo.2	-	12					PPP2R2A_uc003xek.2_Intron|KCTD9_uc011lad.1_RNA	NM_017634	NP_060104			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity				0		all_cancers(63;0.0164)|Ovarian(32;0.000878)|all_epithelial(46;0.00542)|Breast(100;0.0164)|Hepatocellular(4;0.114)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Epithelial(17;2.39e-12)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0438)														---	---	---	---
PBK	55872	broad.mit.edu	37	8	27690542	27690542	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27690542delA	uc003xgi.2	-						PBK_uc011lap.1_Intron	NM_018492	NP_060962			PDZ binding kinase						mitosis		ATP binding|protein binding|protein serine/threonine kinase activity				0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28158144	28158144	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28158144delA								ELP3 (109477 upstream) : PNOC (16505 downstream)																																			---	---	---	---
HMBOX1	79618	broad.mit.edu	37	8	28827549	28827549	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28827549delT	uc003xhd.3	+						HMBOX1_uc010lvd.2_Intron|HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_Intron|HMBOX1_uc003xhe.2_Intron|HMBOX1_uc011lay.1_Intron|HMBOX1_uc003xhf.2_5'Flank|HMBOX1_uc003xhg.2_5'Flank	NM_001135726	NP_001129198			homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)														---	---	---	---
WRN	7486	broad.mit.edu	37	8	30938371	30938371	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30938371delT	uc003xio.3	+						WRN_uc011lbd.1_5'Flank|WRN_uc011lbe.1_5'Flank	NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	8	34732162	34732162	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34732162delA								None (None upstream) : UNC5D (360813 downstream)																																			---	---	---	---
FGFR1	2260	broad.mit.edu	37	8	38291845	38291849	+	Intron	DEL	TGCTT	-	-	rs151115715	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38291845_38291849delTGCTT	uc003xlp.2	-						FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Intron|FGFR1_uc011lbs.1_Intron|FGFR1_uc011lbt.1_Intron|FGFR1_uc011lbu.1_Intron|FGFR1_uc011lbv.1_Intron|FGFR1_uc011lbw.1_Intron|FGFR1_uc011lbx.1_Intron|FGFR1_uc003xlv.2_Intron|FGFR1_uc003xlu.2_Intron|FGFR1_uc003xlw.1_Intron	NM_023110	NP_075598			fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42186868	42186869	+	Intron	DEL	TC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42186868_42186869delTC	uc003xow.1	+						IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	47703944	47703944	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47703944delT								None (None upstream) : BEYLA (48564 downstream)																																			---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65528843	65528843	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65528843delA	uc003xvj.2	-							NM_004820	NP_004811			cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)																---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68028523	68028523	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68028523delA	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73480397	73480397	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73480397delA	uc003xzb.2	+	2	1016	c.428delA	c.(427-429)CAAfs	p.Q143fs		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	143	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81790454	81790455	+	IGR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81790454_81790455insT								ZNF704 (3438 upstream) : PAG1 (89593 downstream)																																			---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
CCNE2	9134	broad.mit.edu	37	8	95903888	95903895	+	Intron	DEL	AAAAAAAA	-	-	rs78334619		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95903888_95903895delAAAAAAAA	uc003yhc.2	-						CCNE2_uc003yhd.2_Intron	NM_057749	NP_477097			cyclin E2						cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	cytosol|nucleoplasm	protein kinase binding				0	Breast(36;8.75e-07)																	---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100833442	100833442	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100833442delA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101438881	101438882	+	IGR	INS	-	ACT	ACT	rs143966994		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101438881_101438882insACT								RNF19A (116554 upstream) : ANKRD46 (83105 downstream)																																			---	---	---	---
RRM2B	50484	broad.mit.edu	37	8	103220753	103220753	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103220753delA	uc003ykn.2	-						RRM2B_uc003yko.2_Intron|RRM2B_uc010mbv.1_Intron|RRM2B_uc010mbw.1_Intron|RRM2B_uc010mbx.1_Intron|RRM2B_uc010mby.1_Intron	NM_015713	NP_056528			ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process|DNA repair|nucleobase, nucleoside and nucleotide interconversion	nucleoplasm	ribonucleoside-diphosphate reductase activity|transition metal ion binding			ovary(2)	2	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)										Direct_reversal_of_damage|Modulation_of_nucleotide_pools					---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103358988	103358988	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103358988delA	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986			ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104581282	104581282	+	Intron	DEL	T	-	-	rs13266056		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104581282delT	uc003ylp.2	+							NM_001100117	NP_001093587			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106208519	106208519	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106208519delT								LRP12 (607299 upstream) : ZFPM2 (122628 downstream)																																			---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108315770	108315770	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108315770delA	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron|ANGPT1_uc003ymp.3_Intron	NM_001146	NP_001137			angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113421012	113421012	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113421012delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117739520	117739520	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117739520delA	uc003yoa.2	-						EIF3H_uc003yob.2_Intron|EIF3H_uc011lhz.1_Intron	NM_003756	NP_003747			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)																	---	---	---	---
TRMT12	55039	broad.mit.edu	37	8	125464614	125464615	+	3'UTR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125464614_125464615insT	uc003yra.3	+	1						NM_017956	NP_060426			homolog of yeast tRNA methyltransferase 12						tRNA processing		methyltransferase activity			upper_aerodigestive_tract(1)	1	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	138676649	138676649	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138676649delT								None (None upstream) : FAM135B (465619 downstream)																																			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139601386	139601386	+	3'UTR	DEL	A	-	-	rs72284088		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139601386delA	uc003yvd.2	-	65					COL22A1_uc011ljo.1_3'UTR	NM_152888	NP_690848			collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145763001	145763001	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145763001delC	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	NM_025251	NP_079527			KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
ERMP1	79956	broad.mit.edu	37	9	5812235	5812235	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5812235delA	uc003zjm.1	-						ERMP1_uc011lme.1_Intron|ERMP1_uc010mhs.1_Intron	NM_024896	NP_079172			aminopeptidase Fxna						proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)														---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8497368	8497368	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8497368delA	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						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)			---	---	---	---
HAUS6	54801	broad.mit.edu	37	9	19062839	19062839	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19062839delT	uc003znk.2	-						HAUS6_uc011lmz.1_Intron|HAUS6_uc003znl.1_Intron|HAUS6_uc003znm.1_Intron	NM_017645	NP_060115			HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2																		---	---	---	---
HAUS6	54801	broad.mit.edu	37	9	19082749	19082750	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19082749_19082750insA	uc003znk.2	-						HAUS6_uc011lmz.1_Intron|HAUS6_uc003znl.1_Intron|HAUS6_uc003znm.1_Intron	NM_017645	NP_060115			HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2																		---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20448401	20448401	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20448401delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron|MLLT3_uc011lng.1_Intron	NM_004529	NP_004520			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)				T	MLL	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	9	30800838	30800839	+	IGR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30800838_30800839insT								None (None upstream) : None (None downstream)																																			---	---	---	---
PTENP1	11191	broad.mit.edu	37	9	33675365	33675365	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33675365delA	uc003zth.3	-	1						NR_023917				SubName: Full=Phosphatase and tensin homolog 2; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	39817161	39817161	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39817161delA								LOC653501 (308273 upstream) : FAM74A1 (83039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66333430	66333430	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66333430delA								FAM74A4 (839044 upstream) : LOC442421 (163040 downstream)																																			---	---	---	---
UBQLN1	29979	broad.mit.edu	37	9	86300771	86300772	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86300771_86300772insA	uc004amv.2	-						UBQLN1_uc004amw.2_Intron	NM_013438	NP_038466			ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0																		---	---	---	---
AGTPBP1	23287	broad.mit.edu	37	9	88211378	88211378	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88211378delA	uc011ltd.1	-						AGTPBP1_uc004aod.3_Intron|AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054			ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7																		---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88667264	88667264	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88667264delT	uc004aol.2	-						GOLM1_uc010mqd.1_Intron|GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
ZCCHC6	79670	broad.mit.edu	37	9	88957837	88957837	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88957837delA	uc004aoq.2	-						ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron|ZCCHC6_uc004aov.2_Intron|ZCCHC6_uc004aow.2_Intron	NM_024617	NP_078893			zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	89875500	89875504	+	Intron	DEL	AAAAA	-	-	rs142686931		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89875500_89875504delAAAAA	uc004apb.1	-											Homo sapiens cDNA clone IMAGE:30346008.																														---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90113866	90113866	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90113866delT	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_5'Flank|DAPK1_uc011lth.1_5'Flank	NM_004938	NP_004929			death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
C9orf44	158314	broad.mit.edu	37	9	94904432	94904432	+	Intron	DEL	G	-	-	rs34310564		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94904432delG	uc004arp.1	+							NR_027341				Homo sapiens cDNA FLJ13600 fis, clone PLACE1009947.												0																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95432026	95432026	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95432026delG	uc004asl.1	-							NM_022755	NP_073592			inositol 1,3,4,5,6-pentakisphosphate 2-kinase						inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																		---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96422612	96422612	+	Frame_Shift_Del	DEL	A	-	-	rs76832193		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96422612delA	uc004aub.2	+	12	1615	c.1468delA	c.(1468-1470)AAAfs	p.K490fs	PHF2_uc011lug.1_Frame_Shift_Del_p.K373fs|PHF2_uc004auc.2_5'Flank	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2	490	Pro-rich.|Lys-rich.				liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
C9orf102	375748	broad.mit.edu	37	9	98678837	98678838	+	Intron	INS	-	A	A	rs144815828	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98678837_98678838insA	uc004avt.3	+						C9orf102_uc010mrx.1_Intron|C9orf102_uc011lum.1_Intron|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.2_Intron	NM_001010895	NP_001010895			RAD26L hypothetical protein						DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	98910246	98910247	+	IGR	DEL	AA	-	-	rs139074595		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98910246_98910247delAA								NCRNA00092 (126209 upstream) : HSD17B3 (87342 downstream)																																			---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101751672	101751672	+	Intron	DEL	G	-	-	rs142671851	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101751672delG	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
C9orf125	84302	broad.mit.edu	37	9	104239493	104239494	+	Intron	INS	-	AAAC	AAAC	rs67389871	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104239493_104239494insAAAC	uc004bbm.2	-						uc004bbl.1_5'Flank	NM_032342	NP_115718			hypothetical protein LOC84302							integral to membrane					0		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
TMEM38B	55151	broad.mit.edu	37	9	108536066	108536066	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108536066delT	uc004bcu.1	+						TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582			transmembrane protein 38B							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114126061	114126061	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114126061delT	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114135312	114135312	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114135312delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
C9orf84	158401	broad.mit.edu	37	9	114520878	114520878	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114520878delA	uc004bfr.2	-						C9orf84_uc011lwt.1_Intron|C9orf84_uc004bfs.1_Intron|C9orf84_uc004bfq.2_Intron|C9orf84_uc010mug.2_Intron	NM_173521	NP_775792			hypothetical protein LOC158401 isoform 1											ovary(2)	2																		---	---	---	---
C9orf80	58493	broad.mit.edu	37	9	115451949	115451949	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115451949delT	uc004bgg.2	-						C9orf80_uc010muk.2_Intron	NM_021218	NP_067041			SOSSC protein						DNA repair|response to ionizing radiation	SOSS complex	protein binding				0																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119748440	119748440	+	Intron	DEL	C	-	-	rs34599827		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119748440delC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
RABEPK	10244	broad.mit.edu	37	9	127995785	127995785	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127995785delT	uc004bpi.2	+						RABEPK_uc004bpj.2_Intron|RABEPK_uc004bpk.2_Intron|RABEPK_uc004bpl.1_Intron|RABEPK_uc004bpm.2_Intron	NM_005833	NP_005824			Rab9 effector protein with kelch motifs						receptor-mediated endocytosis|vesicle docking involved in exocytosis	endosome membrane|plasma membrane				ovary(1)	1																		---	---	---	---
WDR34	89891	broad.mit.edu	37	9	131397627	131397627	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131397627delA	uc004bvq.1	-						WDR34_uc004bvs.1_Intron|WDR34_uc004bvr.1_Intron	NM_052844	NP_443076			WD repeat domain 34							cytoplasm				central_nervous_system(2)|skin(1)	3																OREG0019522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C9orf78	51759	broad.mit.edu	37	9	132596001	132596001	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132596001delA	uc004byp.2	-						C9orf78_uc004byo.2_5'Flank|C9orf78_uc004byq.1_5'UTR|USP20_uc004bys.2_5'Flank|USP20_uc004byr.2_5'Flank|USP20_uc004byt.1_5'Flank	NM_016520	NP_057604			chromosome 9 open reading frame 78												0		Ovarian(14;0.00556)																---	---	---	---
NCS1	23413	broad.mit.edu	37	9	132985258	132985259	+	Intron	DEL	GC	-	-	rs145828712	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132985258_132985259delGC	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101			frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0																		---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136249407	136249409	+	Intron	DEL	ATA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136249407_136249409delATA	uc004cdk.2	+						C9orf96_uc004cdl.2_Intron	NM_153710	NP_714921			hypothetical protein LOC169436								ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
RNU6ATAC	100151684	broad.mit.edu	37	9	137032203	137032203	+	5'Flank	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137032203delT	uc010nap.1	-							NR_023344				Homo sapiens RNA, U6atac small nuclear (U12-dependent splicing) (RNU6ATAC), non-coding RNA.												0																		---	---	---	---
OBP2A	29991	broad.mit.edu	37	9	138439915	138439915	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138439915delG	uc004cgb.2	+						OBP2A_uc004cgc.2_Intron|OBP2A_uc010nau.2_Intron|OBP2A_uc010nav.2_Intron	NM_014582	NP_055397			odorant binding protein 2A precursor						response to stimulus|sensory perception of smell	extracellular region	odorant binding|transporter activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)														---	---	---	---
NACC2	138151	broad.mit.edu	37	9	138907999	138907999	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138907999delT	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254			BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0																		---	---	---	---
BEND7	222389	broad.mit.edu	37	10	13494739	13494739	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13494739delA	uc001imm.2	-						BEND7_uc001iml.2_Intron|BEND7_uc001imn.2_Intron|BEND7_uc001imo.3_Intron	NM_152751	NP_689964			BEN domain containing 7 isoform 1								protein binding			ovary(1)|breast(1)	2																		---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21977574	21977575	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21977574_21977575delAA	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001irb.2_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	10	26958525	26958527	+	IGR	DEL	AAG	-	-	rs138608083		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26958525_26958527delAAG								LOC731789 (16143 upstream) : PDSS1 (28068 downstream)																																			---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28270269	28270269	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28270269delA	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron|ARMC4_uc010qdu.1_Intron	NM_018076	NP_060546			armadillo repeat containing 4								binding			ovary(4)|skin(2)	6																		---	---	---	---
CREM	1390	broad.mit.edu	37	10	35456559	35456559	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35456559delT	uc001iyb.2	+						CREM_uc001ixx.2_Intron|CREM_uc001ixy.2_Intron|CREM_uc001ixz.2_Intron|CREM_uc001iya.2_Intron|CREM_uc001iyc.2_Intron|CREM_uc001iyd.2_Intron|CREM_uc001iye.2_Intron|CREM_uc001iyf.2_5'UTR|CREM_uc001iyg.2_5'UTR	NM_181571	NP_853549			cAMP responsive element modulator isoform a						cell differentiation|multicellular organismal development|signal transduction|spermatogenesis	nucleus	cAMP response element binding protein binding|protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GJD4	219770	broad.mit.edu	37	10	35897554	35897554	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35897554delA	uc001iyy.1	+	2	1271	c.1113delA	c.(1111-1113)TGAfs	p.*371fs		NM_153368	NP_699199	Q96KN9	CXD4_HUMAN	connexin40.1	371					cell communication	connexon complex|integral to membrane				large_intestine(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	45145608	45145611	+	IGR	DEL	TCCT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45145608_45145611delTCCT								CXCL12 (265066 upstream) : TMEM72 (261153 downstream)																																			---	---	---	---
FAM21C	253725	broad.mit.edu	37	10	46248590	46248590	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46248590delT	uc001jcu.2	+						FAM21C_uc001jcs.1_Intron|FAM21C_uc001jct.2_Intron|FAM21C_uc010qfi.1_Intron|FAM21C_uc010qfj.1_5'Flank	NM_015262	NP_056077			hypothetical protein LOC253725											ovary(1)	1																		---	---	---	---
CSTF2T	23283	broad.mit.edu	37	10	53457289	53457289	+	3'UTR	DEL	A	-	-	rs143102624		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53457289delA	uc001jjp.2	-	1					PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050			cleavage stimulation factor, 3' pre-RNA, subunit						mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)														---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64969014	64969014	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64969014delA	uc001jmn.2	-						JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Intron|JMJD1C_uc010qiq.1_Intron|JMJD1C_uc009xpi.2_Intron|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc009xpk.1_5'Flank	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
SLC25A16	8034	broad.mit.edu	37	10	70243182	70243182	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70243182delT	uc001joi.2	-	9					SLC25A16_uc010qix.1_3'UTR|SLC25A16_uc010qiy.1_3'UTR|SLC25A16_uc001joj.2_3'UTR	NM_152707	NP_689920			solute carrier family 25, member 16						coenzyme biosynthetic process|pantothenate metabolic process	integral to membrane|mitochondrial inner membrane	binding|solute:solute antiporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70304123	70304123	+	IGR	DEL	T	-	-	rs71716010		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70304123delT								SLC25A16 (16539 upstream) : TET1 (15994 downstream)																																			---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70497583	70497583	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70497583delT	uc001joo.2	+						CCAR1_uc001jol.1_Intron|CCAR1_uc001jom.1_Intron|CCAR1_uc009xpx.1_Intron|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Intron|CCAR1_uc010qja.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707			cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75560546	75560546	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75560546delC	uc009xrl.2	+						KIAA0913_uc001jve.2_Intron|KIAA0913_uc001jvf.2_Intron|KIAA0913_uc001jvh.2_Intron|KIAA0913_uc001jvi.2_Intron|KIAA0913_uc010qkr.1_Intron|KIAA0913_uc001jvj.2_Intron|KIAA0913_uc009xrn.1_3'UTR	NM_015037	NP_055852			hypothetical protein LOC23053								zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
VDAC2	7417	broad.mit.edu	37	10	76981855	76981855	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76981855delA	uc001jwz.2	+						VDAC2_uc010qld.1_Intron|VDAC2_uc001jxa.2_Intron|VDAC2_uc010qle.1_Intron	NM_003375	NP_003366			voltage-dependent anion channel 2							mitochondrial nucleoid|mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)													---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79603068	79603069	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79603068_79603069insA	uc001jzk.2	-						DLG5_uc001jzj.2_Intron|DLG5_uc009xru.1_Intron|DLG5_uc001jzl.3_5'Flank	NM_004747	NP_004738			discs large homolog 5						cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	81632947	81632948	+	IGR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81632947_81632948insT								LOC650623 (184299 upstream) : MBL1P (31706 downstream)																																			---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85910380	85910380	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85910380delT	uc001kcs.1	+						GHITM_uc010qma.1_Intron|GHITM_uc010qmb.1_Intron	NM_014394	NP_055209			growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
C10orf4	118924	broad.mit.edu	37	10	95429632	95429632	+	Intron	DEL	A	-	-	rs79307310		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95429632delA	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron	NM_145246	NP_660289			FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)																---	---	---	---
LGI1	9211	broad.mit.edu	37	10	95552720	95552720	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95552720delT	uc001kjc.3	+						LGI1_uc010qnv.1_Intron|LGI1_uc001kjd.3_Intron|LGI1_uc009xui.2_Intron|LGI1_uc001kje.2_Intron	NM_005097	NP_005088			leucine-rich, glioma inactivated 1 precursor						axon guidance|cell proliferation|positive regulation of cell growth|positive regulation of synaptic transmission	cell junction|extracellular space|synapse	receptor binding			ovary(2)|central_nervous_system(1)|skin(1)	4		Colorectal(252;0.124)																---	---	---	---
ARL3	403	broad.mit.edu	37	10	104449587	104449587	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104449587delA	uc001kwa.2	-							NM_004311	NP_004302			ADP-ribosylation factor-like 3						cell cycle|cytokinesis|small GTPase mediated signal transduction	centrosome|cytoplasmic microtubule|Golgi membrane|midbody|nucleus|photoreceptor connecting cilium|spindle microtubule	GDP binding|GTP binding|metal ion binding|microtubule binding				0		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)														---	---	---	---
VWA2	340706	broad.mit.edu	37	10	116014989	116014990	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116014989_116014990delTT	uc001lbl.1	+						VWA2_uc001lbk.1_Intron|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898			von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)														---	---	---	---
PNLIPRP2	5408	broad.mit.edu	37	10	118396277	118396277	+	Intron	DEL	G	-	-	rs148140777	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118396277delG	uc001lcq.2	+						PNLIPRP2_uc009xyv.1_Intron	NM_005396	NP_005387			pancreatic lipase-related protein 2						galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			large_intestine(1)	1				all cancers(201;0.015)														---	---	---	---
VAX1	11023	broad.mit.edu	37	10	118897630	118897632	+	5'UTR	DEL	GGC	-	-	rs71677026		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118897630_118897632delGGC	uc009xyx.2	-	1					VAX1_uc001ldb.1_5'UTR	NM_001112704	NP_001106175			ventral anterior homeobox 1 isoform a							nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)														---	---	---	---
FAM45A	404636	broad.mit.edu	37	10	120879760	120879760	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120879760delA	uc001ldw.2	+						FAM45A_uc010qsv.1_Intron|FAM45A_uc010qsw.1_Intron|FAM45A_uc010qsx.1_Intron|FAM45A_uc010qsy.1_Intron|FAM45A_uc010qsz.1_Intron	NM_207009	NP_996892			hypothetical protein LOC404636											ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	122079208	122079208	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122079208delT								SEC23IP (377963 upstream) : PPAPDC1A (137258 downstream)																																			---	---	---	---
BUB3	9184	broad.mit.edu	37	10	124920172	124920172	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124920172delT	uc001lhe.2	+						BUB3_uc009yah.2_Intron|BUB3_uc001lhf.3_Intron|BUB3_uc001lhd.2_Intron|BUB3_uc010qud.1_Intron	NM_004725	NP_004716			budding uninhibited by benzimidazoles 3 isoform						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|attachment of spindle microtubules to kinetochore|cell division|meiosis|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	condensed chromosome kinetochore|cytosol|nucleus	protein binding			ovary(1)	1		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)																---	---	---	---
CHST15	51363	broad.mit.edu	37	10	125805078	125805078	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125805078delT	uc001lhl.2	-						CHST15_uc001lhm.2_Intron|CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976			B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1																		---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135093332	135093332	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135093332delG	uc001lmg.1	-	18	3004	c.2647delC	c.(2647-2649)CAAfs	p.Q883fs	ADAM8_uc010quz.1_5'Flank|ADAM8_uc009ybi.2_5'Flank|ADAM8_uc010qva.1_5'Flank|ADAM8_uc009ybj.1_5'Flank|TUBGCP2_uc001lmf.1_Frame_Shift_Del_p.Q476fs|TUBGCP2_uc010qvc.1_Frame_Shift_Del_p.Q911fs|TUBGCP2_uc009ybk.1_Frame_Shift_Del_p.Q906fs|TUBGCP2_uc010qvd.1_Frame_Shift_Del_p.Q753fs|TUBGCP2_uc001lmh.1_RNA	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	883					G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
PDDC1	347862	broad.mit.edu	37	11	770899	770899	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:770899delA	uc001lrc.2	-	8	686	c.661delT	c.(661-663)TGAfs	p.*221fs	PDDC1_uc001lrb.2_5'Flank|PDDC1_uc010qwm.1_Frame_Shift_Del_p.*171fs|PDDC1_uc001lrd.2_Intron|PDDC1_uc001lrf.1_3'UTR|PDDC1_uc001lrg.1_RNA|PDDC1_uc009ycg.2_3'UTR|PDDC1_uc010qwn.1_RNA|PDDC1_uc010qwo.1_RNA|PDDC1_uc010qwp.1_3'UTR|PDDC1_uc010qwq.1_3'UTR|PDDC1_uc010qwr.1_3'UTR|PDDC1_uc010qws.1_3'UTR	NM_182612	NP_872418	Q8NB37	PDDC1_HUMAN	Parkinson disease 7 domain containing 1	221						extracellular region					0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;3.66e-26)|Epithelial(43;2.43e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-19)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1264717	1264717	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1264717delC	uc009ycr.1	+	48	8647	c.8521delC	c.(8521-8523)CCCfs	p.P2841fs	MUC5B_uc001ltb.2_Frame_Shift_Del_p.P2206fs	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	2203	7 X Cys-rich subdomain repeats.|Thr-rich.			P -> S (in Ref. 4; CAA96577).	cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
BRSK2	9024	broad.mit.edu	37	11	1466880	1466880	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1466880delC	uc001lti.2	+	11	1443	c.1057delC	c.(1057-1059)CCCfs	p.P353fs	BRSK2_uc009ycv.1_Frame_Shift_Del_p.P353fs|BRSK2_uc001lth.1_Frame_Shift_Del_p.P353fs|BRSK2_uc001ltj.2_Frame_Shift_Del_p.P353fs|BRSK2_uc001ltk.2_RNA|BRSK2_uc001ltl.2_Frame_Shift_Del_p.P353fs|BRSK2_uc001ltm.2_Frame_Shift_Del_p.P399fs|BRSK2_uc001ltn.2_RNA|BRSK2_uc010qwx.1_RNA	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	353					establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)														---	---	---	---
STIM1	6786	broad.mit.edu	37	11	4091365	4091367	+	In_Frame_Del	DEL	GAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4091365_4091367delGAA	uc001lyv.2	+	6	1291_1293	c.723_725delGAA	c.(721-726)ATGAAG>ATG	p.K243del	STIM1_uc009yef.2_In_Frame_Del_p.K243del|STIM1_uc009yeg.2_In_Frame_Del_p.K70del	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	243	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5662310	5662311	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5662310_5662311insT	uc001mbf.2	+						HBG2_uc001mak.1_Intron|TRIM34_uc001mbh.2_Intron|TRIM34_uc009yeq.2_Intron|TRIM34_uc001mbi.2_Intron|TRIM34_uc001mbj.2_Intron|TRIM78P_uc009yer.2_5'Flank	NM_001003819	NP_001003819			tripartite motif-containing 6 and tripartite							intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	9628209	9628210	+	IGR	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9628209_9628210delAA								WEE1 (16898 upstream) : SWAP70 (57418 downstream)																																			---	---	---	---
SBF2	81846	broad.mit.edu	37	11	9838292	9838292	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9838292delA	uc001mib.2	-						SBF2_uc001mid.2_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
USP47	55031	broad.mit.edu	37	11	11969772	11969772	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11969772delT	uc001mjs.2	+						USP47_uc001mjr.2_Intron|USP47_uc009ygi.2_5'Flank	NM_017944	NP_060414			ubiquitin specific protease 47						base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
SAA4	6291	broad.mit.edu	37	11	18257512	18257512	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18257512delA	uc001mny.2	-							NM_006512	NP_006503			serum amyloid A4, constitutive precursor						acute-phase response	high-density lipoprotein particle					0																		---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18316379	18316379	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18316379delA	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608			Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3														Hermansky-Pudlak_syndrome				---	---	---	---
LDHAL6A	160287	broad.mit.edu	37	11	18500558	18500560	+	3'UTR	DEL	TTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18500558_18500560delTTT	uc001mop.1	+	8					LDHAL6A_uc001moq.2_3'UTR	NM_001144071	NP_001137543			lactate dehydrogenase A-like 6A						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)													---	---	---	---
E2F8	79733	broad.mit.edu	37	11	19259637	19259637	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19259637delT	uc001mpm.2	-	3	580	c.58delA	c.(58-60)ACAfs	p.T20fs	E2F8_uc009yhv.2_RNA|E2F8_uc001mpn.3_Frame_Shift_Del_p.T20fs|E2F8_uc001mpo.1_Frame_Shift_Del_p.T20fs	NM_024680	NP_078956	A0AVK6	E2F8_HUMAN	E2F family member 8	20					cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1																		---	---	---	---
ELP4	26610	broad.mit.edu	37	11	31785302	31785302	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31785302delT	uc001mtb.2	+						ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913			elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)																	---	---	---	---
WT1	7490	broad.mit.edu	37	11	32451979	32451980	+	Intron	DEL	AG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32451979_32451980delAG	uc001mtn.1	-						WT1_uc001mtl.1_Intron|WT1_uc001mtm.1_Intron|WT1_uc001mto.1_Intron|WT1_uc001mtp.1_Intron|WT1_uc001mtq.1_Intron|WT1_uc009yjs.1_Intron	NM_024426	NP_077744			Wilms tumor 1 isoform D						adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding		EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1)	687	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)					D|Mis|N|F|S	EWSR1	Wilms|desmoplastic small round cell tumor	Wilms			Denys-Drash_syndrome|Frasier_syndrome|Familial_Wilms_tumor|Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				---	---	---	---
PRRG4	79056	broad.mit.edu	37	11	32852020	32852020	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32852020delT	uc001mtx.2	+							NM_024081	NP_076986			proline rich Gla (G-carboxyglutamic acid) 4							extracellular region|Golgi apparatus|integral to membrane	calcium ion binding				0	Breast(20;0.206)																	---	---	---	---
CSTF3	1479	broad.mit.edu	37	11	33182669	33182669	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33182669delA	uc001muh.2	-						CSTF3_uc001mui.2_Intron|CSTF3_uc001muj.2_Intron|uc001muk.2_5'Flank	NM_001326	NP_001317			cleavage stimulation factor subunit 3 isoform 1						mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0																OREG0020867	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43419441	43419441	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43419441delT	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron|TTC17_uc001mxj.2_Intron	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46775145	46775145	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46775145delT	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938			colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
NDUFS3	4722	broad.mit.edu	37	11	47600766	47600767	+	Intron	DEL	AG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47600766_47600767delAG	uc001nga.2	+						NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_5'Flank|KBTBD4_uc001nfx.2_5'Flank|KBTBD4_uc001nfz.2_5'Flank|KBTBD4_uc001nfy.2_5'Flank|NDUFS3_uc010rhn.1_Intron	NM_004551	NP_004542			NADH dehydrogenase (ubiquinone) Fe-S protein 3						induction of apoptosis|mitochondrial electron transport, NADH to ubiquinone|negative regulation of cell growth|reactive oxygen species metabolic process|transport	mitochondrial respiratory chain complex I	electron carrier activity|NADH dehydrogenase (ubiquinone) activity|protein binding				0					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	48967951	48967951	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48967951delA								OR4A47 (456679 upstream) : FOLH1 (200237 downstream)																																			---	---	---	---
FOLH1	2346	broad.mit.edu	37	11	49204798	49204798	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49204798delA	uc001ngy.2	-						FOLH1_uc001ngz.2_Intron|FOLH1_uc009yly.2_Intron|FOLH1_uc009ylz.2_Intron|FOLH1_uc009yma.2_Intron	NM_004476	NP_004467			folate hydrolase 1 isoform 1						proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)													---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57582848	57582848	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57582848delT	uc001nmc.3	+						CTNND1_uc001nlh.1_Intron|CTNND1_uc001nlu.3_Intron|CTNND1_uc001nlt.3_Intron|CTNND1_uc001nls.3_Intron|CTNND1_uc001nlw.3_Intron|CTNND1_uc001nmf.3_Intron|CTNND1_uc001nmd.3_Intron|CTNND1_uc001nlk.3_Intron|CTNND1_uc001nme.3_Intron|CTNND1_uc001nll.3_Intron|CTNND1_uc001nmg.3_Intron|CTNND1_uc001nlj.3_Intron|CTNND1_uc001nlr.3_Intron|CTNND1_uc001nlp.3_Intron|CTNND1_uc001nlx.3_Intron|CTNND1_uc001nlz.3_Intron|CTNND1_uc009ymn.2_Intron|CTNND1_uc001nlm.3_Intron|CTNND1_uc001nly.3_Intron|CTNND1_uc001nmb.3_Intron|CTNND1_uc001nma.3_Intron|CTNND1_uc001nmi.3_Intron|CTNND1_uc001nmh.3_Intron|CTNND1_uc001nlq.3_Intron|CTNND1_uc001nln.3_Intron|CTNND1_uc001nli.3_Intron|CTNND1_uc001nlo.3_Intron|CTNND1_uc001nlv.3_Intron	NM_001085458	NP_001078927			catenin, delta 1 isoform 1ABC						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	58117335	58117335	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58117335delA								OR10W1 (81603 upstream) : OR5B17 (8265 downstream)																																			---	---	---	---
CPSF7	79869	broad.mit.edu	37	11	61187363	61187363	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61187363delC	uc001nrq.2	-						CPSF7_uc001nro.2_Intron|CPSF7_uc001nrp.2_Intron|CPSF7_uc001nrr.2_Intron|CPSF7_uc001nrs.1_Intron	NM_001136040	NP_001129512			pre-mRNA cleavage factor I, 59 kDa subunit						mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1																		---	---	---	---
SF3B2	10992	broad.mit.edu	37	11	65835245	65835245	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65835245delC	uc001ogy.1	+						PACS1_uc001ogz.1_5'Flank|PACS1_uc001oha.1_5'Flank	NM_006842	NP_006833			splicing factor 3B subunit 2						interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3																OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KDM2A	22992	broad.mit.edu	37	11	66983146	66983147	+	Intron	DEL	AA	-	-	rs113780245	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66983146_66983147delAA	uc001ojw.2	+						KDM2A_uc001ojx.2_Intron|KDM2A_uc001ojy.2_Intron	NM_012308	NP_036440			F-box and leucine-rich repeat protein 11						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	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|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
TBC1D10C	374403	broad.mit.edu	37	11	67176565	67176565	+	Frame_Shift_Del	DEL	C	-	-	rs147560025		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67176565delC	uc001ola.2	+	9	983	c.954delC	c.(952-954)ATCfs	p.I318fs	PPP1CA_uc001okx.1_Intron|TBC1D10C_uc001okz.2_Frame_Shift_Del_p.P254fs|TBC1D10C_uc001olb.2_RNA	NM_198517	NP_940919	Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	318						intracellular	Rab GTPase activator activity				0			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)															---	---	---	---
FGF4	2249	broad.mit.edu	37	11	69588345	69588345	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69588345delC	uc001opg.1	-						FGF4_uc010rqj.1_Intron	NM_002007	NP_001998			fibroblast growth factor 4 precursor						cell-cell signaling|chondroblast differentiation|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|mesenchymal cell proliferation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade	extracellular region	growth factor activity|heparin binding				0	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)													---	---	---	---
ANO1	55107	broad.mit.edu	37	11	69971949	69971950	+	Intron	INS	-	A	A	rs35617632		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69971949_69971950insA	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513			anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76224308	76224308	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76224308delA	uc001oxl.2	+						C11orf30_uc010rsa.1_Intron|C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Intron|C11orf30_uc010rsc.1_Intron|C11orf30_uc001oxn.2_Intron|C11orf30_uc010rsd.1_Intron	NM_020193	NP_064578			EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76239630	76239635	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76239630_76239635delTTTTTT	uc001oxl.2	+						C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Intron|C11orf30_uc010rsc.1_Intron|C11orf30_uc001oxn.2_Intron|C11orf30_uc010rsd.1_Intron|C11orf30_uc001oxo.1_Intron|C11orf30_uc010rse.1_Intron	NM_020193	NP_064578			EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77436580	77436580	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77436580delA	uc001oyn.2	-							NM_016578	NP_057662			remodeling and spacing factor 1						CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
TRIM49	57093	broad.mit.edu	37	11	89536749	89536750	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89536749_89536750insT	uc001pdb.2	-							NM_020358	NP_065091			ring finger protein 18							intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
TAF1D	79101	broad.mit.edu	37	11	93469128	93469128	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93469128delT	uc001ped.2	-	6					SNORA8_uc001pec.2_5'Flank|TAF1D_uc001pdz.2_Intron|TAF1D_uc001pea.1_Intron|SNORD5_uc009ywf.1_5'Flank|SNORA18_uc009ywg.1_5'Flank|MIR1304_hsa-mir-1304|MI0006371_5'Flank|SNORA40_uc009ywh.2_5'Flank	NM_024116	NP_077021			TATA box binding protein (TBP)-associated						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding				0																		---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	102984164	102984164	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102984164delT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	102985853	102985853	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102985853delT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103048288	103048288	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103048288delA	uc001pho.2	+	38	6022	c.5878delA	c.(5878-5880)AAAfs	p.K1960fs	DYNC2H1_uc001phn.1_Frame_Shift_Del_p.K1960fs|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1960	AAA 2 (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	110846586	110846586	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110846586delA								ARHGAP20 (262674 upstream) : C11orf53 (280121 downstream)																																			---	---	---	---
IL18	3606	broad.mit.edu	37	11	112024223	112024223	+	Intron	DEL	T	-	-	rs78854082		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024223delT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553			interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)														---	---	---	---
PTS	5805	broad.mit.edu	37	11	112104139	112104139	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112104139delT	uc001pnj.3	+						PTS_uc009yyo.2_Intron	NM_000317	NP_000308			6-pyruvoyltetrahydropterin synthase						cellular amino acid metabolic process|central nervous system development|tetrahydrobiopterin biosynthetic process	mitochondrion	6-pyruvoyltetrahydropterin synthase activity|metal ion binding				0		all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519)														---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	112832277	112832278	+	5'UTR	DEL	GG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112832277_112832278delGG	uc009yyq.1	+	1					NCAM1_uc001pno.2_5'UTR|uc001pnn.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	113662178	113662178	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113662178delA								CLDN25 (10971 upstream) : USP28 (6420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115497786	115497787	+	IGR	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115497786_115497787delTT								CADM1 (122545 upstream) : None (None downstream)																																			---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116906807	116906808	+	Intron	DEL	TT	-	-	rs77063239		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116906807_116906808delTT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
SIDT2	51092	broad.mit.edu	37	11	117063143	117063143	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117063143delC	uc001pqh.1	+						SIDT2_uc010rxe.1_Intron|SIDT2_uc001pqg.2_Intron|SIDT2_uc001pqi.1_Intron|SIDT2_uc001pqj.1_5'Flank	NM_001040455	NP_001035545			SID1 transmembrane family, member 2 precursor							integral to membrane|lysosomal membrane					0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120317937	120317937	+	Intron	DEL	T	-	-	rs79430904		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120317937delT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
CRTAM	56253	broad.mit.edu	37	11	122724521	122724521	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122724521delA	uc001pyj.2	+							NM_019604	NP_062550			class-I MHC-restricted T cell associated						cell recognition|detection of tumor cell|positive regulation of cytokine secretion|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	integral to membrane|plasma membrane	receptor binding			ovary(1)	1		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)														---	---	---	---
PATE1	160065	broad.mit.edu	37	11	125618436	125618437	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125618436_125618437insT	uc001qct.2	+						PATE1_uc009zbr.2_Intron	NM_138294	NP_612151			expressed in prostate and testis precursor							extracellular region					0																		---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1863751	1863751	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1863751delA	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827			adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)															---	---	---	---
DYRK4	8798	broad.mit.edu	37	12	4723002	4723002	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4723002delT	uc001qmx.2	+	13					DYRK4_uc001qmy.1_3'UTR|DYRK4_uc001qmz.1_3'UTR|DYRK4_uc001qna.1_3'UTR|DYRK4_uc010ser.1_3'UTR	NM_003845	NP_003836			dual-specificity tyrosine-(Y)-phosphorylation							Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)															---	---	---	---
VWF	7450	broad.mit.edu	37	12	6058813	6058813	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6058813delA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543			von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
LPCAT3	10162	broad.mit.edu	37	12	7092803	7092803	+	Intron	DEL	A	-	-	rs75408212		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7092803delA	uc001qsi.2	-						EMG1_uc010sfv.1_Intron|LPCAT3_uc010sfw.1_Intron|LPCAT3_uc009zfp.2_Intron|LPCAT3_uc010sfx.1_Intron|LPCAT3_uc009zfq.1_Intron	NM_005768	NP_005759			lysophosphatidylcholine acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity			ovary(1)	1																		---	---	---	---
CLEC4D	338339	broad.mit.edu	37	12	8666271	8666271	+	5'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8666271delA	uc001qun.2	+	1						NM_080387	NP_525126			C-type lectin domain family 4, member D						innate immune response	integral to membrane	sugar binding				0	Lung SC(5;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	9555195	9555196	+	IGR	INS	-	C	C	rs140281398	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9555195_9555196insC								LOC642846 (88511 upstream) : DDX12 (15092 downstream)																																			---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18690984	18690984	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18690984delA	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561			phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)																---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19406761	19406761	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19406761delA	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19514518	19514518	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19514518delA	uc001reb.2	+	23	3074	c.2988delA	c.(2986-2988)TTAfs	p.L996fs	PLEKHA5_uc010sie.1_Frame_Shift_Del_p.L1157fs|PLEKHA5_uc001rea.2_Frame_Shift_Del_p.L1054fs|PLEKHA5_uc009zin.2_Frame_Shift_Del_p.L754fs|PLEKHA5_uc010sif.1_Frame_Shift_Del_p.L985fs|PLEKHA5_uc010sig.1_Frame_Shift_Del_p.L978fs|PLEKHA5_uc010sih.1_Frame_Shift_Del_p.L951fs|PLEKHA5_uc001rec.1_Frame_Shift_Del_p.L805fs|PLEKHA5_uc009zio.2_Frame_Shift_Del_p.L262fs	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A	996							1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21242746	21242746	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21242746delT	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron					SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
KIAA0528	9847	broad.mit.edu	37	12	22625136	22625137	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22625136_22625137delAA	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron	NM_014802	NP_055617			hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
KIAA0528	9847	broad.mit.edu	37	12	22625276	22625276	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22625276delA	uc001rfq.2	-	18	2341	c.2113delT	c.(2113-2115)TATfs	p.Y705fs	KIAA0528_uc010sir.1_Frame_Shift_Del_p.Y520fs|KIAA0528_uc010sis.1_Frame_Shift_Del_p.Y705fs|KIAA0528_uc010sit.1_Frame_Shift_Del_p.Y707fs|KIAA0528_uc010siu.1_Frame_Shift_Del_p.Y705fs|KIAA0528_uc001rfr.2_Frame_Shift_Del_p.Y696fs	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	705							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26640150	26640150	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26640150delT	uc001rhg.2	-	40	5822	c.5405delA	c.(5404-5406)AAGfs	p.K1802fs	ITPR2_uc009zjg.1_5'UTR	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	1802	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31630952	31630952	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31630952delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FGD4	121512	broad.mit.edu	37	12	32772566	32772566	+	Intron	DEL	A	-	-	rs75798711		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32772566delA	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc010ske.1_Intron|FGD4_uc001rlb.1_Intron	NM_139241	NP_640334			FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)																	---	---	---	---
DNM1L	10059	broad.mit.edu	37	12	32896263	32896264	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32896263_32896264insA	uc001rld.2	+						DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192			dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40247410	40247410	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40247410delT	uc010skm.1	-						C12orf40_uc009zjv.1_Intron|SLC2A13_uc001rme.1_Intron	NM_052885	NP_443117			solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)													HNSCC(50;0.14)			---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40265442	40265442	+	Intron	DEL	T	-	-	rs78698425		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40265442delT	uc010skm.1	-						C12orf40_uc009zjv.1_Intron|SLC2A13_uc001rme.1_Intron	NM_052885	NP_443117			solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)													HNSCC(50;0.14)			---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45782253	45782253	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45782253delT	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron|ANO6_uc010slg.1_Intron	NM_001025356	NP_001020527			anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2																		---	---	---	---
TIMELESS	8914	broad.mit.edu	37	12	56824461	56824461	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56824461delT	uc001slf.2	-						TIMELESS_uc001slg.2_Intron	NM_003920	NP_003911			timeless homolog						cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8																		---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57860075	57860075	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57860075delG	uc001snx.2	+	8	893	c.815delG	c.(814-816)TGGfs	p.W272fs	GLI1_uc009zpq.2_Frame_Shift_Del_p.W144fs	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	272	C2H2-type 2.				epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15			GBM - Glioblastoma multiforme(3;3.99e-32)															---	---	---	---
MARS	4141	broad.mit.edu	37	12	57884564	57884574	+	Intron	DEL	TTTTTTTTTTT	-	-	rs35674919		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57884564_57884574delTTTTTTTTTTT	uc001sog.2	+						ARHGAP9_uc001sod.2_5'Flank|ARHGAP9_uc001soe.1_5'Flank|MARS_uc001sof.1_Intron|MARS_uc010srp.1_Intron|MARS_uc010srq.1_Intron	NM_004990	NP_004981			methionyl-tRNA synthetase						methionyl-tRNA aminoacylation	cytosol	ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding			ovary(3)|central_nervous_system(1)|pancreas(1)	5			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)													---	---	---	---
OS9	10956	broad.mit.edu	37	12	58110063	58110063	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58110063delG	uc001spj.2	+						OS9_uc010srx.1_Intron|OS9_uc001spk.2_Intron|OS9_uc001spl.2_Intron|OS9_uc001spm.2_Intron|OS9_uc001spn.2_Intron|OS9_uc010sry.1_Intron|OS9_uc010srz.1_Intron	NM_006812	NP_006803			osteosarcoma amplified 9, endoplasmic reticulum						ER-associated protein catabolic process|protein retention in ER lumen|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to endoplasmic reticulum stress	endoplasmic reticulum lumen|Hrd1p ubiquitin ligase complex	glycoprotein binding|protein binding|sugar binding			ovary(1)	1	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)															---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64265417	64265418	+	Intron	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64265417_64265418insT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	66431539	66431539	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66431539delA								HMGA2 (71471 upstream) : LLPH (85311 downstream)																																			---	---	---	---
PTPRB	5787	broad.mit.edu	37	12	70986495	70986495	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70986495delA	uc001swb.3	-						PTPRB_uc010sto.1_Intron|PTPRB_uc010stp.1_Intron|PTPRB_uc001swc.3_Intron|PTPRB_uc001swa.3_Intron|PTPRB_uc001swd.3_Intron|PTPRB_uc009zrr.1_Intron|PTPRB_uc001swe.2_Intron	NM_002837	NP_002828			protein tyrosine phosphatase, receptor type, B						angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)															---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71523013	71523013	+	Intron	DEL	T	-	-	rs112700480		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71523013delT	uc009zrt.1	-						TSPAN8_uc001swk.1_Intron|TSPAN8_uc001swj.1_Intron	NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	73525130	73525130	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73525130delA								TRHDE (465709 upstream) : None (None downstream)																																			---	---	---	---
PAWR	5074	broad.mit.edu	37	12	79988067	79988067	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79988067delA	uc001syx.2	-							NM_002583	NP_002574			PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0																		---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85554294	85554294	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85554294delT	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	91035369	91035370	+	IGR	INS	-	GAAGGAAGGAAGGAAG	GAAGGAAGGAAGGAAG	rs151197546	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91035369_91035370insGAAGGAAGGAAGGAAG								LOC338758 (929641 upstream) : C12orf12 (310623 downstream)																																			---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95451201	95451202	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95451201_95451202delAA	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97073209	97073209	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97073209delA	uc001tet.1	+							NM_198520	NP_940922			hypothetical protein LOC374467											skin(6)|ovary(1)	7																		---	---	---	---
TMPO	7112	broad.mit.edu	37	12	98925326	98925326	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98925326delT	uc001tfj.2	+						TMPO_uc001tfi.1_Intron|TMPO_uc001tfk.2_Intron|TMPO_uc001tfl.2_Intron|TMPO_uc001tfh.1_Intron	NM_001032283	NP_001027454			thymopoietin isoform beta							integral to membrane|nuclear inner membrane	DNA binding|lamin binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	100402758	100402758	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100402758delT								ANKS1B (24326 upstream) : UHRF1BP1L (28107 downstream)																																			---	---	---	---
DEPDC4	120863	broad.mit.edu	37	12	100657163	100657163	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100657163delT	uc001thi.2	-						DEPDC4_uc001thh.1_Intron|DEPDC4_uc001thj.1_Intron|DEPDC4_uc009ztv.1_Intron|DEPDC4_uc001thk.1_Intron|DEPDC4_uc001thl.1_Intron	NM_152317	NP_689530			DEP domain containing 4						intracellular signal transduction						0																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101738703	101738703	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101738703delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
KIAA1033	23325	broad.mit.edu	37	12	105512166	105512166	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105512166delA	uc001tld.2	+						KIAA1033_uc010swr.1_Intron|KIAA1033_uc010sws.1_Intron	NM_015275	NP_056090			hypothetical protein LOC23325						endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2																		---	---	---	---
KIAA1033	23325	broad.mit.edu	37	12	105540436	105540436	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105540436delT	uc001tld.2	+						KIAA1033_uc010swr.1_Intron|KIAA1033_uc010sws.1_Intron	NM_015275	NP_056090			hypothetical protein LOC23325						endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2																		---	---	---	---
APPL2	55198	broad.mit.edu	37	12	105601642	105601642	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105601642delA	uc001tlf.1	-						APPL2_uc010swt.1_Intron|APPL2_uc001tlg.1_Intron|APPL2_uc010swu.1_Intron|APPL2_uc009zuq.2_Intron	NM_018171	NP_060641			adaptor protein, phosphotyrosine interaction, PH						cell cycle|cell proliferation|signal transduction	early endosome membrane|nucleus	protein binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109609906	109609906	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109609906delT	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
TCHP	84260	broad.mit.edu	37	12	110342658	110342658	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110342658delT	uc001tpn.2	+						TCHP_uc001tpo.1_Intron|TCHP_uc001tpp.2_Intron	NM_001143852	NP_001137324			trichoplein						apoptosis|negative regulation of cell growth	apical cortex|centrosome|keratin filament|mitochondrion|plasma membrane	protein binding			skin(1)	1																		---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112096441	112096442	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112096441_112096442delAA	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759			BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1																		---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112107551	112107551	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112107551delA	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759			BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1																		---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112117150	112117150	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112117150delA	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759			BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	119145415	119145416	+	IGR	INS	-	TGGTGA	TGGTGA	rs28483306		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119145415_119145416insTGGTGA								SUDS3 (289576 upstream) : SRRM4 (273980 downstream)																																			---	---	---	---
MSI1	4440	broad.mit.edu	37	12	120809497	120809498	+	5'Flank	DEL	AA	-	-	rs112962110		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120809497_120809498delAA	uc001tye.1	-							NM_002442	NP_002433			musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SFRS9	8683	broad.mit.edu	37	12	120899703	120899703	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120899703delA	uc001tyi.2	-	4						NM_003769	NP_003760			splicing factor, arginine/serine-rich 9						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
COQ5	84274	broad.mit.edu	37	12	120960838	120960838	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120960838delA	uc001tyn.2	-						COQ5_uc001tyo.2_Intron|COQ5_uc010szj.1_Intron	NM_032314	NP_115690			coenzyme Q5 homolog, methyltransferase						ubiquinone biosynthetic process	mitochondrion	methyltransferase activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121229157	121229157	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121229157delT	uc001tzd.2	-						SPPL3_uc009zwz.2_Intron	NM_139015	NP_620584			signal peptide peptidase 3							integral to membrane	aspartic-type endopeptidase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122975248	122975248	+	Intron	DEL	T	-	-	rs11318334		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122975248delT	uc001ucn.2	-						ZCCHC8_uc009zxp.2_Intron|ZCCHC8_uc009zxq.2_Intron	NM_017612	NP_060082			zinc finger, CCHC domain containing 8							catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123055783	123055783	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123055783delT	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124397614	124397614	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124397614delC	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
ULK1	8408	broad.mit.edu	37	12	132398252	132398256	+	Intron	DEL	AAAAC	-	-	rs68126752		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132398252_132398256delAAAAC	uc001uje.2	+							NM_003565	NP_003556			Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19960085	19960085	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19960085delT								LOC100101938 (40972 upstream) : TPTE2 (36936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20144119	20144119	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20144119delA								TPTE2 (8405 upstream) : MPHOSPH8 (63761 downstream)																																			---	---	---	---
FGF9	2254	broad.mit.edu	37	13	22246488	22246488	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22246488delA	uc001uog.2	+							NM_002010	NP_002001			fibroblast growth factor 9 precursor						cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|male gonad development|positive regulation of cell division	extracellular space	growth factor activity|heparin binding				0		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)														---	---	---	---
TNFRSF19	55504	broad.mit.edu	37	13	24167428	24167428	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24167428delA	uc001uov.1	+						TNFRSF19_uc001uot.2_Intron|TNFRSF19_uc010tcu.1_Intron|TNFRSF19_uc001uow.2_Intron|TNFRSF19_uc001uou.2_Intron	NM_018647	NP_061117			tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)														---	---	---	---
RPL21	6144	broad.mit.edu	37	13	27830554	27830554	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27830554delT	uc001ura.2	+							NM_000982	NP_000973			ribosomal protein L21						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0		Lung SC(185;0.0156)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0287)|OV - Ovarian serous cystadenocarcinoma(117;0.118)|Epithelial(112;0.139)|GBM - Glioblastoma multiforme(144;0.21)														---	---	---	---
ATP5EP2	432369	broad.mit.edu	37	13	28519334	28519334	+	5'Flank	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28519334delA	uc001uru.2	+							NR_002162				Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit pseudogene 2 (ATP5EP2), transcript variant 6, non-coding RNA.											ovary(1)	1																		---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28919697	28919697	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28919697delA	uc001usb.3	-						FLT1_uc001usa.3_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28932006	28932012	+	Intron	DEL	TTTTTTT	-	-	rs71816101		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28932006_28932012delTTTTTTT	uc001usb.3	-							NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FLT1	2321	broad.mit.edu	37	13	29041804	29041804	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29041804delT	uc001usb.3	-						FLT1_uc010aar.1_Intron|FLT1_uc001usc.3_Intron|FLT1_uc010tdp.1_Intron|FLT1_uc001usd.2_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32900364	32900364	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32900364delT	uc001uub.1	+						BRCA2_uc001uua.1_Intron	NM_000059	NP_000050			breast cancer 2, early onset						cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35756714	35756714	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35756714delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37605615	37605615	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37605615delT	uc001uwg.2	-						FAM48A_uc010abt.2_Intron|FAM48A_uc001uwh.2_Intron|FAM48A_uc001uwi.2_Intron|FAM48A_uc001uwj.2_Intron|FAM48A_uc001uwk.2_Intron|FAM48A_uc010tes.1_Intron|FAM48A_uc001uwl.1_Intron	NM_001014286	NP_001014308			family with sequence similarity 48, member A						autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)														---	---	---	---
CSNK1A1L	122011	broad.mit.edu	37	13	37679145	37679145	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37679145delT	uc001uwm.1	-	1	657	c.249delA	c.(247-249)AAAfs	p.K83fs		NM_145203	NP_660204	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	83	Protein kinase.				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)	1		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)														---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38357629	38357630	+	Intron	DEL	TT	-	-	rs7339215	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38357629_38357630delTT	uc001uws.2	-						TRPC4_uc010abv.2_5'Flank|TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263			transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39600600	39600600	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39600600delA	uc001uwy.2	-						C13orf23_uc001uwz.2_Intron	NM_025138	NP_079414			hypothetical protein LOC80209 isoform 1											ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
LHFP	10186	broad.mit.edu	37	13	39917882	39917882	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39917882delT	uc001uxf.2	-	4						NM_005780	NP_005771			lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)				T	HMGA2	lipoma								---	---	---	---
COG6	57511	broad.mit.edu	37	13	40301747	40301747	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40301747delT	uc001uxh.2	+						COG6_uc001uxi.2_Intron|COG6_uc010acb.2_Intron	NM_020751	NP_065802			component of oligomeric golgi complex 6 isoform						protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42393543	42393543	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42393543delA	uc001uyj.2	-						KIAA0564_uc001uyk.2_Intron	NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42788583	42788583	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42788583delA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Intron|DGKH_uc001uyn.1_Intron|DGKH_uc001uyo.1_Intron|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46716269	46716270	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46716269_46716270delAA	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
SUCLA2	8803	broad.mit.edu	37	13	48570880	48570881	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48570880_48570881insA	uc001vbs.2	-						SUCLA2_uc010tgb.1_Intron|SUCLA2_uc010tgc.1_Intron|SUCLA2_uc010tgd.1_Intron|SUCLA2_uc001vbt.1_Intron|SUCLA2_uc001vbu.1_Intron	NM_003850	NP_003841			succinate-CoA ligase, ADP-forming, beta subunit						succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)													---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49649272	49649272	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49649272delT	uc001vcm.2	+						FNDC3A_uc001vcl.1_Intron|FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49761480	49761481	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49761480_49761481delTT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49761894	49761894	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49761894delT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
CDADC1	81602	broad.mit.edu	37	13	49848636	49848636	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49848636delA	uc001vcu.2	+						CDADC1_uc010tgk.1_Intron|CDADC1_uc001vcv.2_Intron	NM_030911	NP_112173			cytidine and dCMP deaminase domain containing 1								hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)														---	---	---	---
INTS6	26512	broad.mit.edu	37	13	51936274	51936274	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51936274delT	uc001vfk.2	-	18					SERPINE3_uc010tgp.1_Intron|INTS6_uc001vfi.2_3'UTR|INTS6_uc001vfj.2_3'UTR|INTS6_uc001vfl.2_3'UTR	NM_012141	NP_036273			integrator complex subunit 6 isoform a						snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity			ovary(1)|lung(1)	2		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61057789	61057789	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61057789delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	66497431	66497432	+	IGR	DEL	AG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66497431_66497432delAG								None (None upstream) : PCDH9 (379535 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72049399	72049399	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72049399delA	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937			dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77780725	77780725	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77780725delA	uc001vkf.2	-						MYCBP2_uc010aev.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)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77834802	77834803	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77834802_77834803delAA	uc001vkf.2	-						MYCBP2_uc010aev.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	84481623	84481623	+	IGR	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84481623delG								SLITRK1 (25095 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85798922	85798922	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85798922delT								None (None upstream) : SLITRK6 (568000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87863040	87863040	+	IGR	DEL	T	-	-	rs144228386	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87863040delT								None (None upstream) : SLITRK5 (461830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88546433	88546433	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88546433delT								SLITRK5 (214565 upstream) : None (None downstream)																																			---	---	---	---
TGDS	23483	broad.mit.edu	37	13	95233466	95233466	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95233466delA	uc001vlw.2	-						TGDS_uc001vlx.2_Intron	NM_014305	NP_055120			TDP-glucose 4,6-dehydratase						cellular metabolic process		coenzyme binding|dTDP-glucose 4,6-dehydratase activity|protein binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
GPR180	160897	broad.mit.edu	37	13	95271823	95271823	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95271823delT	uc001vly.2	+						GPR180_uc001vlz.2_Intron|GPR180_uc010afi.2_Intron	NM_180989	NP_851320			G protein-coupled receptor 180 precursor							integral to membrane				breast(1)	1	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
DZIP1	22873	broad.mit.edu	37	13	96276979	96276980	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96276979_96276980insA	uc001vmk.2	-						DZIP1_uc001vml.2_Intron	NM_198968	NP_945319			DAZ interacting protein 1 isoform 2						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)															---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103289390	103289390	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103289390delA	uc001vpi.3	+							NM_003291	NP_003282			tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103289645	103289645	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103289645delA	uc001vpi.3	+							NM_003291	NP_003282			tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
CDC16	8881	broad.mit.edu	37	13	115002411	115002411	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115002411delA	uc001vuk.1	+						CDC16_uc010tkm.1_Intron|CDC16_uc001vul.1_Intron|CDC16_uc001vum.1_Intron|CDC16_uc001vun.1_Intron|CDC16_uc001vuo.1_Intron	NM_003903	NP_003894			anaphase-promoting complex, subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|mitosis|mitotic cell cycle spindle assembly checkpoint|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 K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19339542	19339542	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19339542delA								None (None upstream) : OR11H12 (38052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19408019	19408019	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19408019delA								OR11H12 (29447 upstream) : POTEG (145346 downstream)																																			---	---	---	---
STXBP6	29091	broad.mit.edu	37	14	25325269	25325269	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25325269delA	uc001wpu.2	-	4	1039	c.324delT	c.(322-324)TTTfs	p.F108fs	STXBP6_uc001wpv.2_Frame_Shift_Del_p.F108fs|STXBP6_uc001wpw.2_Frame_Shift_Del_p.F108fs|STXBP6_uc001wpx.1_RNA	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn	108					vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)														---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31843897	31843897	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31843897delA	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron|HEATR5A_uc001wrg.1_Intron|HEATR5A_uc010tpk.1_Intron	NM_015473	NP_056288			HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)														---	---	---	---
NUBPL	80224	broad.mit.edu	37	14	32257177	32257177	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32257177delA	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428			nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)														---	---	---	---
PPP2R3C	55012	broad.mit.edu	37	14	35564160	35564160	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35564160delA	uc001wss.2	-						PPP2R3C_uc001wst.2_Intron|PPP2R3C_uc010tpr.1_Intron|PPP2R3C_uc001wsu.2_Intron	NM_017917	NP_060387			serine/threonine-protein phosphatase 2A							centrosome|nucleus	calcium ion binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)														---	---	---	---
MIPOL1	145282	broad.mit.edu	37	14	37754647	37754647	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37754647delA	uc001wuc.2	+	8	1121	c.618delA	c.(616-618)CTAfs	p.L206fs	MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Frame_Shift_Del_p.L175fs|MIPOL1_uc001wud.2_Frame_Shift_Del_p.L206fs|MIPOL1_uc010ams.2_Frame_Shift_Del_p.L206fs|MIPOL1_uc001wue.2_Frame_Shift_Del_p.L175fs|MIPOL1_uc010amt.2_Frame_Shift_Del_p.L25fs	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1	206	Potential.									ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)														---	---	---	---
MIPOL1	145282	broad.mit.edu	37	14	37754802	37754803	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37754802_37754803delTT	uc001wuc.2	+						MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Intron|MIPOL1_uc001wud.2_Intron|MIPOL1_uc010ams.2_Intron|MIPOL1_uc001wue.2_Intron|MIPOL1_uc010amt.2_Intron	NM_138731	NP_620059			mirror-image polydactyly 1											ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)														---	---	---	---
TRAPPC6B	122553	broad.mit.edu	37	14	39627730	39627730	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39627730delT	uc001wut.1	-						TRAPPC6B_uc001wuu.1_Intron|TRAPPC6B_uc001wuv.1_Intron|TRAPPC6B_uc010tqd.1_Intron	NM_001079537	NP_001073005			trafficking protein particle complex 6B isoform						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)														---	---	---	---
MIA2	117153	broad.mit.edu	37	14	39703369	39703370	+	Frame_Shift_Del	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39703369_39703370delAA	uc001wux.2	+	1	245_246	c.51_52delAA	c.(49-54)ACAAAGfs	p.T17fs	MIA2_uc010amy.1_5'UTR	NM_054024	NP_473365	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	17_18						extracellular region				ovary(1)|breast(1)	2	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	45330467	45330467	+	IGR	DEL	T	-	-	rs138459383		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45330467delT								FSCB (353968 upstream) : C14orf28 (36040 downstream)																																			---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50930796	50930796	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50930796delT	uc001wya.2	-	12	1113	c.793delA	c.(793-795)AGAfs	p.R265fs	MAP4K5_uc001wyb.2_Frame_Shift_Del_p.R265fs|MAP4K5_uc010anv.1_Frame_Shift_Del_p.R265fs	NM_006575	NP_006566	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase	265	Protein kinase.				activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity	p.R265fs*8(1)		large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	54361815	54361818	+	IGR	DEL	CTTC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54361815_54361818delCTTC								DDHD1 (741769 upstream) : BMP4 (54639 downstream)																																			---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55241532	55241539	+	Intron	DEL	AAAAAAAA	-	-	rs35827295		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55241532_55241539delAAAAAAAA	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbg.2_Intron	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58604646	58604646	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58604646delA	uc001xdc.2	-						C14orf37_uc010tro.1_Intron|C14orf37_uc001xdd.2_Intron|C14orf37_uc001xde.2_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
C14orf135	64430	broad.mit.edu	37	14	60581403	60581403	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60581403delT	uc001xer.3	+						C14orf135_uc001xeq.2_Intron	NM_022495	NP_071940			hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63881778	63881778	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63881778delT	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64636831	64636831	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64636831delT	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc010aqa.2_Intron|SYNE2_uc001xgq.2_Intron	NM_015180	NP_055995			spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64867679	64867679	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64867679delT	uc001xhb.2	+						MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Intron	NM_005956	NP_005947			methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
C14orf50	145376	broad.mit.edu	37	14	65041151	65041151	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65041151delT	uc001xhl.1	+							NM_172365	NP_758953			hypothetical protein LOC145376											skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00382)|all cancers(60;0.00427)|BRCA - Breast invasive adenocarcinoma(234;0.0488)														---	---	---	---
GPX2	2877	broad.mit.edu	37	14	65409455	65409456	+	5'UTR	DEL	AG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65409455_65409456delAG	uc010tsn.1	-	1					CHURC1_uc010tsj.1_Intron|CHURC1_uc010tsk.1_Intron|FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|GPX2_uc001xhy.1_RNA	NM_002083	NP_002074			glutathione peroxidase 2						response to oxidative stress	cytoplasm	electron carrier activity|glutathione peroxidase activity			ovary(1)	1				all cancers(60;0.00117)|OV - Ovarian serous cystadenocarcinoma(108;0.00557)|BRCA - Breast invasive adenocarcinoma(234;0.00971)	Glutathione(DB00143)													---	---	---	---
ZFYVE26	23503	broad.mit.edu	37	14	68217931	68217931	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68217931delT	uc001xka.2	-						ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkb.2_Intron	NM_015346	NP_056161			zinc finger, FYVE domain containing 26						cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)														---	---	---	---
PTGR2	145482	broad.mit.edu	37	14	74340951	74340951	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74340951delC	uc001xow.2	+						PTGR2_uc010tue.1_Intron|PTGR2_uc001xox.2_Intron|ZNF410_uc001xoy.1_Intron	NM_001146154	NP_001139626			prostaglandin reductase 2						prostaglandin metabolic process		15-oxoprostaglandin 13-oxidase activity|zinc ion binding				0																		---	---	---	---
ABCD4	5826	broad.mit.edu	37	14	74772359	74772359	+	5'Flank	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74772359delT	uc001xpr.2	-						ABCD4_uc001xps.2_5'Flank|ABCD4_uc001xpt.2_5'Flank|ABCD4_uc010tur.1_5'Flank|ABCD4_uc001xpu.2_5'Flank|ABCD4_uc001xpv.2_5'Flank	NM_005050	NP_005041			ATP-binding cassette, sub-family D, member 4							ATP-binding cassette (ABC) transporter complex|integral to membrane|peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			upper_aerodigestive_tract(2)|large_intestine(1)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00153)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76352963	76352963	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76352963delT	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xrz.2_Intron|TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91883954	91883954	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91883954delC	uc010aty.2	-						CCDC88C_uc010twk.1_5'Flank|CCDC88C_uc001xzl.3_Intron	NM_001080414	NP_001073883			DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92604781	92604781	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92604781delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92623949	92623949	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92623949delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
EML1	2009	broad.mit.edu	37	14	100376521	100376522	+	Intron	INS	-	AT	AT			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100376521_100376522insAT	uc001ygs.2	+						EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425			echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	103615607	103615613	+	IGR	DEL	AAAAAAC	-	-	rs150545566		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103615607_103615613delAAAAAAC								TNFAIP2 (11831 upstream) : EIF5 (184880 downstream)																																			---	---	---	---
INF2	64423	broad.mit.edu	37	14	105208074	105208074	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105208074delC	uc010tyi.1	+						ADSSL1_uc001ypd.2_Intron|ADSSL1_uc001ype.2_Intron|ADSSL1_uc001ypf.2_Intron	NM_022489	NP_071934			inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	20710570	20710570	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20710570delA	uc001ytg.2	-						uc010tyx.1_Intron|uc001yth.3_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	25975503	25975503	+	Intron	DEL	G	-	-	rs57788199		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25975503delG	uc010ayu.2	-							NM_024490	NP_077816			ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28388214	28388214	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28388214delA	uc001zbj.2	-							NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37187070	37187070	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37187070delA	uc001zjr.2	-						MEIS2_uc001zjl.2_Intron|MEIS2_uc010ucj.1_Intron|MEIS2_uc001zjm.2_Intron|MEIS2_uc001zjn.2_Intron|MEIS2_uc001zjo.2_Intron|MEIS2_uc001zjp.2_Intron|MEIS2_uc001zjs.2_Intron|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron|MEIS2_uc001zjj.2_Intron|MEIS2_uc001zjk.2_Intron	NM_170675	NP_733775			Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)														---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38793548	38793548	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38793548delG	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730			RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)														---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40917332	40917333	+	Frame_Shift_Del	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40917332_40917333delAA	uc010bbs.1	+	11	5109_5110	c.4948_4949delAA	c.(4948-4950)AAAfs	p.K1650fs	CASC5_uc010ucq.1_Frame_Shift_Del_p.K1474fs|CASC5_uc001zme.2_Frame_Shift_Del_p.K1624fs|CASC5_uc010bbt.1_Frame_Shift_Del_p.K1624fs	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1	1650					acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)														---	---	---	---
INO80	54617	broad.mit.edu	37	15	41387663	41387663	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41387663delA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	41455942	41455943	+	IGR	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41455942_41455943insA								INO80 (47602 upstream) : EXD1 (18990 downstream)																																			---	---	---	---
CAPN3	825	broad.mit.edu	37	15	42676609	42676609	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42676609delA	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron	NM_000070	NP_000061			calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	44024095	44024095	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44024095delA								CKMT1A (32676 upstream) : CATSPER2P1 (4053 downstream)																																			---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44949207	44949209	+	Intron	DEL	AAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44949207_44949209delAAA	uc001ztx.2	-						SPG11_uc010ueh.1_Intron|SPG11_uc010uei.1_Intron|SPG11_uc001zua.1_Intron	NM_025137	NP_079413			spatacsin isoform 1						cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
SLC28A2	9153	broad.mit.edu	37	15	45561372	45561372	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45561372delA	uc001zva.2	+							NM_004212	NP_004203			solute carrier family 28 (sodium-coupled						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)														---	---	---	---
MYEF2	50804	broad.mit.edu	37	15	48444345	48444345	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48444345delT	uc001zwi.3	-						MYEF2_uc001zwg.3_5'Flank|MYEF2_uc001zwh.3_5'UTR|MYEF2_uc001zwj.3_Intron	NM_016132	NP_057216			myelin expression factor 2						transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|nucleotide binding|RNA binding			lung(2)|ovary(1)	3		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48763001	48763001	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48763001delA	uc001zwx.1	-						FBN1_uc010beo.1_5'Flank	NM_000138	NP_000129			fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
CEP152	22995	broad.mit.edu	37	15	49097636	49097636	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49097636delT	uc001zwy.2	-						CEP152_uc001zwz.2_Intron|CEP152_uc001zxa.1_Intron	NM_014985	NP_055800			centrosomal protein 152kDa						centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)														---	---	---	---
GABPB1	2553	broad.mit.edu	37	15	50571062	50571062	+	Intron	DEL	A	-	-	rs71993721		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50571062delA	uc001zyb.2	-						GABPB1_uc001zya.2_Intron|GABPB1_uc010ufg.1_Intron	NM_005254	NP_005245			GA binding protein transcription factor, beta						positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)	1																		---	---	---	---
PIGB	9488	broad.mit.edu	37	15	55625949	55625949	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55625949delA	uc002act.2	+						PIGB_uc010ugg.1_Intron	NM_004855	NP_004846			phosphatidylinositol glycan, class B						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)														---	---	---	---
PIGB	9488	broad.mit.edu	37	15	55631503	55631503	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55631503delT	uc002act.2	+	7	1149	c.833delT	c.(832-834)ATTfs	p.I278fs	PIGB_uc010ugg.1_Frame_Shift_Del_p.I83fs	NM_004855	NP_004846	Q92521	PIGB_HUMAN	phosphatidylinositol glycan, class B	278					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	56852469	56852469	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56852469delT	uc002ads.2	-											Homo sapiens cDNA clone IMAGE:5275275.																														---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57545439	57545439	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57545439delT	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_Intron|TCF12_uc010ugp.1_Intron|TCF12_uc010ugq.1_Intron|TCF12_uc010ugr.1_Intron	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59376343	59376343	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59376343delC	uc002afv.2	+	9	2592	c.2313delC	c.(2311-2313)CGCfs	p.R771fs	RNF111_uc002afs.2_Frame_Shift_Del_p.R771fs|RNF111_uc002aft.2_Frame_Shift_Del_p.R780fs|RNF111_uc002afu.2_Frame_Shift_Del_p.R770fs|RNF111_uc002afw.2_Frame_Shift_Del_p.R780fs|RNF111_uc002afx.2_Frame_Shift_Del_p.R297fs|RNF111_uc002afy.2_5'Flank	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	771	Pro-rich.				multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
FAM81A	145773	broad.mit.edu	37	15	59813411	59813411	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59813411delA	uc002agc.2	+							NM_152450	NP_689663			hypothetical protein LOC145773											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	60257613	60257613	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60257613delA								BNIP2 (275971 upstream) : FOXB1 (38808 downstream)																																			---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62209976	62209976	+	Intron	DEL	A	-	-	rs34386874		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62209976delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron|VPS13C_uc002ahd.1_5'Flank	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62242755	62242755	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62242755delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62250933	62250933	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62250933delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
SCAMP5	192683	broad.mit.edu	37	15	75311041	75311041	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75311041delT	uc002azk.1	+						SCAMP5_uc002azl.1_Intron|SCAMP5_uc002azm.1_Intron|SCAMP5_uc002azn.1_Intron|SCAMP5_uc010uly.1_Intron	NM_138967	NP_620417			secretory carrier membrane protein 5						exocytosis|negative regulation of endocytosis|positive regulation of calcium ion-dependent exocytosis|positive regulation of cytokine secretion|protein transport|response to endoplasmic reticulum stress	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane|trans-Golgi network membrane	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75541371	75541372	+	IGR	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75541371_75541372delTT								C15orf39 (36863 upstream) : GOLGA6C (9527 downstream)																																			---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75702784	75702784	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75702784delA	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron	NM_015477	NP_056292			transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81179965	81179965	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81179965delC	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159			KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83360356	83360356	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83360356delA	uc010uoh.1	-						AP3B2_uc010uoi.1_Intron|AP3B2_uc010uoj.1_Intron|AP3B2_uc010uok.1_Intron	NM_004644	NP_004635			adaptor-related protein complex 3, beta 2						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
BNC1	646	broad.mit.edu	37	15	83935885	83935885	+	Intron	DEL	A	-	-	rs78524914		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83935885delA	uc002bjt.1	-						BNC1_uc010uos.1_Intron	NM_001717	NP_001708			basonuclin 1						epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85449886	85449886	+	Intron	DEL	T	-	-	rs71397830		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85449886delT	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86182454	86182454	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86182454delA	uc002blv.1	+						AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron|AKAP13_uc010bnf.1_Intron|AKAP13_uc010bne.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
WDR93	56964	broad.mit.edu	37	15	90265499	90265499	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90265499delT	uc002boj.2	+						WDR93_uc010bnr.2_Intron|WDR93_uc010upz.1_Intron	NM_020212	NP_064597			WD repeat domain 93						electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
ZNF710	374655	broad.mit.edu	37	15	90616288	90616288	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90616288delC	uc002bov.1	+							NM_198526	NP_940928			zinc finger protein 710						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)															---	---	---	---
BLM	641	broad.mit.edu	37	15	91308328	91308328	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91308328delT	uc002bpr.2	+						BLM_uc010uqh.1_Intron|BLM_uc010uqi.1_Intron|BLM_uc010bnx.2_Intron|BLM_uc002bps.1_Intron	NM_000057	NP_000048			Bloom syndrome protein						double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)					Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93510492	93510492	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93510492delT	uc002bsp.2	+						CHD2_uc002bso.1_Intron	NM_001271	NP_001262			chromodomain helicase DNA binding protein 2						regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)															---	---	---	---
TM2D3	80213	broad.mit.edu	37	15	102185369	102185369	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102185369delA	uc002bxi.2	-						TM2D3_uc010usg.1_Intron|TM2D3_uc002bxh.2_Intron|TM2D3_uc002bxj.2_Intron|TM2D3_uc002bxk.2_Intron	NM_078474	NP_510883			TM2 domain containing 3 isoform a							integral to membrane				ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
LOC100134368	100134368	broad.mit.edu	37	16	437288	437288	+	Intron	DEL	A	-	-	rs137908843		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:437288delA	uc002cgw.1	+						uc002cgx.3_3'UTR	NR_024453				Homo sapiens cDNA clone IMAGE:3636396, partial cds.												0																		---	---	---	---
CLUAP1	23059	broad.mit.edu	37	16	3569691	3569691	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3569691delA	uc002cvk.1	+						CLUAP1_uc002cvj.1_Intron|CLUAP1_uc002cvl.1_Intron|CLUAP1_uc002cvm.1_Intron	NM_015041	NP_055856			clusterin associated protein 1 isoform 1							nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
DNAJA3	9093	broad.mit.edu	37	16	4487633	4487633	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4487633delA	uc002cwk.2	+						DNAJA3_uc002cwl.2_Intron|DNAJA3_uc010uxk.1_Intron	NM_005147	NP_005138			DnaJ (Hsp40) homolog, subfamily A, member 3						activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11066725	11066725	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11066725delT	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
LITAF	9516	broad.mit.edu	37	16	11647266	11647267	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11647266_11647267insA	uc002daz.2	-						LITAF_uc002dba.2_Intron|LITAF_uc002dbb.2_Intron|LITAF_uc002dbc.2_Intron|LITAF_uc002dbd.2_Intron	NM_004862	NP_004853			lipopolysaccharide-induced TNF-alpha factor						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|lysosomal membrane	signal transducer activity|WW domain binding			liver(1)	1																		---	---	---	---
ZC3H7A	29066	broad.mit.edu	37	16	11867975	11867975	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11867975delA	uc002dbk.2	-						ZC3H7A_uc002dbl.2_Intron|ZC3H7A_uc002dbm.1_Intron	NM_014153	NP_054872			zinc finger CCCH-type containing 7A							nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
RUNDC2A	84127	broad.mit.edu	37	16	12142010	12142011	+	Intron	INS	-	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12142010_12142011insG	uc002dbw.1	+							NM_032167	NP_115543			RUN domain containing 2A											ovary(1)	1								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
ERCC4	2072	broad.mit.edu	37	16	14016110	14016110	+	Intron	DEL	T	-	-	rs113434368		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14016110delT	uc002dce.2	+						ERCC4_uc010bva.2_Intron	NM_005236	NP_005227			excision repair cross-complementing rodent						double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair	nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex	damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity			lung(4)|ovary(3)|skin(2)|pancreas(1)	10								Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
TMC7	79905	broad.mit.edu	37	16	19020932	19020932	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19020932delA	uc002dfq.2	+						TMC7_uc010vao.1_Intron|TMC7_uc002dfp.2_Intron|TMC7_uc010vap.1_Intron	NM_024847	NP_079123			transmembrane channel-like 7 isoform a							integral to membrane				skin(2)|ovary(1)	3																		---	---	---	---
THUMPD1	55623	broad.mit.edu	37	16	20748117	20748117	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20748117delT	uc002dho.2	-	4					THUMPD1_uc010vaz.1_3'UTR|THUMPD1_uc002dhp.2_Intron	NM_017736	NP_060206			THUMP domain containing 1												0																		---	---	---	---
METTL9	51108	broad.mit.edu	37	16	21664118	21664118	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21664118delT	uc002dje.2	+						uc002diq.3_Intron|METTL9_uc002djf.2_Intron|IGSF6_uc002djg.1_5'Flank|IGSF6_uc010vbi.1_5'Flank	NM_016025	NP_057109			methyltransferase like 9 isoform 1											ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0759)														---	---	---	---
USP31	57478	broad.mit.edu	37	16	23117811	23117811	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23117811delA	uc002dll.2	-							NM_020718	NP_065769			ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)														---	---	---	---
GGA2	23062	broad.mit.edu	37	16	23486475	23486476	+	Intron	DEL	AC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23486475_23486476delAC	uc002dlq.2	-						GGA2_uc010bxo.1_Intron	NM_015044	NP_055859			ADP-ribosylation factor binding protein 2						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0386)														---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	23847674	23847675	+	Intron	DEL	GC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23847674_23847675delGC	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
INO80E	283899	broad.mit.edu	37	16	30007665	30007665	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30007665delA	uc002dvg.1	+	1	135	c.34delA	c.(34-36)AAAfs	p.K12fs	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvh.1_RNA|INO80E_uc002dvi.1_Frame_Shift_Del_p.K12fs|INO80E_uc002dvj.1_RNA|INO80E_uc002dvk.1_Frame_Shift_Del_p.K12fs|HIRIP3_uc002dve.2_5'Flank|HIRIP3_uc002dvf.2_5'Flank	NM_173618	NP_775889	Q8NBZ0	IN80E_HUMAN	INO80 complex subunit E	12	Potential.				DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex				skin(1)	1																		---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47292700	47292700	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47292700delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47599131	47599131	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47599131delT	uc002eev.3	+						PHKB_uc002eeu.3_Intron	NM_000293	NP_000284			phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53263000	53263000	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53263000delT	uc002ehb.2	+	7	2438	c.2274delT	c.(2272-2274)CATfs	p.H758fs	CHD9_uc002egy.2_Frame_Shift_Del_p.H758fs|CHD9_uc002eha.1_Frame_Shift_Del_p.H758fs|CHD9_uc002ehc.2_Frame_Shift_Del_p.H758fs|CHD9_uc002ehd.2_Frame_Shift_Del_p.H284fs	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	758	Chromo 1.				cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53326632	53326632	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53326632delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53348724	53348724	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53348724delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	54491407	54491407	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54491407delT								IRX3 (171029 upstream) : IRX5 (473704 downstream)																																			---	---	---	---
MT1F	4494	broad.mit.edu	37	16	56693131	56693131	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56693131delT	uc002ejt.2	+	3						NM_005949	NP_005940			metallothionein 1F							cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0																		---	---	---	---
GPR114	221188	broad.mit.edu	37	16	57597177	57597177	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57597177delG	uc002elx.3	+						GPR114_uc010vhr.1_Intron|GPR114_uc002ely.2_Intron	NM_153837	NP_722579			G protein-coupled receptor 114 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1																		---	---	---	---
CSNK2A2	1459	broad.mit.edu	37	16	58201059	58201059	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58201059delT	uc002enc.2	-							NM_001896	NP_001887			casein kinase 2, alpha prime polypeptide						axon guidance|Wnt receptor signaling pathway	cytosol|nucleus	ATP binding|protein N-terminus binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58622855	58622855	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58622855delA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
CES3	23491	broad.mit.edu	37	16	67000964	67000964	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67000964delT	uc002eqt.2	+						CES3_uc010cdz.2_Intron|CES3_uc010cea.2_Intron|CES3_uc010viw.1_5'Flank	NM_024922	NP_079198			carboxylesterase 3 precursor							endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity			ovary(3)|central_nervous_system(2)	5		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)														---	---	---	---
FHOD1	29109	broad.mit.edu	37	16	67267852	67267852	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67267852delG	uc002esl.2	-	13	1866	c.1754delC	c.(1753-1755)CCTfs	p.P585fs	FHOD1_uc010ced.2_Frame_Shift_Del_p.P392fs|FHOD1_uc010vjh.1_Frame_Shift_Del_p.P245fs	NM_013241	NP_037373	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	585	FH1.|Poly-Pro.				actin cytoskeleton organization	cytoplasm|cytoskeleton|nucleus	actin binding	p.P585fs*43(1)		breast(2)|ovary(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)														---	---	---	---
CIRH1A	84916	broad.mit.edu	37	16	69184860	69184860	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69184860delC	uc002ews.3	+						CIRH1A_uc002ewr.2_Intron|CIRH1A_uc002ewt.3_Intron|CIRH1A_uc010cfi.2_Intron|CIRH1A_uc010cfj.1_Intron	NM_032830	NP_116219			cirhin							nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)														---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70935161	70935161	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70935161delT	uc002ezr.2	-							NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
PLCG2	5336	broad.mit.edu	37	16	81934374	81934376	+	In_Frame_Del	DEL	ATC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81934374_81934376delATC	uc002fgt.2	+	14	1503_1505	c.1351_1353delATC	c.(1351-1353)ATCdel	p.I453del	PLCG2_uc010chg.1_In_Frame_Del_p.I453del	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	453	PI-PLC X-box.				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																		---	---	---	---
FBXO31	79791	broad.mit.edu	37	16	87368028	87368030	+	Intron	DEL	AGA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87368028_87368030delAGA	uc002fjw.2	-						FBXO31_uc010vot.1_Intron|FBXO31_uc002fjv.2_Intron	NM_024735	NP_079011			F-box protein 31						cell cycle|cyclin catabolic process|mitotic cell cycle G1/S transition DNA damage checkpoint|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	SCF ubiquitin ligase complex	cyclin binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0272)														---	---	---	---
ZC3H18	124245	broad.mit.edu	37	16	88691141	88691141	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88691141delC	uc002fky.2	+	12	2230	c.2030delC	c.(2029-2031)ACCfs	p.T677fs	ZC3H18_uc010voz.1_Frame_Shift_Del_p.T701fs|ZC3H18_uc010chw.2_RNA|ZC3H18_uc002fkz.2_5'Flank	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	677	Ser-rich.					nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)														---	---	---	---
ZNF778	197320	broad.mit.edu	37	16	89291883	89291883	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89291883delT	uc002fmv.2	+						ZNF778_uc010vpf.1_Intron|ZNF778_uc002fmw.1_Intron|ZNF778_uc010vpg.1_Intron	NM_182531	NP_872337			zinc finger protein 778						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)														---	---	---	---
MNT	4335	broad.mit.edu	37	17	2298768	2298768	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2298768delG	uc002fur.2	-							NM_020310	NP_064706			MAX binding protein						multicellular organismal development|negative regulation of cell proliferation|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			skin(1)	1				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)														---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2570628	2570628	+	Intron	DEL	A	-	-	rs76296857		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2570628delA	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron|PAFAH1B1_uc010vqz.1_5'Flank	NM_000430	NP_000421			platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2866623	2866624	+	Intron	INS	-	C	C	rs77735094		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2866623_2866624insC	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
MINK1	50488	broad.mit.edu	37	17	4800452	4800452	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4800452delC	uc010vsl.1	+						MINK1_uc010vsk.1_Intron|MINK1_uc010vsm.1_Intron|MINK1_uc010vsn.1_Intron|MINK1_uc010vso.1_Intron|MINK1_uc010vsp.1_Intron|C17orf107_uc010ckr.2_5'Flank|C17orf107_uc002fzl.3_5'Flank	NM_153827	NP_722549			misshapen-like kinase 1 isoform 3						JNK cascade	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
NUP88	4927	broad.mit.edu	37	17	5307293	5307293	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5307293delA	uc002gbo.1	-						NUP88_uc010vsx.1_Intron|NUP88_uc010cle.1_Intron|NUP88_uc010vsy.1_Intron	NM_002532	NP_002523			nucleoporin 88kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1																		---	---	---	---
ALOX12	239	broad.mit.edu	37	17	6909374	6909379	+	Intron	DEL	GGGGCC	-	-	rs5819132		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6909374_6909379delGGGGCC	uc002gdx.3	+						uc002gdy.1_Intron	NM_000697	NP_000688			arachidonate 12-lipoxygenase						anti-apoptosis|cellular component movement|fatty acid oxidation|leukotriene biosynthetic process|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of cell proliferation|superoxide anion generation	cytosol|sarcolemma	arachidonate 12-lipoxygenase activity|hepoxilin-epoxide hydrolase activity|iron ion binding|lipoxygenase activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
C17orf49	124944	broad.mit.edu	37	17	6919049	6919049	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6919049delC	uc002gec.2	+						C17orf49_uc002geb.3_Intron|C17orf49_uc002ged.2_Intron|C17orf49_uc002gee.2_Intron|C17orf49_uc010vti.1_Intron	NM_174893	NP_777553			hypothetical protein LOC124944 isoform 2						chromatin modification	MLL1 complex|NURF complex	DNA binding			large_intestine(1)	1																		---	---	---	---
TMEM107	84314	broad.mit.edu	37	17	8077041	8077041	+	3'UTR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8077041delT	uc002gkg.3	-	5					TMEM107_uc002gkh.3_3'UTR|TMEM107_uc002gki.3_3'UTR|TMEM107_uc002gkj.3_RNA	NM_183065	NP_898888			transmembrane protein 107 isoform 2							integral to membrane					0																		---	---	---	---
LOC220594	220594	broad.mit.edu	37	17	18418850	18418850	+	RNA	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18418850delC	uc010cqe.2	-	3		c.2295delG			LOC220594_uc010cqf.2_RNA|LOC220594_uc002gty.2_RNA	NR_003554				Homo sapiens mRNA for TL132.												0																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18776163	18776164	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18776163_18776164delTT	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26946487	26946487	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26946487delA	uc002hbu.2	-						KIAA0100_uc002hbt.2_Intron	NM_014680	NP_055495			hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	27348210	27348211	+	IGR	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27348210_27348211delTT								SEZ6 (14752 upstream) : PIPOX (21707 downstream)																																			---	---	---	---
CRYBA1	1411	broad.mit.edu	37	17	27572452	27572452	+	5'Flank	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27572452delA	uc002hdw.2	+							NM_005208	NP_005199			crystallin, beta A3						visual perception	soluble fraction	structural constituent of eye lens				0			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)															---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28029815	28029815	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28029815delA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002heq.2_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747			slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
CPD	1362	broad.mit.edu	37	17	28706682	28706683	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28706682_28706683insC	uc002hfb.1	+	1	699_700	c.684_685insC	c.(682-687)GAACCCfs	p.E228fs	CPD_uc010wbo.1_5'Flank|CPD_uc010wbp.1_5'Flank	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor	228_229	Extracellular (Potential).|Carboxypeptidase-like 1.				proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2																		---	---	---	---
C17orf42	79736	broad.mit.edu	37	17	29226631	29226631	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29226631delA	uc002hfu.2	-						C17orf42_uc002hfv.2_Intron|C17orf42_uc002hfw.2_3'UTR	NM_024683	NP_078959			hypothetical protein LOC79736						oxidative phosphorylation|regulation of transcription, DNA-dependent|transcription from mitochondrial promoter	mitochondrial nucleoid|ribonucleoprotein complex	DNA polymerase processivity factor activity|nucleic acid binding|protein binding			ovary(1)	1		all_cancers(10;4.64e-07)|all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)																---	---	---	---
NF1	4763	broad.mit.edu	37	17	29528326	29528326	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29528326delT	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29575850	29575851	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29575850_29575851delTT	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron|NF1_uc002hgi.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
UTP6	55813	broad.mit.edu	37	17	30216150	30216150	+	Intron	DEL	A	-	-	rs74645591		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30216150delA	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)																---	---	---	---
RHOT1	55288	broad.mit.edu	37	17	30531121	30531121	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30531121delT	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron	NM_018307	NP_060777			ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)																---	---	---	---
C17orf75	64149	broad.mit.edu	37	17	30661628	30661629	+	Intron	INS	-	CA	CA			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30661628_30661629insCA	uc002hhg.2	-							NM_022344	NP_071739			hypothetical protein LOC64149						spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31103177	31103177	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31103177delA	uc002hho.1	-						MYO1D_uc002hhp.1_Intron|MYO1D_uc010wcb.1_Intron	NM_015194	NP_056009			myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)															---	---	---	---
NLE1	54475	broad.mit.edu	37	17	33466212	33466212	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33466212delA	uc002hiy.1	-						NLE1_uc010ctn.1_Intron|NLE1_uc002hiz.1_Intron	NM_018096	NP_060566			Notchless gene homolog isoform a							nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)																---	---	---	---
MRPL45	84311	broad.mit.edu	37	17	36462377	36462379	+	Intron	DEL	AAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36462377_36462379delAAA	uc002hpy.2	+							NM_032351	NP_115727			mitochondrial ribosomal protein L45 precursor						intracellular protein transport|translation	mitochondrial inner membrane presequence translocase complex|ribosome	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|structural constituent of ribosome				0	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)																---	---	---	---
PSMD3	5709	broad.mit.edu	37	17	38140453	38140456	+	Intron	DEL	AAAA	-	-	rs34306234		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38140453_38140456delAAAA	uc002htn.1	+						PSMD3_uc010wen.1_Intron|PSMD3_uc010weo.1_Intron	NM_002809	NP_002800			proteasome 26S non-ATPase subunit 3						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|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	enzyme regulator activity|protein binding			ovary(1)|pancreas(1)	2	Colorectal(19;0.000442)																	---	---	---	---
STAT5A	6776	broad.mit.edu	37	17	40457521	40457521	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40457521delA	uc002hzj.1	+						STAT5A_uc010cya.1_Intron|STAT5A_uc010cyb.1_Intron|STAT5A_uc010cyc.1_Intron|STAT5A_uc010cyd.1_5'Flank|STAT5A_uc010cye.1_5'Flank	NM_003152	NP_003143			signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)														---	---	---	---
NAGLU	4669	broad.mit.edu	37	17	40685495	40685495	+	5'Flank	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40685495delT	uc002hzv.2	+							NM_000263	NP_000254			alpha-N-acetylglucosaminidase precursor							lysosome	alpha-N-acetylglucosaminidase activity				0		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	40905438	40905438	+	IGR	DEL	A	-	-	rs150921188	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40905438delA								EZH1 (8367 upstream) : LOC100190938 (86 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41796307	41796309	+	IGR	DEL	TTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41796307_41796309delTTT								MEOX1 (57045 upstream) : SOST (34790 downstream)																																			---	---	---	---
G6PC3	92579	broad.mit.edu	37	17	42151308	42151308	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42151308delA	uc002iex.2	+						G6PC3_uc002iey.2_Intron|G6PC3_uc010czo.2_Intron|G6PC3_uc002iez.2_Intron|G6PC3_uc002ifb.2_5'Flank|G6PC3_uc002ifc.2_5'Flank	NM_138387	NP_612396			glucose-6-phosphatase catalytic subunit 3						gluconeogenesis|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	glucose-6-phosphatase activity			skin(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.113)														---	---	---	---
PLEKHM1	9842	broad.mit.edu	37	17	43515408	43515408	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43515408delT	uc002ija.2	-						PLEKHM1_uc010wjm.1_Intron|PLEKHM1_uc002ijb.2_Intron	NM_014798	NP_055613			pleckstrin homology domain containing, family M						intracellular signal transduction	cytoplasm	metal ion binding				0	Renal(3;0.0405)																	---	---	---	---
WNT3	7473	broad.mit.edu	37	17	44851007	44851007	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44851007delC	uc002ikv.2	-							NM_030753	NP_110380			wingless-type MMTV integration site family,						canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|cellular response to retinoic acid|dorsal/ventral axis specification|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic pattern specification|head morphogenesis|hemopoietic stem cell proliferation|inner ear morphogenesis|limb bud formation|mammary gland epithelium development|mesoderm formation|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|positive regulation of cell proliferation|Spemann organizer formation at the anterior end of the primitive streak|Wnt receptor signaling pathway, calcium modulating pathway	early endosome|extracellular space|late endosome|membrane fraction|membrane raft|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|signal transducer activity			lung(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.0257)															---	---	---	---
NPEPPS	9520	broad.mit.edu	37	17	45691166	45691166	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45691166delA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_Intron|NPEPPS_uc002ils.1_Intron	NM_006310	NP_006301			aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0																		---	---	---	---
KPNB1	3837	broad.mit.edu	37	17	45734125	45734125	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45734125delA	uc002ilt.1	+						KPNB1_uc010wkw.1_Intron|KPNB1_uc010wkx.1_5'Flank	NM_002265	NP_002256			karyopherin beta 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ABI3	51225	broad.mit.edu	37	17	47295005	47295005	+	Intron	DEL	C	-	-	rs113223751		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47295005delC	uc002iop.1	+						ABI3_uc002ioq.1_Intron	NM_016428	NP_057512			NESH protein isoform 1						cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)												HNSCC(55;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48363388	48363395	+	IGR	DEL	ATTCCTTA	-	-	rs12951054	by1000genomes;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48363388_48363395delATTCCTTA								TMEM92 (4544 upstream) : XYLT2 (59998 downstream)																																			---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48693840	48693841	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48693840_48693841delTT	uc002irk.1	+						CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Intron|CACNA1G_uc002irq.1_Intron|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Intron|CACNA1G_uc002irx.1_Intron|CACNA1G_uc002iry.1_Intron|CACNA1G_uc002irz.1_Intron|CACNA1G_uc002isa.1_Intron|CACNA1G_uc002isb.1_Intron|CACNA1G_uc002isc.1_Intron|CACNA1G_uc002isd.1_Intron|CACNA1G_uc002ise.1_Intron|CACNA1G_uc002isf.1_Intron|CACNA1G_uc002isg.1_Intron|CACNA1G_uc002ish.1_Intron|CACNA1G_uc002isi.1_Intron	NM_018896	NP_061496			voltage-dependent calcium channel alpha 1G						axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49098340	49098340	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49098340delT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56435161	56435161	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56435161delC	uc002iwf.2	-	8	3932	c.1976delG	c.(1975-1977)GGTfs	p.G659fs	RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	659	Pro-rich.|Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
HSF5	124535	broad.mit.edu	37	17	56554230	56554230	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56554230delT	uc002iwi.1	-							NM_001080439	NP_001073908			heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	59667759	59667759	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59667759delA								TBX4 (105290 upstream) : NACA2 (35 downstream)																																			---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59946936	59946936	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59946936delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799			integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59999199	59999199	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59999199delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799			integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60637297	60637297	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60637297delT	uc010ddp.2	+						TLK2_uc002izx.3_Intron|TLK2_uc002izz.3_Intron|TLK2_uc002jaa.3_Intron|TLK2_uc010wpd.1_Intron	NM_006852	NP_006843			tousled-like kinase 2 isoform A						cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2																		---	---	---	---
CCDC47	57003	broad.mit.edu	37	17	61824398	61824398	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61824398delA	uc002jbs.3	-						CCDC47_uc010ddx.2_Intron	NM_020198	NP_064583			coiled-coil domain containing 47 precursor							integral to membrane	protein binding				0																		---	---	---	---
FTSJ3	117246	broad.mit.edu	37	17	61898063	61898064	+	Intron	INS	-	GCTTGAACCTGGAAGACGG	GCTTGAACCTGGAAGACGG	rs142835534	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61898063_61898064insGCTTGAACCTGGAAGACGG	uc002jbz.2	-						FTSJ3_uc002jca.2_Intron	NM_017647	NP_060117			FtsJ homolog 3						RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1																		---	---	---	---
CCDC45	90799	broad.mit.edu	37	17	62521868	62521868	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62521868delT	uc002jem.2	+						CCDC45_uc002jen.2_Intron|CCDC45_uc010wqb.1_Intron	NM_138363	NP_612372			coiled-coil domain containing 45							centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)															---	---	---	---
ABCA6	23460	broad.mit.edu	37	17	67124603	67124603	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67124603delT	uc002jhw.1	-							NM_080284	NP_525023			ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)																	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67290662	67290663	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67290662_67290663insA	uc002jif.2	-						ABCA5_uc002jie.2_Intron|ABCA5_uc002jig.2_Intron|ABCA5_uc002jih.2_Intron|ABCA5_uc010dfe.2_Intron	NM_018672	NP_061142			ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71398047	71398047	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71398047delG	uc010dfm.2	-						SDK2_uc002jjt.3_Intron|SDK2_uc010dfn.2_Intron	NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
FASN	2194	broad.mit.edu	37	17	80043423	80043423	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80043423delG	uc002kdu.2	-	23	4174	c.4057delC	c.(4057-4059)CTCfs	p.L1353fs	FASN_uc002kdw.1_Frame_Shift_Del_p.L569fs	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase	1353				LGDI -> SGH (in Ref. 2; AAA73576).	energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	cytosol|Golgi apparatus|melanosome|plasma membrane	3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339)													---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80152185	80152186	+	Intron	INS	-	TT	TT	rs140430398		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80152185_80152186insTT	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron	NM_198082	NP_932348			coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)															---	---	---	---
ENOSF1	55556	broad.mit.edu	37	18	686115	686115	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:686115delT	uc002kku.3	-						ENOSF1_uc002kkt.3_Intron|ENOSF1_uc010dke.2_Intron|ENOSF1_uc010dkf.2_Intron|ENOSF1_uc002kkv.3_Intron|ENOSF1_uc002kkw.3_Intron|ENOSF1_uc002kkx.3_Intron	NM_017512	NP_059982			enolase superfamily 1 isoform rTS beta						cellular amino acid catabolic process	mitochondrion	isomerase activity|metal ion binding			ovary(1)	1																		---	---	---	---
NDC80	10403	broad.mit.edu	37	18	2585053	2585053	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2585053delA	uc002kli.2	+							NM_006101	NP_006092			kinetochore associated 2						attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1																		---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	6971681	6971681	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6971681delT	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	7026190	7026190	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7026190delA	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
C18orf45	85019	broad.mit.edu	37	18	20945677	20945677	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20945677delA	uc002kuf.2	-						C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_Intron|C18orf45_uc002kug.2_Intron|C18orf45_uc002kuh.2_Intron	NM_032933	NP_116322			hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)																	---	---	---	---
DSC1	1823	broad.mit.edu	37	18	28735961	28735961	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28735961delA	uc002kwn.2	-						DSC1_uc002kwm.2_Intron	NM_024421	NP_077739			desmocollin 1 isoform Dsc1a preproprotein						homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00778)															---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29450471	29450471	+	Intron	DEL	A	-	-	rs35527481		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29450471delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32461881	32461881	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32461881delT	uc010dmn.1	+						DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381			dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
SLC39A6	25800	broad.mit.edu	37	18	33690943	33690943	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33690943delA	uc010dmy.2	-							NM_012319	NP_036451			solute carrier family 39 (zinc transporter),							integral to membrane|lamellipodium membrane	zinc ion transmembrane transporter activity			ovary(1)|pancreas(1)	2																		---	---	---	---
ATP5A1	498	broad.mit.edu	37	18	43670052	43670052	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43670052delG	uc002lbr.1	-						ATP5A1_uc010dnl.1_Intron|ATP5A1_uc002lbs.1_Intron|ATP5A1_uc002lbt.1_Intron|ATP5A1_uc010xct.1_Intron|ATP5A1_uc010dnm.1_Intron	NM_004046	NP_004037			ATP synthase, H+ transporting, mitochondrial F1						ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0																		---	---	---	---
ST8SIA5	29906	broad.mit.edu	37	18	44272373	44272373	+	Intron	DEL	T	-	-	rs77603253		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44272373delT	uc002lcj.1	-						ST8SIA5_uc002lci.1_Intron|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437			ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3																		---	---	---	---
LMAN1	3998	broad.mit.edu	37	18	57000584	57000584	+	Intron	DEL	A	-	-	rs76213902		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57000584delA	uc002lhz.2	-							NM_005570	NP_005561			lectin, mannose-binding, 1 precursor						blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|metal ion binding|unfolded protein binding			skin(1)	1		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	57429216	57429218	+	IGR	DEL	AAG	-	-	rs141641247	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57429216_57429218delAAG								CCBE1 (64572 upstream) : PMAIP1 (137974 downstream)																																			---	---	---	---
PIGN	23556	broad.mit.edu	37	18	59763227	59763227	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59763227delA	uc002lii.3	-						PIGN_uc002lij.3_Intron	NM_176787	NP_789744			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)																---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59958960	59958960	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59958960delT	uc002lil.2	+						KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67807195	67807195	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67807195delA	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67872746	67872747	+	Intron	INS	-	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67872746_67872747insG	uc002lkp.2	-						RTTN_uc010xfb.1_Intron|RTTN_uc002lkq.1_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
POLRMT	5442	broad.mit.edu	37	19	632888	632888	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:632888delG	uc002lpf.1	-	2	195	c.139delC	c.(139-141)CAGfs	p.Q47fs		NM_005035	NP_005026	O00411	RPOM_HUMAN	mitochondrial DNA-directed RNA polymerase	47					transcription initiation from mitochondrial promoter	mitochondrial nucleoid	DNA binding|DNA-directed RNA polymerase activity|protein binding			ovary(1)|pancreas(1)	2		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)														---	---	---	---
HMG20B	10362	broad.mit.edu	37	19	3575530	3575530	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3575530delC	uc002lya.2	+						HMG20B_uc002lyb.2_Intron|HMG20B_uc010xhn.1_Intron	NM_006339	NP_006330			high-mobility group 20B						blood coagulation|cell cycle|chromatin modification	chromosome|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SAFB2	9667	broad.mit.edu	37	19	5604955	5604955	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5604955delA	uc002mcd.2	-							NM_014649	NP_055464			scaffold attachment factor B2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)														---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6414076	6414076	+	3'UTR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6414076delA	uc002mer.3	-	20						NM_003685	NP_003676			KH-type splicing regulatory protein						mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	8414735	8414736	+	IGR	INS	-	G	G	rs59846337		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8414735_8414736insG								KANK3 (6589 upstream) : ANGPTL4 (14275 downstream)																																			---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10266894	10266894	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10266894delT	uc002mng.2	-						DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron	NM_001379	NP_001370			DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
MRPL4	51073	broad.mit.edu	37	19	10367123	10367123	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10367123delA	uc002mnm.2	+						MRPL4_uc002mnn.2_Intron|MRPL4_uc002mno.2_Intron	NM_146387	NP_666499			mitochondrial ribosomal protein L4 isoform a						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	10377498	10377498	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10377498delT								MRPL4 (6764 upstream) : ICAM1 (4019 downstream)																																			---	---	---	---
PRKCSH	5589	broad.mit.edu	37	19	11557826	11557826	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11557826delG	uc002mrt.2	+						PRKCSH_uc002mru.2_Intron|PRKCSH_uc010xlz.1_Intron|PRKCSH_uc010dya.2_Intron|PRKCSH_uc002mrv.1_Intron|PRKCSH_uc010dyb.2_Intron	NM_002743	NP_002734			protein kinase C substrate 80K-H isoform 1						innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding				0																OREG0025258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TNPO2	30000	broad.mit.edu	37	19	12825504	12825507	+	Intron	DEL	ATAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12825504_12825507delATAA	uc002muo.2	-						TNPO2_uc002mup.2_Intron|TNPO2_uc002muq.2_Intron|TNPO2_uc002mur.2_Intron	NM_001136196	NP_001129668			transportin 2 (importin 3, karyopherin beta 2b)						intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12985060	12985060	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12985060delG	uc002mvm.2	+	26	4217	c.4089delG	c.(4087-4089)CCGfs	p.P1363fs		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	1363					cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
FARSA	2193	broad.mit.edu	37	19	13036039	13036039	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13036039delT	uc002mvs.2	-						FARSA_uc002mvt.2_Intron|FARSA_uc010xmv.1_Intron|FARSA_uc010dyy.1_Intron	NM_004461	NP_004452			phenylalanyl-tRNA synthetase, alpha subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13323124	13323125	+	Intron	INS	-	GGG	GGG	rs16048	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13323124_13323125insGGG	uc010dze.2	-						CACNA1A_uc010xnd.1_Intron|CACNA1A_uc002mwx.3_Intron|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc002mwv.3_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CC2D1A	54862	broad.mit.edu	37	19	14030491	14030492	+	Intron	DEL	AA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14030491_14030492delAA	uc002mxo.2	+						CC2D1A_uc002mxn.2_Intron|CC2D1A_uc002mxp.2_Intron|CC2D1A_uc010dzh.2_Intron|CC2D1A_uc002mxq.1_Intron	NM_017721	NP_060191			coiled-coil and C2 domain containing 1A						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)															---	---	---	---
LOC113230	113230	broad.mit.edu	37	19	14182142	14182142	+	5'Flank	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14182142delA	uc002mxz.2	+						LOC113230_uc002mxy.2_5'Flank	NR_024282				RecName: Full=Uncharacterized protein LOC113230;												0																		---	---	---	---
ZNF333	84449	broad.mit.edu	37	19	14810278	14810278	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14810278delT	uc002mzn.2	+						ZNF333_uc010dzq.2_Intron|ZNF333_uc002mzk.3_Intron|ZNF333_uc002mzl.3_Intron|ZNF333_uc002mzm.2_Intron|ZNF333_uc010dzr.1_Intron	NM_032433	NP_115809			zinc finger protein 333						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
C19orf44	84167	broad.mit.edu	37	19	16625243	16625243	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16625243delG	uc002neh.1	+						MED26_uc002nee.2_Intron|C19orf44_uc002neg.2_Intron|C19orf44_uc010eai.1_Intron	NM_032207	NP_115583			hypothetical protein LOC84167												0																		---	---	---	---
HAUS8	93323	broad.mit.edu	37	19	17170524	17170524	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17170524delT	uc002nfe.2	-						HAUS8_uc002nff.2_Intron|HAUS8_uc002nfg.1_Intron|HAUS8_uc002nfh.1_Intron	NM_033417	NP_219485			sarcoma antigen NY-SAR-48 isoform a						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole					0																		---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17994332	17994333	+	Intron	DEL	GG	-	-	rs112211542		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17994332_17994333delGG	uc002nhr.3	+							NM_000453	NP_000444			solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
ZNF486	90649	broad.mit.edu	37	19	20294985	20294985	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20294985delT	uc002nou.2	+							NM_052852	NP_443084			zinc finger protein 486						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF99	7652	broad.mit.edu	37	19	22952626	22952626	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22952626delA	uc010xrh.1	-							NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	23317115	23317115	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23317115delT	uc002nrb.1	+											Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85.																														---	---	---	---
ZNF254	9534	broad.mit.edu	37	19	24289564	24289564	+	Intron	DEL	A	-	-	rs62114842		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24289564delA	uc002nru.2	+						ZNF254_uc010xrk.1_Intron|ZNF254_uc002nrt.1_Intron	NM_203282	NP_975011			zinc finger protein 254						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)																---	---	---	---
DPY19L3	147991	broad.mit.edu	37	19	32944190	32944190	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32944190delT	uc002ntg.2	+						DPY19L3_uc002nth.1_Intron|DPY19L3_uc002nti.1_Intron	NM_207325	NP_997208			dpy-19-like 3							integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)																	---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33439158	33439158	+	Intron	DEL	T	-	-	rs12710001	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33439158delT	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron|CCDC123_uc002nua.2_Intron|CCDC123_uc002nub.1_Intron	NM_032816	NP_116205			coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)																	---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36564439	36564440	+	Intron	DEL	CC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36564439_36564440delCC	uc002odc.2	+						WDR62_uc002odd.2_Intron|WDR62_uc002odb.2_Intron	NM_173636	NP_775907			WD repeat domain 62 isoform 2						cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39066443	39066443	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39066443delA	uc002oit.2	+						RYR1_uc002oiu.2_Intron	NM_000540	NP_000531			skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
TMEM145	284339	broad.mit.edu	37	19	42824786	42824786	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42824786delT	uc002otk.1	+							NM_173633	NP_775904			transmembrane protein 145							integral to membrane					0		Prostate(69;0.00682)																---	---	---	---
KCNN4	3783	broad.mit.edu	37	19	44280870	44280871	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44280870_44280871delTT	uc002oxl.2	-						KCNN4_uc010eiz.2_5'Flank|KCNN4_uc010eja.1_Intron	NM_002250	NP_002241			intermediate conductance calcium-activated						defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	45036669	45036669	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45036669delA								CEACAM20 (3121 upstream) : CEACAM22P (4376 downstream)																																			---	---	---	---
PPP1R13L	10848	broad.mit.edu	37	19	45898859	45898859	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45898859delG	uc002pbn.2	-	7	1266	c.1189delC	c.(1189-1191)CTCfs	p.L397fs	PPP1R13L_uc002pbm.2_5'Flank|PPP1R13L_uc002pbo.2_Frame_Shift_Del_p.L397fs|PPP1R13L_uc002pbp.2_Frame_Shift_Del_p.L397fs	NM_006663	NP_006654	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13	397	Pro-rich.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	transcription corepressor activity|transcription factor binding			skin(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)														---	---	---	---
PNMAL1	55228	broad.mit.edu	37	19	46972012	46972012	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46972012delT	uc002peq.3	-						PNMAL1_uc002per.3_Intron	NM_018215	NP_060685			PNMA-like 1 isoform a												0		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49684788	49684788	+	Intron	DEL	T	-	-	rs140243178		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49684788delT	uc002pmw.2	+						TRPM4_uc010emu.2_Intron|TRPM4_uc010yak.1_Intron|TRPM4_uc002pmx.2_Intron|TRPM4_uc010emv.2_Intron|TRPM4_uc010yal.1_Intron|TRPM4_uc002pmy.2_5'Flank	NM_017636	NP_060106			transient receptor potential cation channel,						dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)														---	---	---	---
TRPM4	54795	broad.mit.edu	37	19	49686205	49686205	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49686205delC	uc002pmw.2	+						TRPM4_uc010emu.2_Intron|TRPM4_uc010yak.1_Intron|TRPM4_uc002pmx.2_Intron|TRPM4_uc010emv.2_Intron|TRPM4_uc010yal.1_Intron|TRPM4_uc002pmy.2_Intron	NM_017636	NP_060106			transient receptor potential cation channel,						dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)														---	---	---	---
CACNG8	59283	broad.mit.edu	37	19	54483340	54483343	+	Intron	DEL	GCGC	-	-	rs2909772		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54483340_54483343delGCGC	uc002qcs.1	+						MIR935_hsa-mir-935|MI0005757_5'Flank	NM_031895	NP_114101			voltage-dependent calcium channel gamma-8						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic density|postsynaptic membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)														---	---	---	---
LILRB5	10990	broad.mit.edu	37	19	54754833	54754833	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54754833delG	uc002qex.2	-						LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Frame_Shift_Del_p.P601fs|LILRB5_uc002qey.2_Intron|LILRB5_uc002qez.2_Intron|LILRB5_uc002qfa.1_3'UTR	NM_006840	NP_006831			leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54810542	54810543	+	IGR	INS	-	CTTCCTT	CTTCCTT	rs140755834	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54810542_54810543insCTTCCTT								LILRA6 (6304 upstream) : LILRA5 (7811 downstream)																																			---	---	---	---
FCAR	2204	broad.mit.edu	37	19	55386627	55386627	+	Intron	DEL	A	-	-	rs76511783		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55386627delA	uc002qhr.1	+						FCAR_uc002qhq.2_Intron|FCAR_uc002qhs.1_Intron|FCAR_uc002qht.1_Intron|FCAR_uc010esi.1_Intron|FCAR_uc002qhu.1_Intron|FCAR_uc002qhv.1_Intron|FCAR_uc002qhw.1_Intron|FCAR_uc002qhx.1_Intron|FCAR_uc002qhy.1_Intron|FCAR_uc002qhz.1_Intron|FCAR_uc002qia.1_Intron	NM_002000	NP_001991			Fc alpha receptor isoform a precursor						immune response	extracellular region|integral to plasma membrane	IgA binding|receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(193;0.0443)														---	---	---	---
AURKC	6795	broad.mit.edu	37	19	57745123	57745123	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57745123delT	uc002qoe.2	+						AURKC_uc002qoc.2_Intron|AURKC_uc002qod.2_Intron|AURKC_uc010etv.2_Intron	NM_001015878	NP_001015878			aurora kinase C isoform 1						cell cycle|cytokinesis	condensed chromosome|cytoplasm|midbody|spindle midzone	ATP binding|protein serine/threonine kinase activity			lung(4)|ovary(2)	6		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;0.0122)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58727943	58727943	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58727943delA								ZNF274 (3016 upstream) : ZNF544 (12127 downstream)																																			---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3577009	3577009	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3577009delT	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
ADAM33	80332	broad.mit.edu	37	20	3655625	3655625	+	Intron	DEL	G	-	-	rs11478045		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3655625delG	uc002wit.2	-						ADAM33_uc002wir.1_Intron|ADAM33_uc002wis.2_5'Flank|ADAM33_uc002wiu.2_Intron|ADAM33_uc002wiw.1_Intron|ADAM33_uc010gba.1_Intron|ADAM33_uc010gbb.1_Intron|ADAM33_uc002wix.1_Intron|ADAM33_uc010zqg.1_Intron|ADAM33_uc010zqh.1_Intron	NM_025220	NP_079496			ADAM metallopeptidase domain 33 isoform alpha						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|ovary(1)|skin(1)	4																		---	---	---	---
TMX4	56255	broad.mit.edu	37	20	7976722	7976722	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7976722delA	uc002wmx.1	-							NM_021156	NP_066979			thioredoxin-related transmembrane protein 4						cell redox homeostasis|electron transport chain|transport	integral to membrane					0																		---	---	---	---
MKKS	8195	broad.mit.edu	37	20	10389197	10389197	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10389197delA	uc002wnt.1	-						MKKS_uc002wnu.1_Intron|MKKS_uc010zrd.1_Intron	NM_018848	NP_061336			McKusick-Kaufman syndrome protein						brain morphogenesis|cerebral cortex development|convergent extension involved in gastrulation|detection of mechanical stimulus involved in sensory perception of sound|fat cell differentiation|flagellum assembly|gonad development|heart looping|hippocampus development|intracellular transport|melanosome transport|photoreceptor cell maintenance|pigment granule aggregation in cell center|protein folding|regulation of cilium beat frequency involved in ciliary motility|sensory perception of smell|social behavior|spermatid development|striatum development	cytosol|microtubule organizing center|motile cilium	ATP binding|unfolded protein binding				0														Bardet-Biedl_syndrome				---	---	---	---
XRN2	22803	broad.mit.edu	37	20	21369830	21369830	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21369830delT	uc002wsf.1	+						XRN2_uc002wsg.1_Intron|XRN2_uc010zsk.1_Intron|XRN2_uc002wsh.1_Intron	NM_012255	NP_036387			5'-3' exoribonuclease 2						cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25900372	25900372	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25900372delA								FAM182B (51586 upstream) : LOC100134868 (90063 downstream)																																			---	---	---	---
PLUNC	51297	broad.mit.edu	37	20	31830265	31830265	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31830265delT	uc002wyv.2	+						PLUNC_uc002wyt.3_Intron|PLUNC_uc002wyu.3_Intron	NM_130852	NP_570913			palate, lung and nasal epithelium associated						innate immune response	extracellular region	lipid binding				0																		---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35677626	35677626	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35677626delA	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
KIAA0406	9675	broad.mit.edu	37	20	36625458	36625458	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36625458delA	uc002xhl.2	-						KIAA0406_uc002xhm.2_Intron	NM_014657	NP_055472			hypothetical protein LOC9675								binding				0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
RPRD1B	58490	broad.mit.edu	37	20	36676670	36676670	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36676670delT	uc002xho.3	+							NM_021215	NP_067038			Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1																		---	---	---	---
LBP	3929	broad.mit.edu	37	20	36999532	36999532	+	Intron	DEL	G	-	-	rs113207369		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36999532delG	uc002xic.1	+							NM_004139	NP_004130			lipopolysaccharide-binding protein precursor						acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
DHX35	60625	broad.mit.edu	37	20	37623284	37623287	+	Intron	DEL	CCCT	-	-	rs35259351	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37623284_37623287delCCCT	uc002xjh.2	+						DHX35_uc010zwa.1_Intron|DHX35_uc010zwb.1_Intron|DHX35_uc010zwc.1_Intron	NM_021931	NP_068750			DEAH (Asp-Glu-Ala-His) box polypeptide 35							catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PLCG1	5335	broad.mit.edu	37	20	39794631	39794631	+	Intron	DEL	C	-	-	rs74464491		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39794631delC	uc002xjp.1	+						PLCG1_uc002xjo.1_Intron|PLCG1_uc010zwe.1_Intron|PLCG1_uc010ggf.2_5'Flank	NM_182811	NP_877963			phospholipase C, gamma 1 isoform b						activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	42047887	42047890	+	IGR	DEL	AGGA	-	-	rs59445924	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42047887_42047890delAGGA								PTPRT (229330 upstream) : SFRS6 (38614 downstream)																																			---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45789429	45789429	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45789429delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235			eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)																---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50286409	50286409	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50286409delA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
NKAIN4	128414	broad.mit.edu	37	20	61874139	61874139	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61874139delG	uc002yek.2	-							NM_152864	NP_690603			Na+/K+ transporting ATPase interacting 4							integral to membrane|plasma membrane					0	all_cancers(38;2.72e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	21112407	21112408	+	IGR	DEL	GA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21112407_21112408delGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21646916	21646917	+	IGR	INS	-	AGGAAGGT	AGGAAGGT	rs142229684	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21646916_21646917insAGGAAGGT								None (None upstream) : C21orf131 (467997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21797194	21797194	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21797194delT								None (None upstream) : C21orf131 (317720 downstream)																																			---	---	---	---
JAM2	58494	broad.mit.edu	37	21	27074452	27074452	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27074452delA	uc002ylp.1	+						JAM2_uc011ace.1_Intron|JAM2_uc002ylq.1_Intron|JAM2_uc011acf.1_Intron|JAM2_uc010glh.1_Intron|JAM2_uc002ylr.1_Intron|JAM2_uc010gli.1_Intron	NM_021219	NP_067042			junctional adhesion molecule 2 precursor						blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0																		---	---	---	---
ATP5J	522	broad.mit.edu	37	21	27097750	27097752	+	Intron	DEL	TTT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27097750_27097752delTTT	uc002yls.2	-						ATP5J_uc002ylt.2_Intron|ATP5J_uc002ylu.2_Intron|ATP5J_uc002ylv.2_Intron|ATP5J_uc002ylw.2_Intron	NM_001685	NP_001676			ATP synthase, H+ transporting, mitochondrial F0						ATP catabolic process|respiratory electron transport chain		hydrogen ion transmembrane transporter activity				0																		---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27134768	27134768	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27134768delT	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031			GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30319939	30319939	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30319939delA	uc002ymr.2	-							NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34115632	34115632	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34115632delA	uc002yqn.2	-						GCFC1_uc002yql.2_Intron|GCFC1_uc002yqm.2_Intron|GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron	NM_016631	NP_057715			GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	34213737	34213737	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34213737delT								C21orf62 (27684 upstream) : OLIG2 (184502 downstream)																																			---	---	---	---
IFNAR1	3454	broad.mit.edu	37	21	34717524	34717524	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34717524delT	uc002yrn.2	+						IFNAR1_uc011adv.1_Intron	NM_000629	NP_000620			interferon-alpha receptor 1 precursor						JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	integral to plasma membrane	type I interferon receptor activity			central_nervous_system(1)|skin(1)	2					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)													---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38845339	38845339	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38845339delT	uc002ywk.2	+						DYRK1A_uc002ywh.1_Intron|DYRK1A_uc002ywi.2_Intron|DYRK1A_uc002ywj.2_Intron|DYRK1A_uc002ywl.2_Intron|DYRK1A_uc002ywm.2_Intron	NM_001396	NP_001387			dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4																		---	---	---	---
LCA5L	150082	broad.mit.edu	37	21	40794907	40794907	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40794907delT	uc002yxu.2	-	5	1145	c.832delA	c.(832-834)ATAfs	p.I278fs	LCA5L_uc002yxv.2_Frame_Shift_Del_p.I278fs|LCA5L_uc002yxw.1_Frame_Shift_Del_p.I278fs|LCA5L_uc002yxx.1_Frame_Shift_Del_p.I140fs|LCA5L_uc002yxy.2_RNA	NM_152505	NP_689718	O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	278											0		Prostate(19;1.2e-06)																---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43223282	43223282	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43223282delA	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43546367	43546367	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43546367delC	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc002zal.1_Intron|UMODL1_uc010gpa.1_5'Flank	NM_001004416	NP_001004416			uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
TMPRSS3	64699	broad.mit.edu	37	21	43792676	43792677	+	3'UTR	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43792676_43792677insA	uc002zbb.2	-	13					TMPRSS3_uc002zay.2_3'UTR|TMPRSS3_uc002zaz.2_3'UTR|TMPRSS3_uc002zba.2_3'UTR|TMPRSS3_uc002zbc.2_3'UTR	NM_024022	NP_076927			transmembrane protease, serine 3 isoform 1						cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity			ovary(2)|breast(1)	3																		---	---	---	---
GNB1L	54584	broad.mit.edu	37	22	19780677	19780677	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19780677delA	uc002zqe.1	-						GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqf.1_Intron	NM_053004	NP_443730			guanine nucleotide binding protein						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	internal side of plasma membrane|intracellular				breast(1)	1	Colorectal(54;0.0993)																	---	---	---	---
ZDHHC8	29801	broad.mit.edu	37	22	20130522	20130522	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20130522delC	uc002zrq.2	+	10	1475	c.1369delC	c.(1369-1371)CCCfs	p.P457fs	ZDHHC8_uc002zrr.1_Frame_Shift_Del_p.P457fs|ZDHHC8_uc010gsa.2_Frame_Shift_Del_p.P263fs	NM_013373	NP_037505	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC domain containing 8	457	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Colorectal(54;0.0993)																	---	---	---	---
MED15	51586	broad.mit.edu	37	22	20918696	20918697	+	Intron	DEL	TC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20918696_20918697delTC	uc002zsp.2	+						MED15_uc002zsn.1_Intron|MED15_uc002zso.2_Intron|MED15_uc002zsq.2_Intron|MED15_uc010gso.2_Intron|MED15_uc002zsr.2_Intron|MED15_uc011ahs.1_Intron|MED15_uc011aht.1_Intron|MED15_uc002zss.2_Intron|MED15_uc011ahu.1_5'Flank	NM_001003891	NP_001003891			mediator complex subunit 15 isoform a						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)													OREG0026319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HSCB	150274	broad.mit.edu	37	22	29138427	29138427	+	Intron	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29138427delG	uc003aea.2	+						CHEK2_uc003adt.1_5'Flank|CHEK2_uc003adu.1_5'Flank|CHEK2_uc003adv.1_5'Flank|CHEK2_uc003adw.1_5'Flank|CHEK2_uc003adx.1_5'Flank|CHEK2_uc003ady.1_5'Flank|CHEK2_uc003adz.1_5'Flank	NM_172002	NP_741999			J-type co-chaperone HSC20 precursor						iron-sulfur cluster assembly|protein folding	mitochondrion	chaperone binding|heat shock protein binding|metal ion binding			kidney(1)	1																		---	---	---	---
BPIL2	254240	broad.mit.edu	37	22	32828267	32828267	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32828267delC	uc003amn.2	-						BPIL2_uc010gwo.2_Intron|BPIL2_uc011amb.1_Intron	NM_174932	NP_777592			bactericidal/permeability-increasing							extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	34492105	34492106	+	IGR	INS	-	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34492105_34492106insT								LARGE (173521 upstream) : ISX (970023 downstream)																																			---	---	---	---
KCTD17	79734	broad.mit.edu	37	22	37458553	37458553	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37458553delT	uc010gxb.2	+						KCTD17_uc011amv.1_Intron|KCTD17_uc010gxc.2_Intron	NM_024681	NP_078957			potassium channel tetramerisation domain							voltage-gated potassium channel complex	identical protein binding|voltage-gated potassium channel activity				0																		---	---	---	---
CSNK1E	1454	broad.mit.edu	37	22	38776882	38776883	+	Intron	DEL	TG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38776882_38776883delTG	uc003avm.1	-						LOC400927_uc010gxm.2_Intron|LOC400927_uc011ans.1_Intron|LOC400927_uc011ant.1_Intron|LOC400927_uc003avr.1_Intron	NM_152221	NP_689407			casein kinase 1 epsilon						DNA repair|G2/M transition of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|signal transduction	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Melanoma(58;0.045)																	---	---	---	---
NHP2L1	4809	broad.mit.edu	37	22	42076082	42076082	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42076082delA	uc003bat.2	-						NHP2L1_uc003bau.2_Intron|NHP2L1_uc003bav.2_Intron|NHP2L1_uc003baw.2_Intron	NM_005008	NP_004999			NHP2 non-histone chromosome protein 2-like 1						nuclear mRNA splicing, via spliceosome|ribosome biogenesis	box C/D snoRNP complex|nucleoplasm|spliceosomal complex	protein binding|RNA binding				0																		---	---	---	---
SMC1B	27127	broad.mit.edu	37	22	45754476	45754477	+	Intron	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45754476_45754477insA	uc003bgc.2	-						SMC1B_uc003bgd.2_Intron	NM_148674	NP_683515			SMC1 structural maintenance of chromosomes						chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
TTC38	55020	broad.mit.edu	37	22	46674364	46674364	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46674364delA	uc003bhi.2	+						TTC38_uc011aqx.1_Intron	NM_017931	NP_060401			tetratricopeptide repeat domain 38								binding			ovary(1)	1																		---	---	---	---
GTSE1	51512	broad.mit.edu	37	22	46722679	46722679	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46722679delT	uc011aqy.1	+						GTSE1_uc011aqz.1_Intron|GTSE1_uc003bhl.1_3'UTR|GTSE1_uc003bhm.1_Intron|GTSE1_uc003bhn.2_5'Flank	NM_016426	NP_057510			G-2 and S-phase expressed 1						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process	cytoplasmic microtubule				ovary(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)														---	---	---	---
TRABD	80305	broad.mit.edu	37	22	50636990	50636990	+	3'UTR	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50636990delC	uc003bjq.1	+	10					TRABD_uc003bjr.1_3'UTR|TRABD_uc003bjs.1_3'UTR|TRABD_uc003bjt.1_3'UTR|TRABD_uc003bju.1_3'UTR|TRABD_uc003bjv.2_Intron|TRABD_uc003bjw.1_3'UTR|SELO_uc011arr.1_5'Flank	NM_025204	NP_079480			TraB domain containing												0		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)														---	---	---	---
ACR	49	broad.mit.edu	37	22	51183154	51183154	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51183154delG	uc003bnh.3	+	5	797	c.785delG	c.(784-786)TGGfs	p.W262fs		NM_001097	NP_001088	P10323	ACRO_HUMAN	acrosin precursor	262	Peptidase S1.				acrosome matrix dispersal|activation of adenylate cyclase activity	acrosomal matrix|protein complex	amidase activity|copper ion binding|DNA binding|drug binding|fucose binding|mannose binding|protein binding|serine-type endopeptidase activity|zinc ion binding				0		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
SHOX	6473	broad.mit.edu	37	X	601953	601953	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:601953delA	uc004cph.1	+						SHOX_uc004cpi.2_Intron	NM_000451	NP_000442			short stature homeobox isoform SHOXa						skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		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)																---	---	---	---
IL3RA	3563	broad.mit.edu	37	X	1467568	1467569	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1467568_1467569delTT	uc004cps.2	+						IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174			interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		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)			Sargramostim(DB00020)													---	---	---	---
ASMT	438	broad.mit.edu	37	X	1741892	1741892	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1741892delA	uc004cqd.2	+						ASMT_uc010ncy.2_Intron|ASMT_uc004cqe.2_Intron	NM_004043	NP_004034			acetylserotonin O-methyltransferase						melatonin biosynthetic process|translation	cytosol	acetylserotonin O-methyltransferase activity|S-methyltransferase activity			skin(1)	1		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
EGFL6	25975	broad.mit.edu	37	X	13645058	13645058	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13645058delT	uc004cvi.2	+						EGFL6_uc004cvj.2_Intron	NM_015507	NP_056322			epidermal growth factor-like protein 6						cell adhesion|cell cycle|cell differentiation|multicellular organismal development	basement membrane|extracellular space|membrane	calcium ion binding|integrin binding			breast(2)	2																		---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18664273	18664273	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18664273delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron|RS1_uc004cyo.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19663793	19663793	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19663793delA	uc004czm.2	-						SH3KBP1_uc011mje.1_Intron|SH3KBP1_uc011mjf.1_Intron|SH3KBP1_uc004czl.2_Intron	NM_031892	NP_114098			SH3-domain kinase binding protein 1 isoform a						apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0																		---	---	---	---
CXorf23	256643	broad.mit.edu	37	X	19983022	19983022	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19983022delT	uc004czp.2	-						CXorf23_uc010nfn.2_Intron|CXorf23_uc011mjg.1_Intron|CXorf23_uc004czo.2_Intron	NM_198279	NP_938020			hypothetical protein LOC256643							mitochondrion				lung(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	21844464	21844466	+	IGR	DEL	AAA	-	-	rs76688696		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21844464_21844466delAAA								SMPX (68234 upstream) : MBTPS2 (13190 downstream)																																			---	---	---	---
SMS	6611	broad.mit.edu	37	X	21995929	21995929	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21995929delA	uc004dag.2	+						SMS_uc011mjq.1_Intron|SMS_uc004daf.1_Intron|SMS_uc010nfs.2_5'Flank|SMS_uc010nft.2_5'Flank	NM_004595	NP_004586			spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)													---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22151761	22151761	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22151761delA	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435			phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	24383621	24383621	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24383621delT								FAM48B1 (81 upstream) : PDK3 (99723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35077922	35077922	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35077922delT								FAM47B (114888 upstream) : MAGEB16 (738537 downstream)																																			---	---	---	---
CXorf22	170063	broad.mit.edu	37	X	35969183	35969183	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35969183delA	uc004ddj.2	+						CXorf22_uc010ngv.2_Intron	NM_152632	NP_689845			hypothetical protein LOC170063											large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
CXorf22	170063	broad.mit.edu	37	X	35993612	35993612	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35993612delT	uc004ddj.2	+						CXorf22_uc010ngv.2_Intron	NM_152632	NP_689845			hypothetical protein LOC170063											large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
CXorf30	645090	broad.mit.edu	37	X	36392862	36392862	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36392862delT	uc011mkc.1	+							NM_001098843	NP_001092313			hypothetical protein LOC645090											lung(2)|breast(1)	3																		---	---	---	---
USP9X	8239	broad.mit.edu	37	X	41069679	41069679	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41069679delT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679			ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
MAOA	4128	broad.mit.edu	37	X	43587703	43587703	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43587703delA	uc004dfy.2	+						MAOA_uc011mkw.1_Intron	NM_000240	NP_000231			monoamine oxidase A						behavior|neurotransmitter biosynthetic process|neurotransmitter catabolic process|neurotransmitter secretion|xenobiotic metabolic process	integral to membrane|mitochondrial outer membrane	primary amine oxidase activity|protein binding			breast(2)|ovary(1)	3					Almotriptan(DB00918)|Carbidopa(DB00190)|Clonazepam(DB01068)|Dopamine(DB00988)|Fluvoxamine(DB00176)|Ginkgo biloba(DB01381)|Imipramine(DB00458)|Isocarboxazid(DB01247)|Levodopa(DB01235)|Linezolid(DB00601)|Lorazepam(DB00186)|Moclobemide(DB01171)|Nicotine(DB00184)|Norepinephrine(DB00368)|Phenelzine(DB00780)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pseudoephedrine(DB00852)|Rasagiline(DB01367)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	53834858	53834859	+	IGR	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53834858_53834859insA								HUWE1 (121185 upstream) : PHF8 (128255 downstream)																																			---	---	---	---
HEPH	9843	broad.mit.edu	37	X	65426913	65426913	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65426913delC	uc011moz.1	+						HEPH_uc004dwn.2_Intron|HEPH_uc004dwo.2_Intron|HEPH_uc010nkr.2_Intron|HEPH_uc011mpa.1_Intron|HEPH_uc010nks.2_Intron	NM_138737	NP_620074			hephaestin isoform a						cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9																		---	---	---	---
GDPD2	54857	broad.mit.edu	37	X	69645042	69645043	+	Intron	DEL	CT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69645042_69645043delCT	uc004dyh.2	+						GDPD2_uc010nkx.1_Intron|GDPD2_uc010nky.1_Intron|GDPD2_uc011mpk.1_Intron|GDPD2_uc011mpl.1_Intron|GDPD2_uc011mpm.1_Intron	NM_017711	NP_060181			osteoblast differentiation promoting factor						glycerol metabolic process|lipid metabolic process	cytoplasm|cytoskeleton|integral to membrane|plasma membrane	glycerophosphodiester phosphodiesterase activity|glycerophosphoinositol inositolphosphodiesterase activity|metal ion binding			ovary(2)	2	Renal(35;0.156)																	---	---	---	---
ITGB1BP2	26548	broad.mit.edu	37	X	70521865	70521866	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70521865_70521866delTT	uc004dzr.1	+						BCYRN1_uc011mpt.1_Intron|ITGB1BP2_uc004dzs.1_5'UTR	NM_012278	NP_036410			integrin beta 1 binding protein 2						muscle organ development|signal transduction		SH3 domain binding			ovary(1)	1	Renal(35;0.156)																	---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70639873	70639874	+	Intron	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70639873_70639874delTT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nld.1_Intron|TAF1_uc010nle.1_Intron|TAF1_uc010nlf.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
HDAC8	55869	broad.mit.edu	37	X	71656476	71656477	+	Intron	INS	-	AGGA	AGGA			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71656476_71656477insAGGA	uc004eau.2	-						HDAC8_uc011mqe.1_Intron|HDAC8_uc011mqf.1_Intron|HDAC8_uc011mqg.1_Intron	NM_018486	NP_060956			histone deacetylase 8						chromatin assembly or disassembly|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nuclear chromosome	histone deacetylase activity (H3-K16 specific)|metal ion binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription factor binding				0	Renal(35;0.156)				Vorinostat(DB02546)													---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74604701	74604701	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74604701delA	uc004ecg.2	-						ZDHHC15_uc004ech.2_Intron|ZDHHC15_uc011mqo.1_Intron	NM_144969	NP_659406			zinc finger, DHHC-type containing 15 isoform 1							integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74651360	74651360	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74651360delA	uc004ecg.2	-						ZDHHC15_uc004ech.2_Intron|ZDHHC15_uc011mqo.1_Intron	NM_144969	NP_659406			zinc finger, DHHC-type containing 15 isoform 1							integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
ATP7A	538	broad.mit.edu	37	X	77299140	77299140	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77299140delT	uc004ecx.3	+							NM_000052	NP_000043			ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	83996004	83996004	+	IGR	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83996004delT								HDX (238546 upstream) : UBE2DNL (193153 downstream)																																			---	---	---	---
CENPI	2491	broad.mit.edu	37	X	100401470	100401470	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100401470delA	uc004egx.2	+						CENPI_uc011mrg.1_Intron	NM_006733	NP_006724			centromere protein I						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1																		---	---	---	---
RNF128	79589	broad.mit.edu	37	X	105970804	105970804	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105970804delA	uc004eml.2	+						RNF128_uc004emk.2_Intron	NM_194463	NP_919445			ring finger protein 128 isoform 1							endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
COL4A5	1287	broad.mit.edu	37	X	107840210	107840211	+	Intron	DEL	TG	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107840210_107840211delTG	uc004enz.1	+						COL4A5_uc011mso.1_Intron|COL4A5_uc004eob.1_Intron	NM_033380	NP_203699			type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110416183	110416184	+	Intron	DEL	TC	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110416183_110416184delTC	uc004epa.2	+						PAK3_uc010npt.1_Intron|PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron|PAK3_uc004eoz.2_Intron|PAK3_uc011mst.1_Intron|PAK3_uc010npv.1_Intron|PAK3_uc010npw.1_Intron	NM_001128173	NP_001121645			p21-activated kinase 3 isoform d						multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10															TSP Lung(19;0.15)			---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114856519	114856519	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114856519delT	uc004eqd.2	+						PLS3_uc010nqf.2_Intron|PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114877477	114877477	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114877477delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron|PLS3_uc011mti.1_Intron|PLS3_uc011mtj.1_Intron|PLS3_uc011mtk.1_5'Flank|PLS3_uc011mtl.1_5'Flank	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117679509	117679509	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117679509delT	uc004eqp.2	+							NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
CXorf56	63932	broad.mit.edu	37	X	118694020	118694020	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118694020delA	uc004erk.1	-						CXorf56_uc004erj.1_Intron|CXorf56_uc011mtu.1_Intron	NM_022101	NP_071384			hypothetical protein LOC63932								protein binding				0																		---	---	---	---
LAMP2	3920	broad.mit.edu	37	X	119575940	119575940	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119575940delA	uc004est.3	-						LAMP2_uc004ess.3_Intron|LAMP2_uc011mtz.1_Intron|LAMP2_uc011mua.1_Intron|LAMP2_uc010nqp.1_Intron	NM_002294	NP_002285			lysosomal-associated membrane protein 2 isoform						platelet activation|platelet degranulation	endosome membrane|integral to membrane|late endosome|lysosomal membrane|membrane fraction|plasma membrane|platelet dense granule membrane				ovary(1)	1																		---	---	---	---
PHF6	84295	broad.mit.edu	37	X	133512257	133512257	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133512257delT	uc004exj.2	+						PHF6_uc004exk.2_Intron|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Intron|PHF6_uc010nrr.2_Intron|PHF6_uc004exi.2_Intron	NM_001015877	NP_001015877			PHD finger protein 6 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
PHF6	84295	broad.mit.edu	37	X	133527689	133527689	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133527689delT	uc004exj.2	+						PHF6_uc004exk.2_Intron|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Intron|PHF6_uc010nrr.2_Intron|PHF6_uc004exi.2_Intron	NM_001015877	NP_001015877			PHD finger protein 6 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
FAM122C	159091	broad.mit.edu	37	X	133979590	133979590	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133979590delT	uc004exz.1	+						FAM122C_uc011mvq.1_Intron|FAM122C_uc004exy.1_Intron	NM_138819	NP_620174			hypothetical protein LOC159091												0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
SLC9A6	10479	broad.mit.edu	37	X	135095352	135095352	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135095352delA	uc004ezj.2	+						SLC9A6_uc004ezk.2_Intron	NM_006359	NP_006350			solute carrier family 9 (sodium/hydrogen						regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	135181860	135181861	+	IGR	INS	-	TC	TC	rs142657727		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135181860_135181861insTC								SLC9A6 (52434 upstream) : FHL1 (47000 downstream)																																			---	---	---	---
HTATSF1	27336	broad.mit.edu	37	X	135593401	135593402	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135593401_135593402insA	uc004ezw.2	+	10	1919_1920	c.1497_1498insA	c.(1495-1500)CCTAAAfs	p.P499fs	HTATSF1_uc004ezx.2_Frame_Shift_Ins_p.P499fs	NM_001163280	NP_001156752	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	499_500	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|viral genome replication	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MCF2	4168	broad.mit.edu	37	X	138670607	138670607	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138670607delA	uc004fau.2	-						MCF2_uc004fav.2_Intron|MCF2_uc011mwl.1_Intron|MCF2_uc010nsh.1_Intron|MCF2_uc011mwm.1_Intron|MCF2_uc011mwn.1_Intron|MCF2_uc004faw.2_Intron|MCF2_uc011mwo.1_Intron	NM_005369	NP_005360			MCF.2 cell line derived transforming sequence						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	139114824	139114824	+	IGR	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139114824delA								CXorf66 (67147 upstream) : SOX3 (470328 downstream)																																			---	---	---	---
SPANXC	64663	broad.mit.edu	37	X	140355351	140355351	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140355351delA	uc004fbl.2	-											Homo sapiens nuclear-associated protein SPAN-Xa (SPANX) mRNA, complete cds.							cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)																	---	---	---	---
MAGEC1	9947	broad.mit.edu	37	X	140991551	140991552	+	5'Flank	INS	-	C	C	rs140228818		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140991551_140991552insC	uc004fbt.2	+						MAGEC1_uc010nsl.1_5'Flank	NM_005462	NP_005453			melanoma antigen family C, 1								protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)														HNSCC(15;0.026)			---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147011446	147011446	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147011446delT	uc010nst.2	+						FMR1_uc011mwz.1_Intron|FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_Intron|FMR1_uc011mxa.1_5'Flank	NM_002024	NP_002015			fragile X mental retardation 1						mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													Fragile_X_syndrome				---	---	---	---
MTMR1	8776	broad.mit.edu	37	X	149898488	149898488	+	Intron	DEL	A	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149898488delA	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feg.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819			myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	150162649	150162651	+	IGR	DEL	AAA	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150162649_150162651delAAA								HMGB3 (3403 upstream) : GPR50 (182408 downstream)																																			---	---	---	---
PLXNB3	5365	broad.mit.edu	37	X	153039867	153039867	+	Intron	DEL	C	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153039867delC	uc004fii.2	+						PLXNB3_uc010nuk.2_Intron|PLXNB3_uc011mzd.1_Intron|PLXNB3_uc004fij.1_5'Flank|SRPK3_uc004fik.2_5'Flank	NM_005393	NP_005384			plexin B3 isoform 1						axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PLXNB3	5365	broad.mit.edu	37	X	153042691	153042691	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153042691delG	uc004fii.2	+	30	5130	c.4956delG	c.(4954-4956)GAGfs	p.E1652fs	PLXNB3_uc010nuk.2_Frame_Shift_Del_p.E1675fs|PLXNB3_uc011mzd.1_Frame_Shift_Del_p.E1291fs|SRPK3_uc004fik.2_5'UTR	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3 isoform 1	1652	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	153680002	153680003	+	IGR	DEL	TT	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153680002_153680003delTT								FAM50A (1001 upstream) : PLXNA3 (6620 downstream)																																			---	---	---	---
PLXNA3	55558	broad.mit.edu	37	X	153691584	153691584	+	Intron	DEL	T	-	-			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153691584delT	uc004flm.2	+							NM_017514	NP_059984			plexin A3 precursor						axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
NOC2L	26155	broad.mit.edu	37	1	889451	889451	+	Missense_Mutation	SNP	G	A	A	rs150111944	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:889451G>A	uc001abz.3	-	7	769	c.710C>T	c.(709-711)CCG>CTG	p.P237L	NOC2L_uc001aby.3_Missense_Mutation_p.P34L|NOC2L_uc009vjq.2_Missense_Mutation_p.P237L	NM_015658	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog	237						nucleolus	protein binding			ovary(1)|skin(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)														---	---	---	---
CPSF3L	54973	broad.mit.edu	37	1	1250901	1250901	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1250901G>A	uc001aee.1	-	5	585	c.527C>T	c.(526-528)ACG>ATG	p.T176M	CPSF3L_uc009vjy.1_RNA|CPSF3L_uc001aef.1_Missense_Mutation_p.T182M|CPSF3L_uc009vjz.1_Missense_Mutation_p.T154M|CPSF3L_uc010nyj.1_Missense_Mutation_p.T147M|CPSF3L_uc001aeg.1_Missense_Mutation_p.T52M|CPSF3L_uc001aeh.1_Missense_Mutation_p.T75M|CPSF3L_uc001aei.1_Missense_Mutation_p.T78M|CPSF3L_uc001aej.1_Intron|CPSF3L_uc001aek.1_Translation_Start_Site	NM_017871	NP_060341	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor	176						Golgi apparatus|nucleus	hydrolase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)														---	---	---	---
TAS1R3	83756	broad.mit.edu	37	1	1269811	1269811	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1269811C>T	uc010nyk.1	+	6	2526	c.2526C>T	c.(2524-2526)GAC>GAT	p.D842D		NM_152228	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3 precursor	842	Cytoplasmic (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste|sensory perception of umami taste	plasma membrane	protein heterodimerization activity|taste receptor activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)	Aspartame(DB00168)													---	---	---	---
PLCH2	9651	broad.mit.edu	37	1	2411332	2411332	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2411332G>A	uc001aji.1	+	3	705	c.431G>A	c.(430-432)CGC>CAC	p.R144H	PLCH2_uc010nyz.1_5'Flank|PLCH2_uc009vle.1_5'Flank|PLCH2_uc001ajj.1_5'Flank|PLCH2_uc001ajk.1_5'Flank	NM_014638	NP_055453	O75038	PLCH2_HUMAN	phospholipase C, eta 2	144	PH.|Necessary for plasma membrane localization (By similarity).				intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)														---	---	---	---
MMEL1	79258	broad.mit.edu	37	1	2535312	2535312	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2535312T>C	uc001ajy.2	-						MMEL1_uc009vlg.1_Intron	NM_033467	NP_258428			membrane metallo-endopeptidase-like 1						proteolysis	extracellular region|integral to membrane|intracellular membrane-bounded organelle	metal ion binding|metalloendopeptidase activity				0	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)														---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3347517	3347517	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3347517C>T	uc001akf.2	+	15	3446	c.3366C>T	c.(3364-3366)GAC>GAT	p.D1122D	PRDM16_uc001akc.2_Silent_p.D1121D|PRDM16_uc001akd.2_Silent_p.D1121D|PRDM16_uc001ake.2_Silent_p.D1122D|PRDM16_uc009vlh.2_Silent_p.D822D	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	1122	Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6215763	6215763	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6215763C>T	uc001amb.1	-	4	502	c.402G>A	c.(400-402)TCG>TCA	p.S134S		NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	134					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)														---	---	---	---
PLEKHG5	57449	broad.mit.edu	37	1	6529516	6529516	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6529516T>C	uc001ano.1	-						PLEKHG5_uc001ann.1_Intron|PLEKHG5_uc001anq.1_Intron|PLEKHG5_uc001anp.1_Intron|PLEKHG5_uc001anj.1_Intron|PLEKHG5_uc009vma.1_Intron|PLEKHG5_uc010nzr.1_Intron|PLEKHG5_uc001ank.1_Intron|PLEKHG5_uc009vmb.1_Intron|PLEKHG5_uc001anl.1_Intron|PLEKHG5_uc001anm.1_Intron|PLEKHG5_uc001anr.1_5'Flank	NM_001042663	NP_001036128			pleckstrin homology domain containing family G						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
DNAJC11	55735	broad.mit.edu	37	1	6698426	6698426	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6698426T>C	uc001aof.2	-	12	1360	c.1254_splice	c.e12-1	p.K418_splice	DNAJC11_uc010nzt.1_Intron|DNAJC11_uc001aog.2_Splice_Site_p.K366_splice|DNAJC11_uc010nzu.1_Splice_Site_p.K328_splice	NM_018198	NP_060668			DnaJ (Hsp40) homolog, subfamily C, member 11						protein folding		heat shock protein binding|unfolded protein binding			ovary(1)|skin(1)	2	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7797375	7797375	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7797375C>T	uc001aoi.2	+	15	3610	c.3403C>T	c.(3403-3405)CGG>TGG	p.R1135W	CAMTA1_uc010nzv.1_Missense_Mutation_p.R222W|CAMTA1_uc001aok.3_Missense_Mutation_p.R178W|CAMTA1_uc001aoj.2_Missense_Mutation_p.R91W	NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	1135					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)														---	---	---	---
PIK3CD	5293	broad.mit.edu	37	1	9778917	9778917	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9778917G>A	uc001aqb.3	+	9	1394	c.1186G>A	c.(1186-1188)GCC>ACC	p.A396T	PIK3CD_uc010oaf.1_Missense_Mutation_p.A396T|PIK3CD_uc001aqe.3_Missense_Mutation_p.A361T	NM_005026	NP_005017	O00329	PK3CD_HUMAN	catalytic phosphatidylinositol 3-kinase delta	396					phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11300580	11300580	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11300580G>A	uc001asd.2	-	11	1687	c.1566C>T	c.(1564-1566)TAC>TAT	p.Y522Y		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	522					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
FBXO44	93611	broad.mit.edu	37	1	11718932	11718932	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11718932C>T	uc001asm.2	+						FBXO44_uc001ask.2_Intron|FBXO44_uc001asl.2_Intron|FBXO44_uc001asn.2_Intron|FBXO44_uc010oar.1_Intron|FBXO44_uc010oas.1_Intron	NM_033182	NP_149438			F-box protein 44 isoform 1						protein catabolic process	SCF ubiquitin ligase complex	protein binding			ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
NPPA	4878	broad.mit.edu	37	1	11906083	11906083	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11906083A>G	uc001ati.2	-						CLCN6_uc010oav.1_Intron|CLCN6_uc010oaw.1_Intron|CLCN6_uc010oax.1_Intron|CLCN6_uc010oay.1_Intron|CLCN6_uc010oaz.1_Intron|CLCN6_uc010oba.1_Intron	NM_006172	NP_006163			natriuretic peptide precursor A preproprotein						cGMP biosynthetic process|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size	extracellular region	hormone activity			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
TNFRSF1B	7133	broad.mit.edu	37	1	12251952	12251952	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12251952C>T	uc001att.2	+	4	518	c.429C>T	c.(427-429)TGC>TGT	p.C143C	TNFRSF1B_uc001atu.2_5'UTR|TNFRSF1B_uc009vnk.2_RNA	NM_001066	NP_001057	P20333	TNR1B_HUMAN	tumor necrosis factor receptor 2 precursor	143	TNFR-Cys 3.|Extracellular (Potential).				apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity			liver(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)|Infliximab(DB00065)													---	---	---	---
TNFRSF1B	7133	broad.mit.edu	37	1	12262065	12262065	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12262065C>T	uc001att.2	+	9	1031	c.942C>T	c.(940-942)CCC>CCT	p.P314P	TNFRSF1B_uc001atu.2_Silent_p.P119P|TNFRSF1B_uc009vnk.2_RNA	NM_001066	NP_001057	P20333	TNR1B_HUMAN	tumor necrosis factor receptor 2 precursor	314	Cytoplasmic (Potential).				apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity			liver(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)|Infliximab(DB00065)													---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12416561	12416561	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12416561T>C	uc001atv.2	+	49	10119	c.9978T>C	c.(9976-9978)GCT>GCC	p.A3326A	VPS13D_uc001atw.2_Silent_p.A3301A|VPS13D_uc001atx.2_Silent_p.A2513A	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3325					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
LOC649330	649330	broad.mit.edu	37	1	12907413	12907413	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12907413C>A	uc009vno.2	-	1	825	c.730G>T	c.(730-732)GCA>TCA	p.A244S	HNRNPCL1_uc010obf.1_Missense_Mutation_p.A244S	NM_001146181	NP_001139653	B7ZW38	B7ZW38_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	244							nucleic acid binding|nucleotide binding				0																		---	---	---	---
LOC649330	649330	broad.mit.edu	37	1	12907705	12907705	+	Missense_Mutation	SNP	T	G	G	rs2359482	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12907705T>G	uc009vno.2	-	1	533	c.438A>C	c.(436-438)CAA>CAC	p.Q146H	HNRNPCL1_uc010obf.1_Missense_Mutation_p.Q146H	NM_001146181	NP_001139653	B7ZW38	B7ZW38_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	146							nucleic acid binding|nucleotide binding				0																		---	---	---	---
LOC649330	649330	broad.mit.edu	37	1	12907787	12907787	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12907787T>C	uc009vno.2	-	1	451	c.356A>G	c.(355-357)TAT>TGT	p.Y119C	HNRNPCL1_uc010obf.1_Missense_Mutation_p.Y119C	NM_001146181	NP_001139653	B7ZW38	B7ZW38_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	119							nucleic acid binding|nucleotide binding				0																		---	---	---	---
PRAMEF22	653606	broad.mit.edu	37	1	13036638	13036638	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13036638G>A	uc009vnq.1	+	2	710	c.710G>A	c.(709-711)CGC>CAC	p.R237H	PRAMEF5_uc001aur.2_Intron	NM_001100631	NP_001094101	A3QJZ6	PRA22_HUMAN	PRAME family member 22	237											0																		---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16256980	16256980	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16256980A>G	uc001axk.1	+	11	4449	c.4245A>G	c.(4243-4245)CTA>CTG	p.L1415L	SPEN_uc010obp.1_Silent_p.L1374L	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1415	Potential.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
CLCNKB	1188	broad.mit.edu	37	1	16380237	16380237	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16380237G>A	uc001axw.3	+	16	1806	c.1726G>A	c.(1726-1728)GTG>ATG	p.V576M	FAM131C_uc010obz.1_Intron|CLCNKB_uc001axx.3_Missense_Mutation_p.V576M|CLCNKB_uc001axy.3_Missense_Mutation_p.V407M	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb isoform 1	576	CBS 1.				excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			skin(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
C1orf89	79363	broad.mit.edu	37	1	16560163	16560163	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16560163G>A	uc001ayd.2	-	2	631	c.209C>T	c.(208-210)GCG>GTG	p.A70V		NM_030907	NP_112169	Q9BU20	RSG1_HUMAN	hypothetical protein LOC79363	70	Small GTPase-like.				cellular protein localization|cilium assembly|exocytosis|protein transport|regulation of exocytosis|regulation of vesicle fusion|small GTPase mediated signal transduction	cilium|microtubule basal body	GTP binding				0		Colorectal(325;0.000147)|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;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.2e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19443800	19443800	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19443800C>G	uc001bbi.2	-	73	10742	c.10738G>C	c.(10738-10740)GAT>CAT	p.D3580H	UBR4_uc001bbj.1_5'UTR	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3580					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19473420	19473420	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19473420C>A	uc001bbi.2	-	52	7708	c.7704G>T	c.(7702-7704)GAG>GAT	p.E2568D	UBR4_uc001bbk.1_Missense_Mutation_p.E222D	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	2568					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
AKR7A3	22977	broad.mit.edu	37	1	19610481	19610481	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19610481A>G	uc001bbv.1	-							NM_012067	NP_036199			aldo-keto reductase family 7, member A3						cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
AKR7A3	22977	broad.mit.edu	37	1	19610525	19610525	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19610525T>C	uc001bbv.1	-	6	876	c.799A>G	c.(799-801)ACC>GCC	p.T267A		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	267					cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
AKR7A3	22977	broad.mit.edu	37	1	19610544	19610544	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19610544G>A	uc001bbv.1	-	6	857	c.780C>T	c.(778-780)GCC>GCT	p.A260A		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	260					cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20097887	20097887	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20097887C>T	uc001bcn.2	-	5	510	c.268G>A	c.(268-270)GGC>AGC	p.G90S	TMCO4_uc001bcm.2_Missense_Mutation_p.G90S|TMCO4_uc001bco.1_Missense_Mutation_p.G90S|TMCO4_uc001bcp.1_Missense_Mutation_p.G90S|TMCO4_uc009vpn.1_Missense_Mutation_p.G90S|TMCO4_uc001bcq.1_Missense_Mutation_p.G90S	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	90						integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
PINK1	65018	broad.mit.edu	37	1	20971112	20971112	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20971112C>T	uc001bdm.2	+	4	1000	c.906C>T	c.(904-906)CGC>CGT	p.R302R		NM_032409	NP_115785	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1 precursor	302	Protein kinase.|Cytoplasmic (Potential).				cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress	cytosol|integral to membrane|mitochondrial outer membrane	ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding			ovary(2)|central_nervous_system(1)	3		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21031369	21031369	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21031369G>A	uc001bdr.3	-	5	812	c.694C>T	c.(694-696)CGG>TGG	p.R232W	KIF17_uc001bds.3_Missense_Mutation_p.R232W	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a	232	Kinesin-motor.				microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22191363	22191363	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22191363C>T	uc001bfj.2	-	36	4639	c.4599G>A	c.(4597-4599)CCG>CCA	p.P1533P	HSPG2_uc009vqd.2_Silent_p.P1534P	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	1533	Laminin EGF-like 9; second part.				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)													---	---	---	---
MYOM3	127294	broad.mit.edu	37	1	24389608	24389608	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24389608G>A	uc001bin.3	-						MYOM3_uc001bil.3_Intron|MYOM3_uc001bim.3_Intron	NM_152372	NP_689585			myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)														---	---	---	---
MYOM3	127294	broad.mit.edu	37	1	24398454	24398454	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24398454C>T	uc001bin.3	-						MYOM3_uc001bim.3_Intron|MYOM3_uc001bio.2_Intron	NM_152372	NP_689585			myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)														---	---	---	---
CNKSR1	10256	broad.mit.edu	37	1	26515141	26515141	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26515141C>T	uc001bln.3	+	19	1722	c.1664C>T	c.(1663-1665)GCC>GTC	p.A555V	CNKSR1_uc001blm.3_Missense_Mutation_p.A548V|CNKSR1_uc009vsd.2_Missense_Mutation_p.A290V|CNKSR1_uc009vse.2_Missense_Mutation_p.A290V|CNKSR1_uc001blo.2_Missense_Mutation_p.A290V|CATSPER4_uc010oey.1_5'Flank|CATSPER4_uc010oez.1_5'Flank|CATSPER4_uc009vsf.2_5'Flank	NM_006314	NP_006305	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras	555					Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging			lung(1)|kidney(1)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ZNF683	257101	broad.mit.edu	37	1	26691467	26691467	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26691467G>A	uc001bmg.1	-	4	688	c.570C>T	c.(568-570)CAC>CAT	p.H190H	ZNF683_uc001bmh.1_Silent_p.H190H|ZNF683_uc009vsj.1_Silent_p.H190H	NM_173574	NP_775845	Q8IZ20	ZN683_HUMAN	zinc finger protein 683	190					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)														---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27099053	27099053	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27099053G>T	uc001bmv.1	+	13	3842	c.3469G>T	c.(3469-3471)GGA>TGA	p.G1157*	ARID1A_uc001bmt.1_Nonsense_Mutation_p.G1157*|ARID1A_uc001bmu.1_Nonsense_Mutation_p.G1157*|ARID1A_uc001bmw.1_Nonsense_Mutation_p.G774*|ARID1A_uc001bmx.1_Nonsense_Mutation_p.G4*|ARID1A_uc009vsm.1_5'Flank|ARID1A_uc009vsn.1_5'Flank	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1157					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)				Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27105617	27105617	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27105617C>T	uc001bmv.1	+	20	5601	c.5228C>T	c.(5227-5229)ACG>ATG	p.T1743M	ARID1A_uc001bmu.1_Missense_Mutation_p.T1526M|ARID1A_uc001bmx.1_Missense_Mutation_p.T589M|ARID1A_uc009vsm.1_Missense_Mutation_p.T71M|ARID1A_uc009vsn.1_Translation_Start_Site	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1743					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)				Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								---	---	---	---
TMEM222	84065	broad.mit.edu	37	1	27660540	27660540	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27660540C>T	uc001bnr.3	+	4	456	c.403C>T	c.(403-405)CGC>TGC	p.R135C	TMEM222_uc001bns.3_RNA|TMEM222_uc001bnt.3_RNA|TMEM222_uc001bnu.3_RNA	NM_032125	NP_115501	Q9H0R3	TM222_HUMAN	transmembrane protein 222	135	Cytoplasmic (Potential).					integral to membrane	protein binding				0																		---	---	---	---
PPP1R8	5511	broad.mit.edu	37	1	28176655	28176655	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28176655A>G	uc001bov.1	+	7	808	c.754A>G	c.(754-756)AGG>GGG	p.R252G	PPP1R8_uc001bow.1_Missense_Mutation_p.R110G|PPP1R8_uc001box.1_Missense_Mutation_p.R28G|PPP1R8_uc009vtc.1_RNA|PPP1R8_uc009vtd.1_RNA	NM_014110	NP_054829	Q12972	PP1R8_HUMAN	protein phosphatase 1 regulatory inhibitor	252					mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|RNA splicing|transcription, DNA-dependent	cytoplasm|nuclear speck|spliceosomal complex	DNA binding|endonuclease activity|protein binding|protein serine/threonine phosphatase inhibitor activity|ribonuclease E activity|RNA binding				0		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.76e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00248)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29359759	29359759	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29359759T>C	uc001brm.1	+	8	1372	c.1365_splice	c.e8+2	p.E455_splice	EPB41_uc001brg.1_Splice_Site_p.E246_splice|EPB41_uc001brh.1_Splice_Site_p.E246_splice|EPB41_uc001bri.1_Splice_Site_p.E420_splice|EPB41_uc001brj.1_Splice_Site_p.E246_splice|EPB41_uc009vtk.1_Splice_Site_p.E420_splice|EPB41_uc001brk.2_Splice_Site_p.E455_splice|EPB41_uc001brl.1_Splice_Site_p.E455_splice|EPB41_uc009vtl.1_Splice_Site_p.E246_splice|EPB41_uc009vtm.1_Splice_Site_p.E88_splice	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
SFRS4	6429	broad.mit.edu	37	1	29485950	29485950	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29485950G>C	uc001bro.2	-	3	672	c.299C>G	c.(298-300)ACT>AGT	p.T100S	SFRS4_uc010ofy.1_Missense_Mutation_p.T100S|SFRS4_uc009vtp.2_RNA	NM_005626	NP_005617	Q08170	SRSF4_HUMAN	splicing factor, arginine/serine-rich 4	100					mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|RNA binding				0		Colorectal(325;0.00161)|Breast(348;0.0364)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0529)|Lung NSC(340;0.0654)|all_lung(284;0.074)|Ovarian(437;0.104)|Medulloblastoma(700;0.151)		Colorectal(126;1.01e-07)|COAD - Colon adenocarcinoma(152;6.21e-06)|STAD - Stomach adenocarcinoma(196;0.0196)|BRCA - Breast invasive adenocarcinoma(304;0.0531)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.138)														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31413995	31413995	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31413995T>C	uc001bsi.1	-						PUM1_uc001bsf.1_Intron|PUM1_uc001bsg.1_Intron|PUM1_uc001bsh.1_Intron|PUM1_uc001bsj.1_Intron|PUM1_uc010oga.1_Intron|PUM1_uc001bsk.1_Intron|PUM1_uc010ogb.1_Intron|SNORD103A_uc009vts.1_Intron	NM_014676	NP_055491			pumilio 1 isoform 2						cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32157657	32157657	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32157657G>A	uc001btk.1	-	17	1571	c.1206C>T	c.(1204-1206)GGC>GGT	p.G402G	COL16A1_uc001btj.1_Silent_p.G231G|COL16A1_uc001btl.3_Silent_p.G402G	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	402	Triple-helical region 9 (COL9) with 3 imperfections.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
SPOCD1	90853	broad.mit.edu	37	1	32263883	32263883	+	Silent	SNP	G	A	A	rs144387561	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32263883G>A	uc001bts.1	-	9	2128	c.2070C>T	c.(2068-2070)TAC>TAT	p.Y690Y	SPOCD1_uc001btt.2_Translation_Start_Site|SPOCD1_uc001btu.2_Silent_p.Y690Y|SPOCD1_uc001btv.2_Silent_p.Y183Y|SPOCD1_uc001btw.1_Silent_p.Y34Y	NM_144569	NP_653170	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	690	TFIIS central.				transcription, DNA-dependent					ovary(5)|breast(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)														---	---	---	---
MARCKSL1	65108	broad.mit.edu	37	1	32801580	32801580	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32801580C>T	uc001bvd.2	-	1	255	c.55G>A	c.(55-57)GCA>ACA	p.A19T		NM_023009	NP_075385	P49006	MRP_HUMAN	MARCKS-like 1	19						plasma membrane	calmodulin binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
C1orf94	84970	broad.mit.edu	37	1	34663085	34663085	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34663085A>G	uc001bxs.3	+	2	409	c.10A>G	c.(10-12)ATC>GTC	p.I4V	C1orf94_uc001bxt.2_Missense_Mutation_p.I194V	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b	4							protein binding				0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
C1orf212	113444	broad.mit.edu	37	1	35321092	35321092	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35321092C>T	uc001byb.2	-	2	607	c.190G>A	c.(190-192)GTT>ATT	p.V64I		NM_138428	NP_612437			hypothetical protein LOC113444												0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
DLGAP3	58512	broad.mit.edu	37	1	35334196	35334196	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35334196C>T	uc001byc.2	-							NM_001080418	NP_001073887			discs, large (Drosophila) homolog-associated						cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)																---	---	---	---
NCDN	23154	broad.mit.edu	37	1	36031043	36031043	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36031043G>A	uc001bza.2	+	8	2096	c.1969G>A	c.(1969-1971)GCT>ACT	p.A657T	NCDN_uc001bzb.2_Missense_Mutation_p.A657T|NCDN_uc001bzc.2_Missense_Mutation_p.A640T	NM_001014839	NP_001014839	Q9UBB6	NCDN_HUMAN	neurochondrin isoform 1	657					neuron projection development	cytosol|dendrite|neuronal cell body				large_intestine(2)|pancreas(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
THRAP3	9967	broad.mit.edu	37	1	36748267	36748267	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36748267C>T	uc001cae.3	+	3	327	c.103C>T	c.(103-105)CGA>TGA	p.R35*	THRAP3_uc001caf.3_Nonsense_Mutation_p.R35*|THRAP3_uc001cag.1_Nonsense_Mutation_p.R35*	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	35	Arg-rich.|Ser-rich.				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(5)|lung(3)|breast(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)						T	USP6	aneurysmal bone cysts								---	---	---	---
THRAP3	9967	broad.mit.edu	37	1	36769580	36769580	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36769580C>T	uc001cae.3	+	12	3054	c.2830C>T	c.(2830-2832)CGA>TGA	p.R944*	THRAP3_uc001caf.3_Nonsense_Mutation_p.R944*|C1orf113_uc010oia.1_5'Flank	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	944					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(5)|lung(3)|breast(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)						T	USP6	aneurysmal bone cysts								---	---	---	---
EPHA10	284656	broad.mit.edu	37	1	38227422	38227422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38227422G>A	uc009vvi.2	-	3	591	c.505C>T	c.(505-507)CGC>TGC	p.R169C	EPHA10_uc001cbw.3_Missense_Mutation_p.R169C	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	169	Extracellular (Potential).					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
MTF1	4520	broad.mit.edu	37	1	38304325	38304325	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38304325G>A	uc001cce.1	-	4	892	c.751C>T	c.(751-753)CGA>TGA	p.R251*	MTF1_uc009vvj.1_5'UTR	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	251	C2H2-type 4.					nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
UTP11L	51118	broad.mit.edu	37	1	38478539	38478539	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38478539T>C	uc001ccn.3	+	1	154	c.63_splice	c.e1+2	p.Q21_splice	UTP11L_uc009vvm.2_Splice_Site|UTP11L_uc010oil.1_Splice_Site	NM_016037	NP_057121			UTP11-like, U3 small nucleolar						induction of apoptosis|nerve growth factor receptor signaling pathway|nervous system development|rRNA processing	cytoplasm|extracellular space|nucleolus|small-subunit processome	protein binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
ZMPSTE24	10269	broad.mit.edu	37	1	40737716	40737716	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40737716A>G	uc001cfg.2	+							NM_005857	NP_005848			zinc metallopeptidase STE24							endoplasmic reticulum membrane|Golgi membrane|integral to membrane	metal ion binding|metalloexopeptidase activity				0	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)															---	---	---	---
ZNF684	127396	broad.mit.edu	37	1	41007384	41007384	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41007384T>C	uc001cft.1	+	4	489	c.238_splice	c.e4+2	p.E80_splice		NM_152373	NP_689586			zinc finger protein 684						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)															---	---	---	---
ZNF691	51058	broad.mit.edu	37	1	43317175	43317175	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43317175G>A	uc001cih.2	+	2	678	c.627G>A	c.(625-627)ACG>ACA	p.T209T	ZNF691_uc001cig.2_Silent_p.T182T|ZNF691_uc009vwm.2_Silent_p.T202T	NM_015911	NP_056995	Q5VV52	ZN691_HUMAN	zinc finger protein 691	213	C2H2-type 4.					nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
TMEM125	128218	broad.mit.edu	37	1	43738845	43738845	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43738845G>A	uc001cir.2	+	4	1022	c.452G>A	c.(451-453)GGC>GAC	p.G151D	EBNA1BP2_uc001cio.2_5'Flank|TMEM125_uc001cis.2_Missense_Mutation_p.G151D	NM_144626	NP_653227	Q96AQ2	TM125_HUMAN	transmembrane protein 125	151	Helical; (Potential).					integral to membrane				breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
DPH2	1802	broad.mit.edu	37	1	44438134	44438134	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44438134G>T	uc001ckz.2	+	6	1588	c.1393G>T	c.(1393-1395)GGT>TGT	p.G465C	DPH2_uc001cla.2_Missense_Mutation_p.G237C|DPH2_uc010okk.1_Missense_Mutation_p.G330C|DPH2_uc001clb.2_Missense_Mutation_p.G389C|ATP6V0B_uc001clc.2_5'Flank|ATP6V0B_uc001cld.2_5'Flank|ATP6V0B_uc001cle.2_5'Flank|ATP6V0B_uc001clf.2_5'Flank	NM_001384	NP_001375	Q9BQC3	DPH2_HUMAN	diphthamide biosynthesis protein 2 isoform a	465					peptidyl-diphthamide biosynthetic process from peptidyl-histidine	cytoplasm				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)																---	---	---	---
TMEM53	79639	broad.mit.edu	37	1	45120336	45120336	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45120336A>G	uc001cmc.2	-	3	765	c.729T>C	c.(727-729)CGT>CGC	p.R243R	TMEM53_uc001cmb.1_Intron|TMEM53_uc001cmd.2_Silent_p.R170R|TMEM53_uc009vxh.1_Silent_p.R126R|TMEM53_uc010ola.1_Silent_p.R126R	NM_024587	NP_078863	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	243						integral to membrane				ovary(2)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TCTEX1D4	343521	broad.mit.edu	37	1	45271717	45271717	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45271717C>T	uc001cmp.2	-	2	1133	c.624G>A	c.(622-624)TCG>TCA	p.S208S	BTBD19_uc010old.1_5'Flank|BTBD19_uc010ole.1_5'Flank	NM_001013632	NP_001013654	Q5JR98	TC1D4_HUMAN	Tctex1 domain containing 4	208										pancreas(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MKNK1	8569	broad.mit.edu	37	1	47040609	47040609	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47040609C>T	uc001cqb.2	-						MKNK1_uc010omd.1_Intron|MKNK1_uc001cqc.2_Intron|MKNK1_uc009vyi.2_Intron|MKNK1_uc010ome.1_Intron|MKNK1_uc009vyj.2_Intron|MKNK1_uc001cqd.2_Intron|MKNK1_uc010omf.1_Missense_Mutation_p.R133H	NM_003684	NP_003675			MAP kinase-interacting serine/threonine kinase 1						intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
KIAA0494	9813	broad.mit.edu	37	1	47144226	47144226	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47144226A>G	uc001cqk.3	-	11	2372	c.1395T>C	c.(1393-1395)TCT>TCC	p.S465S	KIAA0494_uc010omh.1_Intron|KIAA0494_uc010omj.1_Silent_p.S257S	NM_014774	NP_055589	O75071	K0494_HUMAN	hypothetical protein LOC9813	465	EF-hand 2.						calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TXNDC12	51060	broad.mit.edu	37	1	52492989	52492989	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52492989T>A	uc001cti.2	-	4	522	c.243A>T	c.(241-243)GAA>GAT	p.E81D		NM_015913	NP_056997	O95831	AIFM1_HUMAN	thioredoxin domain containing 12 precursor	329	FAD-dependent oxidoreductase (By similarity).				activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(1)	1																		---	---	---	---
ORC1L	4998	broad.mit.edu	37	1	52840492	52840492	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52840492G>A	uc001ctt.2	-	16	2600	c.2381C>T	c.(2380-2382)ACG>ATG	p.T794M	ORC1L_uc010oni.1_Missense_Mutation_p.T789M|ORC1L_uc001ctu.2_Missense_Mutation_p.T794M|ORC1L_uc009vzd.2_Missense_Mutation_p.T548M	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	794	Necessary and sufficient for ORC complex assembly.				cell cycle checkpoint|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
FAM159A	348378	broad.mit.edu	37	1	53108573	53108573	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53108573T>C	uc001cuf.2	+	2	321	c.221T>C	c.(220-222)GTT>GCT	p.V74A	FAM159A_uc001cug.1_RNA|FAM159A_uc001cuh.2_RNA	NM_001042693	NP_001036158	Q6UWV7	F159A_HUMAN	hypothetical protein LOC348378	74	Helical; (Potential).					integral to membrane					0																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62516732	62516732	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62516732T>C	uc001dab.2	+	31	4239	c.4125_splice	c.e31+2	p.L1375_splice	INADL_uc009waf.1_Splice_Site_p.L1375_splice|INADL_uc001daa.2_Splice_Site_p.L1375_splice|INADL_uc001dad.3_Splice_Site_p.L1072_splice|INADL_uc001dac.2_Splice_Site|INADL_uc010oot.1_Splice_Site_p.L159_splice|INADL_uc009wag.2_Splice_Site_p.L159_splice|INADL_uc010oou.1_Splice_Site_p.L48_splice	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
KANK4	163782	broad.mit.edu	37	1	62740559	62740559	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62740559A>C	uc001dah.3	-	3	594	c.217T>G	c.(217-219)TTC>GTC	p.F73V	KANK4_uc001dai.3_Intron|KANK4_uc001dag.3_5'Flank	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38	73										ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
LEPROT	54741	broad.mit.edu	37	1	65895571	65895571	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65895571T>C	uc001dcf.2	+	3	208	c.119T>C	c.(118-120)ATT>ACT	p.I40T	LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc001dci.2_Intron|LEPR_uc009waq.2_Intron|LEPROT_uc009wap.2_Missense_Mutation_p.I49T	NM_017526	NP_059996	O15243	OBRG_HUMAN	leptin receptor gene-related protein	40	Helical; (Potential).					endosome membrane|Golgi membrane|integral to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)														---	---	---	---
IL23R	149233	broad.mit.edu	37	1	67666492	67666492	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67666492T>C	uc001ddo.2	+	5	649	c.564T>C	c.(562-564)GGT>GGC	p.G188G	IL23R_uc009waz.2_5'UTR|IL23R_uc001ddp.2_RNA|IL23R_uc010opi.1_RNA|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Silent_p.G145G|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_RNA|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Silent_p.G33G|IL23R_uc001ddr.2_RNA|IL23R_uc010opo.1_Silent_p.G47G|IL23R_uc010opp.1_RNA|IL23R_uc010opq.1_Silent_p.G47G|IL23R_uc010opr.1_RNA|IL23R_uc010ops.1_5'UTR|IL23R_uc010opt.1_5'UTR|IL23R_uc010opu.1_5'UTR|IL23R_uc010opv.1_Silent_p.G47G|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_5'UTR|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_5'UTR|IL23R_uc010oqb.1_Silent_p.G47G|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_5'UTR|IL23R_uc010oqf.1_5'UTR|IL23R_uc010oqg.1_5'UTR|IL23R_uc010oqh.1_Intron	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor	188	Extracellular (Potential).|Fibronectin type-III 1.				inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0																		---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72748049	72748049	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72748049C>T	uc001dfw.2	-	1	229	c.129G>A	c.(127-129)GCG>GCA	p.A43A	NEGR1_uc010oqs.1_Silent_p.A43A	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor	43	Ig-like C2-type 1.				cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
LHX8	431707	broad.mit.edu	37	1	75602834	75602834	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75602834C>T	uc001dgo.2	+	4	819	c.155C>T	c.(154-156)CCG>CTG	p.P52L	LHX8_uc001dgq.2_5'UTR	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	52						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
ACADM	34	broad.mit.edu	37	1	76194107	76194107	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76194107T>C	uc001dgw.3	+	2	482	c.52T>C	c.(52-54)TTT>CTT	p.F18L	ACADM_uc010orc.1_Missense_Mutation_p.F18L|ACADM_uc010ord.1_5'UTR|ACADM_uc009wbp.2_Missense_Mutation_p.F22L|ACADM_uc009wbr.2_Missense_Mutation_p.F18L|ACADM_uc010ore.1_Intron|ACADM_uc010orf.1_Intron|ACADM_uc001dgx.3_5'UTR	NM_000016	NP_000007	P11310	ACADM_HUMAN	medium-chain acyl-CoA dehydrogenase isoform a	18					carnitine biosynthetic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|medium-chain fatty acid catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|identical protein binding|medium-chain-acyl-CoA dehydrogenase activity			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
ZZZ3	26009	broad.mit.edu	37	1	78097900	78097900	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78097900G>T	uc001dhq.2	-	5	1616	c.1140C>A	c.(1138-1140)ACC>ACA	p.T380T	ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_Silent_p.T380T|ZZZ3_uc001dhp.2_Silent_p.T380T	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	380					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5																		---	---	---	---
IFI44	10561	broad.mit.edu	37	1	79121150	79121150	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79121150A>C	uc001dip.3	+	5	918	c.794A>C	c.(793-795)GAT>GCT	p.D265A	IFI44_uc010orr.1_Missense_Mutation_p.D265A|IFI44_uc010ors.1_5'UTR	NM_006417	NP_006408	Q8TCB0	IFI44_HUMAN	interferon-induced, hepatitis C-associated	265					response to virus	cytoplasm				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82409459	82409459	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82409459C>T	uc001dit.3	+						LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Intron|LPHN2_uc001div.2_Intron|LPHN2_uc009wcd.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
SPATA1	64173	broad.mit.edu	37	1	85014616	85014616	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85014616C>T	uc001djz.1	+	11	1359	c.1160C>T	c.(1159-1161)CCA>CTA	p.P387L	SPATA1_uc001djy.1_RNA	NM_001081472	NP_001074941			spermatogenesis associated 1											central_nervous_system(1)	1				Epithelial(280;4.36e-10)|all cancers(265;7.1e-09)|BRCA - Breast invasive adenocarcinoma(282;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(397;0.00286)|KIRC - Kidney renal clear cell carcinoma(1967;0.0111)														---	---	---	---
CTBS	1486	broad.mit.edu	37	1	85036346	85036346	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85036346T>C	uc001dka.2	-	2	300	c.235A>G	c.(235-237)ACA>GCA	p.T79A	CTBS_uc001dkc.2_5'UTR|CTBS_uc001dkd.2_5'UTR|CTBS_uc001dkb.2_5'UTR	NM_004388	NP_004379	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl- precursor	79						lysosome	cation binding				0				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)														---	---	---	---
MCOLN3	55283	broad.mit.edu	37	1	85506730	85506730	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85506730C>T	uc001dkp.2	-	3	452	c.359G>A	c.(358-360)AGT>AAT	p.S120N	MCOLN3_uc001dkq.2_Intron|MCOLN3_uc001dkr.2_Missense_Mutation_p.S120N|MCOLN3_uc001dks.3_Translation_Start_Site	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3	120						integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)														---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85666191	85666191	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85666191C>T	uc009wcm.2	-	1	538	c.489G>A	c.(487-489)GGG>GGA	p.G163G	SYDE2_uc001dku.3_Silent_p.G163G	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	163					activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)														---	---	---	---
CLCA1	1179	broad.mit.edu	37	1	86965639	86965639	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86965639A>G	uc001dlt.2	+	14	2785	c.2656A>G	c.(2656-2658)AAT>GAT	p.N886D		NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor	886					calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)														---	---	---	---
CLCA4	22802	broad.mit.edu	37	1	87031502	87031502	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87031502C>T	uc009wcs.2	+	6	797	c.753C>T	c.(751-753)AAC>AAT	p.N251N	CLCA4_uc009wct.2_Silent_p.N14N|CLCA4_uc009wcu.2_Silent_p.N71N	NM_012128	NP_036260	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	251						apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity	p.N251N(1)		ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)														---	---	---	---
GBP3	2635	broad.mit.edu	37	1	89479066	89479066	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89479066T>C	uc001dmt.2	-	6	875	c.670A>G	c.(670-672)ATC>GTC	p.I224V	GBP3_uc010oss.1_Missense_Mutation_p.I145V|GBP3_uc001dmu.2_Missense_Mutation_p.I90V|GBP3_uc001dmv.2_RNA	NM_018284	NP_060754	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	224						integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)														---	---	---	---
GBP3	2635	broad.mit.edu	37	1	89480280	89480280	+	Silent	SNP	G	A	A	rs148546933	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89480280G>A	uc001dmt.2	-	4	583	c.378C>T	c.(376-378)CTC>CTT	p.L126L	GBP3_uc010oss.1_Silent_p.L47L|GBP3_uc001dmu.2_5'UTR|GBP3_uc001dmv.2_RNA	NM_018284	NP_060754	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	126	Helical; (Potential).					integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)														---	---	---	---
LRRC8D	55144	broad.mit.edu	37	1	90400499	90400499	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90400499A>G	uc001dnm.2	+	3	2297	c.1872A>G	c.(1870-1872)AAA>AAG	p.K624K	LRRC8D_uc001dnn.2_Silent_p.K624K	NM_001134479	NP_001127951	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member	624	LRR 5.					integral to membrane	protein binding			ovary(2)	2		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)														---	---	---	---
DPYD	1806	broad.mit.edu	37	1	98165040	98165040	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98165040A>G	uc001drv.2	-	6	684	c.547T>C	c.(547-549)TCT>CCT	p.S183P	DPYD_uc010oub.1_RNA	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	183					'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
AGL	178	broad.mit.edu	37	1	100357205	100357205	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100357205T>C	uc001dsi.1	+	23	3393	c.2993T>C	c.(2992-2994)ATC>ACC	p.I998T	AGL_uc001dsj.1_Missense_Mutation_p.I998T|AGL_uc001dsk.1_Missense_Mutation_p.I998T|AGL_uc001dsl.1_Missense_Mutation_p.I998T|AGL_uc001dsm.1_Missense_Mutation_p.I982T|AGL_uc001dsn.1_Missense_Mutation_p.I981T	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	998	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)														---	---	---	---
VCAM1	7412	broad.mit.edu	37	1	101186043	101186043	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101186043A>G	uc001dti.2	+	2	196	c.76A>G	c.(76-78)AAA>GAA	p.K26E	VCAM1_uc001dtj.2_Missense_Mutation_p.K26E|VCAM1_uc010ouj.1_Missense_Mutation_p.K26E	NM_001078	NP_001069	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1 isoform a	26	Ig-like C2-type 1.|Extracellular (Potential).				heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|leukocyte tethering or rolling|membrane to membrane docking|positive regulation of T cell proliferation|regulation of immune response	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex|apical part of cell|external side of plasma membrane|extracellular space|filopodium|integral to membrane|microvillus|podosome	cell adhesion molecule binding|integrin binding			central_nervous_system(1)	1		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)													---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103573739	103573739	+	5'UTR	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103573739G>A	uc001dul.2	-	1					COL11A1_uc001dum.2_5'UTR|COL11A1_uc001dun.2_5'UTR|COL11A1_uc009weh.2_5'UTR	NM_001854	NP_001845			alpha 1 type XI collagen isoform A						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)														---	---	---	---
SARS	6301	broad.mit.edu	37	1	109778671	109778671	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109778671G>A	uc001dwu.1	+	8	1117	c.1042G>A	c.(1042-1044)GCA>ACA	p.A348T	SARS_uc001dwt.1_Missense_Mutation_p.A348T|SARS_uc001dwv.1_Missense_Mutation_p.A348T|SARS_uc001dww.1_Missense_Mutation_p.A281T|SARS_uc001dwx.1_Missense_Mutation_p.A300T|SARS_uc009wfa.1_Missense_Mutation_p.A348T|SARS_uc001dwy.1_Missense_Mutation_p.A173T|SARS_uc001dwz.1_Missense_Mutation_p.A173T	NM_006513	NP_006504	P49591	SYSC_HUMAN	seryl-tRNA synthetase	348					seryl-tRNA aminoacylation|tRNA processing	cytosol	ATP binding|protein binding|RNA binding|serine-tRNA ligase activity			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)													---	---	---	---
SORT1	6272	broad.mit.edu	37	1	109910092	109910092	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109910092G>T	uc001dxm.1	-	3	427	c.378C>A	c.(376-378)GTC>GTA	p.V126V	SORT1_uc010ovi.1_5'UTR|SORT1_uc009wfb.2_5'UTR	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein	126	Extracellular (Potential).				endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)														---	---	---	---
GSTM3	2947	broad.mit.edu	37	1	110280341	110280341	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110280341T>C	uc001dyo.2	-	7	715	c.405A>G	c.(403-405)CTA>CTG	p.L135L	GSTM3_uc001dyp.2_Silent_p.L132L|GSTM3_uc010ovv.1_Silent_p.L135L	NM_000849	NP_000840	P21266	GSTM3_HUMAN	glutathione S-transferase mu 3	135	GST C-terminal.				establishment of blood-nerve barrier|glutathione metabolic process|response to estrogen stimulus	cytoplasm	glutathione transferase activity|identical protein binding				0		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)													---	---	---	---
KCNC4	3749	broad.mit.edu	37	1	110765914	110765914	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110765914C>T	uc001dzh.2	+	2	1064	c.1007C>T	c.(1006-1008)TCC>TTC	p.S336F	KCNC4_uc001dzf.2_Missense_Mutation_p.S336F|KCNC4_uc009wfr.2_Missense_Mutation_p.S336F|KCNC4_uc001dzg.2_Missense_Mutation_p.S336F|KCNC4_uc001dzi.2_RNA	NM_004978	NP_004969	Q03721	KCNC4_HUMAN	Shaw-related voltage-gated potassium channel	336					synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)														---	---	---	---
KCNC4	3749	broad.mit.edu	37	1	110766270	110766270	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110766270C>T	uc001dzh.2	+	2	1420	c.1363C>T	c.(1363-1365)CTG>TTG	p.L455L	KCNC4_uc001dzf.2_Silent_p.L455L|KCNC4_uc009wfr.2_Silent_p.L455L|KCNC4_uc001dzg.2_Silent_p.L455L|KCNC4_uc001dzi.2_RNA	NM_004978	NP_004969	Q03721	KCNC4_HUMAN	Shaw-related voltage-gated potassium channel	455	Helical; Name=Segment S6; (Potential).				synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)														---	---	---	---
KCNA2	3737	broad.mit.edu	37	1	111147188	111147188	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111147188G>A	uc001dzu.2	-	2	713	c.217C>T	c.(217-219)CGA>TGA	p.R73*	KCNA2_uc009wfv.1_Nonsense_Mutation_p.R73*|KCNA2_uc009wfw.2_Nonsense_Mutation_p.R73*	NM_004974	NP_004965	P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related	73						juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(1)	1		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)														---	---	---	---
CHIA	27159	broad.mit.edu	37	1	111858017	111858017	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111858017G>A	uc001eas.2	+	6	543	c.440G>A	c.(439-441)AGC>AAC	p.S147N	CHIA_uc001ear.2_Missense_Mutation_p.S39N|CHIA_uc001eaq.2_Missense_Mutation_p.S39N|CHIA_uc009wgc.2_Missense_Mutation_p.S39N|CHIA_uc001eat.2_Intron|CHIA_uc001eav.2_5'UTR|CHIA_uc001eau.2_Intron|CHIA_uc009wgd.2_Intron	NM_201653	NP_970615	Q9BZP6	CHIA_HUMAN	acidic chitinase isoform c	147					apoptosis|cell wall chitin metabolic process|chitin catabolic process|digestion|immune response|positive regulation of chemokine secretion|production of molecular mediator involved in inflammatory response|response to acid|response to fungus	cytoplasm|extracellular space	cation binding|chitin binding|chitinase activity|kinase binding|lysozyme activity|sugar binding			ovary(1)	1		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)														---	---	---	---
WNT2B	7482	broad.mit.edu	37	1	113051996	113051996	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113051996C>T	uc001ecb.2	+	1	627	c.112C>T	c.(112-114)CGC>TGC	p.R38C	WNT2B_uc001eca.2_Intron|WNT2B_uc009wgg.2_Intron	NM_024494	NP_078613	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family,	38					chondrocyte differentiation|cornea development in camera-type eye|dorsal/ventral axis specification|forebrain regionalization|hemopoietic stem cell proliferation|iris morphogenesis|lens development in camera-type eye|lung induction|male gonad development|neuron differentiation|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding|signal transducer activity			ovary(2)|breast(2)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113653186	113653186	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113653186T>C	uc001edf.1	+	13	1996	c.1798_splice	c.e13+2	p.E600_splice	LRIG2_uc009wgn.1_Splice_Site_p.E497_splice	NM_014813	NP_055628			leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
PTPN22	26191	broad.mit.edu	37	1	114380688	114380688	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114380688G>C	uc001eds.2	-	13	1464	c.1334C>G	c.(1333-1335)ACA>AGA	p.T445R	PTPN22_uc009wgq.2_Missense_Mutation_p.T390R|PTPN22_uc010owo.1_Missense_Mutation_p.T201R|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Missense_Mutation_p.T445R|PTPN22_uc009wgs.2_Missense_Mutation_p.T318R|PTPN22_uc001edu.2_Missense_Mutation_p.T445R	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type	445					negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
TRIM33	51592	broad.mit.edu	37	1	114952816	114952816	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114952816C>A	uc001eew.2	-	12	2268	c.2184G>T	c.(2182-2184)CCG>CCT	p.P728P	TRIM33_uc010owr.1_Silent_p.P342P|TRIM33_uc010ows.1_Silent_p.P360P|TRIM33_uc001eex.2_Silent_p.P728P	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	728					negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)				T	RET	papillary thyroid								---	---	---	---
ATP1A1	476	broad.mit.edu	37	1	116946596	116946596	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116946596C>T	uc001ege.2	+	22	3381	c.3042C>T	c.(3040-3042)GGC>GGT	p.G1014G	ATP1A1_uc010owv.1_Silent_p.G983G|ATP1A1_uc010oww.1_Silent_p.G1014G|ATP1A1_uc010owx.1_Silent_p.G983G|C1orf203_uc009whb.2_Intron|C1orf203_uc001egg.3_Intron|ATP1A1_uc001egh.2_Silent_p.G156G	NM_000701	NP_000692	P05023	AT1A1_HUMAN	Na+/K+ -ATPase alpha 1 subunit isoform a	1014	Cytoplasmic (Potential).				ATP biosynthetic process	melanosome|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Captopril(DB01197)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Esomeprazole(DB00736)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Ouabain(DB01092)|Pantoprazole(DB00213)|Trichlormethiazide(DB01021)													---	---	---	---
PTGFRN	5738	broad.mit.edu	37	1	117484558	117484558	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117484558G>A	uc001egv.1	+	2	408	c.271G>A	c.(271-273)GAG>AAG	p.E91K		NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator	91	Extracellular (Potential).|Ig-like C2-type 1.					endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)														---	---	---	---
GDAP2	54834	broad.mit.edu	37	1	118455209	118455209	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118455209C>T	uc001ehf.2	-	4	712	c.413G>A	c.(412-414)CGC>CAC	p.R138H	GDAP2_uc001ehg.2_Missense_Mutation_p.R138H	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	138	Macro.									ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)														---	---	---	---
WARS2	10352	broad.mit.edu	37	1	119575812	119575812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119575812G>A	uc001ehn.2	-	6	833	c.805C>T	c.(805-807)CGC>TGC	p.R269C	WARS2_uc010oxf.1_Missense_Mutation_p.R175C|WARS2_uc001ehm.2_3'UTR|WARS2_uc010oxg.1_Missense_Mutation_p.R212C|WARS2_uc010oxh.1_3'UTR	NM_015836	NP_056651	Q9UGM6	SYWM_HUMAN	mitochondrial tryptophanyl tRNA synthetase 2	269					tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity	p.R269C(1)			0	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)													---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144918931	144918931	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144918931G>A	uc001elw.3	-	10	1546	c.1255C>T	c.(1255-1257)CGT>TGT	p.R419C	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.R485C|PDE4DIP_uc001emc.1_Missense_Mutation_p.R419C|PDE4DIP_uc001emd.1_Missense_Mutation_p.R419C|PDE4DIP_uc001emb.1_Missense_Mutation_p.R582C|PDE4DIP_uc001eme.1_5'UTR|PDE4DIP_uc001emf.1_Missense_Mutation_p.R206C	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	419	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
BCL9	607	broad.mit.edu	37	1	147084979	147084979	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147084979C>T	uc001epq.2	+	5	1091	c.351C>T	c.(349-351)AAC>AAT	p.N117N	BCL9_uc010ozr.1_Intron	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	117					Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)							T	IGH@|IGL@	B-ALL								---	---	---	---
BCL9	607	broad.mit.edu	37	1	147086415	147086415	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147086415A>G	uc001epq.2	+	6	1300	c.560A>G	c.(559-561)AAA>AGA	p.K187R	BCL9_uc010ozr.1_Missense_Mutation_p.K113R	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	187					Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)							T	IGH@|IGL@	B-ALL								---	---	---	---
ZNF687	57592	broad.mit.edu	37	1	151263312	151263312	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151263312A>G	uc001exq.2	+	9	3439	c.3341A>G	c.(3340-3342)TAC>TGC	p.Y1114C	ZNF687_uc009wmo.2_Missense_Mutation_p.Y1114C|ZNF687_uc009wmp.2_3'UTR	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	1114					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152192330	152192330	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152192330C>T	uc001ezt.1	-	3	1851	c.1775G>A	c.(1774-1776)GGA>GAA	p.G592E		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	592					keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
FLG	2312	broad.mit.edu	37	1	152283080	152283080	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283080G>A	uc001ezu.1	-	3	4318	c.4282C>T	c.(4282-4284)CGT>TGT	p.R1428C	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1428	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
FLG2	388698	broad.mit.edu	37	1	152328128	152328128	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152328128T>C	uc001ezw.3	-	3	2207	c.2134A>G	c.(2134-2136)AGT>GGT	p.S712G	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	712	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)															---	---	---	---
FLG2	388698	broad.mit.edu	37	1	152329376	152329376	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152329376T>G	uc001ezw.3	-	3	959	c.886A>C	c.(886-888)AGT>CGT	p.S296R	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	296	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)															---	---	---	---
LCE1E	353135	broad.mit.edu	37	1	152759779	152759779	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152759779T>G	uc001fan.2	+	2	57	c.4T>G	c.(4-6)TCC>GCC	p.S2A		NM_178353	NP_848130	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	2					keratinization						0	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
C1orf77	26097	broad.mit.edu	37	1	153617558	153617558	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153617558G>A	uc001fcm.1	+	6	872	c.560G>A	c.(559-561)CGG>CAG	p.R187Q	C1orf77_uc001fcn.1_Missense_Mutation_p.R188Q|C1orf77_uc001fco.1_Missense_Mutation_p.R162Q|C1orf77_uc001fcp.2_RNA	NM_015607	NP_056422	Q9Y3Y2	CHTOP_HUMAN	small protein rich in arginine and glycine	187	Arg/Gly-rich.|Interaction with PRMT1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	protein binding|RNA binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
DENND4B	9909	broad.mit.edu	37	1	153914361	153914361	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153914361G>A	uc001fdd.1	-	6	1440	c.1039C>T	c.(1039-1041)CGC>TGC	p.R347C		NM_014856	NP_055671	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	347	DENN.									ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
CRTC2	200186	broad.mit.edu	37	1	153920984	153920984	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153920984T>G	uc010ped.1	-	13	1881	c.1811A>C	c.(1810-1812)AAC>ACC	p.N604T	DENND4B_uc001fdd.1_5'Flank|CRTC2_uc001fde.3_RNA|CRTC2_uc001fdf.3_Missense_Mutation_p.N140T	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	604					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
AQP10	89872	broad.mit.edu	37	1	154294498	154294498	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154294498C>T	uc001feu.2	+	2	235	c.195C>T	c.(193-195)GCC>GCT	p.A65A	AQP10_uc001fev.2_Silent_p.A65A	NM_080429	NP_536354	Q96PS8	AQP10_HUMAN	aquaporin 10	65	Helical; (Potential).				response to toxin|transmembrane transport|water transport	integral to membrane|plasma membrane	transporter activity			central_nervous_system(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
ADAR	103	broad.mit.edu	37	1	154562368	154562368	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154562368C>T	uc001ffh.2	-	8	2733	c.2533G>A	c.(2533-2535)GCC>ACC	p.A845T	ADAR_uc001ffj.2_Missense_Mutation_p.A800T|ADAR_uc001ffi.2_Missense_Mutation_p.A819T|ADAR_uc001ffk.2_Missense_Mutation_p.A550T	NM_001111	NP_001102	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform a	845					adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)														---	---	---	---
ZBTB7B	51043	broad.mit.edu	37	1	154987252	154987252	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154987252G>A	uc001fgk.3	+	3	274	c.116G>A	c.(115-117)CGG>CAG	p.R39Q	ZBTB7B_uc009wpa.2_Missense_Mutation_p.R39Q|ZBTB7B_uc001fgj.3_Missense_Mutation_p.R73Q|ZBTB7B_uc010peq.1_Missense_Mutation_p.R73Q|ZBTB7B_uc001fgl.3_Missense_Mutation_p.R39Q	NM_015872	NP_056956	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	39	BTB.				cell differentiation|ectoderm development|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)															---	---	---	---
DCST2	127579	broad.mit.edu	37	1	154998843	154998843	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154998843A>T	uc001fgm.2	-	10	1626	c.1546T>A	c.(1546-1548)TTT>ATT	p.F516I	DCST2_uc009wpb.2_RNA	NM_144622	NP_653223	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	516	Helical; (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)															---	---	---	---
TRIM46	80128	broad.mit.edu	37	1	155152138	155152138	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155152138G>A	uc001fhs.1	+	8	1399	c.1316G>A	c.(1315-1317)CGC>CAC	p.R439H	RAG1AP1_uc010pey.1_Intron|TRIM46_uc009wpe.1_RNA|TRIM46_uc001fhq.2_RNA|TRIM46_uc001fhr.2_Missense_Mutation_p.R439H|TRIM46_uc001fht.1_RNA|TRIM46_uc010pfa.1_Missense_Mutation_p.R313H|TRIM46_uc001fhu.1_Missense_Mutation_p.R416H|TRIM46_uc009wpg.1_Missense_Mutation_p.R426H|TRIM46_uc001fhv.3_Missense_Mutation_p.R426H|TRIM46_uc001fhw.1_RNA	NM_025058	NP_079334	Q7Z4K8	TRI46_HUMAN	tripartite motif-containing 46	439	Fibronectin type-III.					intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
RUSC1	23623	broad.mit.edu	37	1	155300265	155300265	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155300265T>C	uc001fkj.2	+	10	2841	c.2612T>C	c.(2611-2613)CTG>CCG	p.L871P	RAG1AP1_uc010pey.1_Intron|RUSC1_uc001fkk.2_Missense_Mutation_p.L765P|RUSC1_uc009wqn.1_RNA|RUSC1_uc009wqo.1_Missense_Mutation_p.L402P|RUSC1_uc001fkl.2_Missense_Mutation_p.L461P|RUSC1_uc001fkp.2_Missense_Mutation_p.L402P|RUSC1_uc001fkq.2_Missense_Mutation_p.L296P|RUSC1_uc010pgb.1_Missense_Mutation_p.L369P|RUSC1_uc009wqp.1_Missense_Mutation_p.L396P|RUSC1_uc001fkn.2_Missense_Mutation_p.L180P|RUSC1_uc001fko.2_RNA|RUSC1_uc001fkr.2_Missense_Mutation_p.L402P|RUSC1_uc001fks.2_Missense_Mutation_p.L138P	NM_001105203	NP_001098673	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1 isoform a	871	SH3.					cytoplasm|nucleolus	SH3/SH2 adaptor activity			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)															---	---	---	---
DAP3	7818	broad.mit.edu	37	1	155707980	155707980	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155707980T>C	uc001flq.2	+	13	1313	c.1144T>C	c.(1144-1146)TTC>CTC	p.F382L	DAP3_uc001flr.2_Missense_Mutation_p.F382L|DAP3_uc001fls.2_Missense_Mutation_p.F382L|DAP3_uc010pgl.1_Missense_Mutation_p.F341L|DAP3_uc001flt.2_Missense_Mutation_p.F348L|DAP3_uc001flu.2_Missense_Mutation_p.F355L|DAP3_uc010pgm.1_Missense_Mutation_p.F348L	NM_033657	NP_387506	P51398	RT29_HUMAN	death-associated protein 3	382					induction of apoptosis by extracellular signals	mitochondrial ribosome|nucleolus|small ribosomal subunit	protein binding			ovary(1)	1	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)																	---	---	---	---
KIAA0907	22889	broad.mit.edu	37	1	155896943	155896943	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155896943G>A	uc001fmi.1	-	5	493	c.469C>T	c.(469-471)CGT>TGT	p.R157C	KIAA0907_uc001fmj.1_Missense_Mutation_p.R157C|KIAA0907_uc009wrk.1_Intron|KIAA0907_uc009wrl.1_RNA|KIAA0907_uc001fml.1_Missense_Mutation_p.R157C|KIAA0907_uc001fmm.2_Missense_Mutation_p.R157C|SCARNA4_uc001fmn.1_5'Flank|KIAA0907_uc001fmo.2_Missense_Mutation_p.R157C	NM_014949	NP_055764	Q7Z7F0	K0907_HUMAN	hypothetical protein LOC22889	157											0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)															---	---	---	---
MEX3A	92312	broad.mit.edu	37	1	156046519	156046519	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156046519A>G	uc001fnd.3	-	2	1409	c.1409T>C	c.(1408-1410)ATG>ACG	p.M470T		NM_001093725	NP_001087194	A1L020	MEX3A_HUMAN	MEX3A protein	470	RING-type.					cytoplasmic mRNA processing body|nucleus	RNA binding|zinc ion binding				0	Hepatocellular(266;0.158)|all_neural(408;0.195)																	---	---	---	---
SMG5	23381	broad.mit.edu	37	1	156220714	156220714	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156220714C>A	uc001foc.3	-	21	3051	c.2902G>T	c.(2902-2904)GGC>TGC	p.G968C	PAQR6_uc010phf.1_5'Flank|PAQR6_uc001fny.1_5'Flank|PAQR6_uc001fnv.1_5'Flank|PAQR6_uc010phg.1_5'Flank|PAQR6_uc001fnx.1_5'Flank|PAQR6_uc001fnw.1_5'Flank|PAQR6_uc001fnz.1_5'Flank|PAQR6_uc010phh.1_5'Flank|PAQR6_uc001foa.1_5'Flank|PAQR6_uc001fob.1_5'Flank|PAQR6_uc001fnu.1_5'Flank|SMG5_uc009wrv.2_Intron	NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay	968	PINc.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)																	---	---	---	---
APOA1BP	128240	broad.mit.edu	37	1	156562003	156562003	+	Splice_Site	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156562003T>G	uc001fph.2	+	2	330	c.291_splice	c.e2+2	p.K97_splice	APOA1BP_uc001fpg.2_Splice_Site_p.K97_splice|APOA1BP_uc001fpi.2_Splice_Site_p.K97_splice|APOA1BP_uc001fpj.2_Splice_Site_p.K14_splice|APOA1BP_uc001fpk.2_5'UTR|APOA1BP_uc010php.1_5'UTR	NM_144772	NP_658985			apolipoprotein A-I binding protein precursor							extracellular region	protein binding			central_nervous_system(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
DARC	2532	broad.mit.edu	37	1	159176246	159176246	+	3'UTR	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159176246T>G	uc001fto.2	+	2					DARC_uc001ftp.3_3'UTR	NM_002036	NP_002027			Duffy blood group antigen isoform b						defense response	integral to membrane|plasma membrane	C-C chemokine binding|chemokine receptor activity			ovary(1)|lung(1)	2	all_hematologic(112;0.0429)																	---	---	---	---
FCER1A	2205	broad.mit.edu	37	1	159277558	159277558	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159277558C>T	uc001ftq.2	+	6	709	c.610C>T	c.(610-612)CTA>TTA	p.L204L		NM_002001	NP_001992	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor	204	Extracellular (Potential).					integral to plasma membrane				lung(2)|skin(2)|prostate(1)	5	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)													---	---	---	---
PIGM	93183	broad.mit.edu	37	1	160000905	160000905	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160000905A>G	uc001fuv.1	-	1	879	c.625T>C	c.(625-627)TAC>CAC	p.Y209H		NM_145167	NP_660150	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	209	Cytoplasmic (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane				ovary(2)|skin(1)	3	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
KCNJ10	3766	broad.mit.edu	37	1	160012141	160012141	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160012141T>C	uc001fuw.1	-	2	332	c.182A>G	c.(181-183)GAC>GGC	p.D61G		NM_002241	NP_002232	P78508	IRK10_HUMAN	potassium inwardly-rectifying channel, subfamily	61	Cytoplasmic (By similarity).					integral to plasma membrane	ATP binding|ATP-activated inward rectifier potassium channel activity			ovary(1)	1	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
ATP1A2	477	broad.mit.edu	37	1	160098475	160098475	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160098475C>T	uc001fvc.2	+	9	1183	c.1051C>T	c.(1051-1053)CGG>TGG	p.R351W	ATP1A2_uc001fvb.2_Missense_Mutation_p.R351W|ATP1A2_uc010piz.1_Missense_Mutation_p.R196W|ATP1A2_uc001fvd.2_Missense_Mutation_p.R87W|ATP1A2_uc009wtg.1_Missense_Mutation_p.R39W	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	351	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)															---	---	---	---
NCSTN	23385	broad.mit.edu	37	1	160326990	160326990	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160326990C>T	uc001fvx.2	+	16	2078	c.1954C>T	c.(1954-1956)CGC>TGC	p.R652C	NCSTN_uc001fvy.2_Missense_Mutation_p.R632C|NCSTN_uc010pjf.1_Missense_Mutation_p.R514C|NCSTN_uc001fvz.2_Missense_Mutation_p.R432C|NCSTN_uc010pjg.1_Missense_Mutation_p.R394C	NM_015331	NP_056146	Q92542	NICA_HUMAN	nicastrin precursor	652	Extracellular (Potential).				amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane|melanosome	protein binding			ovary(1)|lung(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
FAM78B	149297	broad.mit.edu	37	1	166039840	166039840	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166039840A>C	uc001gdr.2	-	3	1014	c.424T>G	c.(424-426)TTC>GTC	p.F142V	FAM78B_uc010plc.1_RNA|FAM78B_uc001gdq.2_5'Flank	NM_001017961	NP_001017961	Q5VT40	FA78B_HUMAN	hypothetical protein LOC149297	142										central_nervous_system(1)|skin(1)	2	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)																	---	---	---	---
DUSP27	92235	broad.mit.edu	37	1	167095702	167095702	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167095702G>A	uc001geb.1	+	5	1334	c.1334G>A	c.(1333-1335)AGC>AAC	p.S445N		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	445					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3																		---	---	---	---
CD247	919	broad.mit.edu	37	1	167408619	167408619	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167408619C>T	uc001gei.3	-	3	326	c.181G>A	c.(181-183)GCC>ACC	p.A61T	CD247_uc001gej.3_Missense_Mutation_p.A61T|CD247_uc001gek.2_Missense_Mutation_p.A61T	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor	61	Cytoplasmic (Potential).|ITAM 1.			DA -> EP (in Ref. 1; AAA60394).	interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)															---	---	---	---
FMO3	2328	broad.mit.edu	37	1	171086310	171086310	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171086310G>A	uc001ghi.2	+	9	1438	c.1327G>A	c.(1327-1329)GCA>ACA	p.A443T	FMO3_uc001ghh.2_Missense_Mutation_p.A443T|FMO3_uc010pmb.1_Missense_Mutation_p.A423T|FMO3_uc010pmc.1_Missense_Mutation_p.A380T	NM_001002294	NP_001002294	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	443					xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
QSOX1	5768	broad.mit.edu	37	1	180153144	180153144	+	Silent	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180153144T>A	uc001gnz.2	+	7	921	c.846T>A	c.(844-846)ACT>ACA	p.T282T	QSOX1_uc001gny.2_Silent_p.T282T|QSOX1_uc001goa.2_Silent_p.T282T	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a	282					cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181735752	181735752	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181735752G>T	uc001gow.2	+						CACNA1E_uc009wxs.2_Intron|CACNA1E_uc001gox.1_Intron|CACNA1E_uc009wxt.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						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																		---	---	---	---
NCF2	4688	broad.mit.edu	37	1	183534900	183534900	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183534900C>T	uc001gqj.3	-	10	1214	c.939G>A	c.(937-939)CCG>CCA	p.P313P	NCF2_uc010pod.1_Silent_p.P268P|NCF2_uc010poe.1_Silent_p.P232P|NCF2_uc001gqk.3_Silent_p.P313P	NM_000433	NP_000424	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	313					cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding			ovary(3)	3																		---	---	---	---
APOBEC4	403314	broad.mit.edu	37	1	183616870	183616870	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183616870T>C	uc001gqn.2	-	2	1319	c.1047A>G	c.(1045-1047)GAA>GAG	p.E349E	RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron	NM_203454	NP_982279	Q8WW27	ABEC4_HUMAN	apolipoprotein B	349					mRNA processing		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185931759	185931759	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185931759C>T	uc001grq.1	+	12	2167	c.1938C>T	c.(1936-1938)ACC>ACT	p.T646T	HMCN1_uc001grr.1_5'UTR	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	646	Ig-like C2-type 3.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186147727	186147727	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186147727T>C	uc001grq.1	+	104	16352	c.16123T>C	c.(16123-16125)TTC>CTC	p.F5375L	HMCN1_uc001grs.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	5375					response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186158785	186158785	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186158785A>G	uc001grq.1	+	107	16912	c.16683A>G	c.(16681-16683)GGA>GGG	p.G5561G	HMCN1_uc001grs.1_Silent_p.G1013G	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	5561					response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
RGS21	431704	broad.mit.edu	37	1	192316502	192316502	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192316502C>T	uc001gsh.2	+	3	245	c.71C>T	c.(70-72)ACG>ATG	p.T24M		NM_001039152	NP_001034241	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	24	RGS.				negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|skin(1)	2																		---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193181570	193181570	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193181570A>G	uc001gtb.2	+	13	1360	c.1117A>G	c.(1117-1119)ACC>GCC	p.T373A		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	373					cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49														Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				---	---	---	---
CFHR3	10878	broad.mit.edu	37	1	196762466	196762466	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196762466A>G	uc001gtl.2	+	6	903	c.816A>G	c.(814-816)GAA>GAG	p.E272E	CFHR3_uc010poy.1_Silent_p.E211E|CFHR1_uc001gtm.2_Intron	NM_021023	NP_066303	Q02985	FHR3_HUMAN	complement factor H-related 3 precursor	272	Sushi 5.					extracellular space					0																		---	---	---	---
ZBTB41	360023	broad.mit.edu	37	1	197128613	197128613	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197128613A>G	uc001gtx.1	-	10	2675	c.2606T>C	c.(2605-2607)ATA>ACA	p.I869T	ZBTB41_uc009wyz.1_RNA	NM_194314	NP_919290	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	869					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197390150	197390150	+	Missense_Mutation	SNP	G	A	A	rs144011428		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197390150G>A	uc001gtz.2	+	6	1327	c.1192G>A	c.(1192-1194)GTC>ATC	p.V398I	CRB1_uc010poz.1_Missense_Mutation_p.V329I|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Missense_Mutation_p.V286I|CRB1_uc010ppb.1_Missense_Mutation_p.V398I|CRB1_uc010ppc.1_RNA|CRB1_uc010ppd.1_5'UTR|CRB1_uc001gub.1_Missense_Mutation_p.V47I	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	398	Extracellular (Potential).|EGF-like 10; calcium-binding (Potential).				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
KIF21B	23046	broad.mit.edu	37	1	200946499	200946499	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200946499G>A	uc001gvs.1	-	31	4483	c.4166C>T	c.(4165-4167)TCG>TTG	p.S1389L	KIF21B_uc001gvr.1_Missense_Mutation_p.S1376L|KIF21B_uc009wzl.1_Missense_Mutation_p.S1389L|KIF21B_uc010ppn.1_Missense_Mutation_p.S1376L	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1389					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6																		---	---	---	---
PKP1	5317	broad.mit.edu	37	1	201282591	201282591	+	Missense_Mutation	SNP	C	T	T	rs144063217		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201282591C>T	uc001gwd.2	+	3	855	c.604C>T	c.(604-606)CGC>TGC	p.R202C	PKP1_uc001gwe.2_Missense_Mutation_p.R202C|PKP1_uc009wzm.2_Intron	NM_000299	NP_000290	Q13835	PKP1_HUMAN	plakophilin 1 isoform 1b	202					cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			ovary(2)	2																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201781716	201781716	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201781716C>T	uc001gwu.2	+	26	5486	c.5139C>T	c.(5137-5139)CTC>CTT	p.L1713L	NAV1_uc001gwx.2_Silent_p.L1322L	NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1716					cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
RNPEP	6051	broad.mit.edu	37	1	201958135	201958135	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201958135C>T	uc001gxd.2	+	2	580	c.551C>T	c.(550-552)ACG>ATG	p.T184M	RNPEP_uc001gxe.2_Translation_Start_Site|RNPEP_uc001gxf.2_Missense_Mutation_p.T53M	NM_020216	NP_064601	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase	184					leukotriene biosynthetic process		epoxide hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)														---	---	---	---
MYOG	4656	broad.mit.edu	37	1	203054894	203054894	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203054894G>A	uc001gzd.2	-	1	484	c.196C>T	c.(196-198)CTG>TTG	p.L66L		NM_002479	NP_002470	P15173	MYOG_HUMAN	myogenin	66					muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	E-box binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity			skin(2)	2																		---	---	---	---
SNRPE	6635	broad.mit.edu	37	1	203830822	203830822	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203830822A>C	uc001hai.2	+	1	83	c.35A>C	c.(34-36)AAG>ACG	p.K12T	SNRPE_uc010pqn.1_RNA	NM_003094	NP_003085	P62304	RUXE_HUMAN	small nuclear ribonucleoprotein polypeptide E	12					histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
DSTYK	25778	broad.mit.edu	37	1	205119814	205119814	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205119814A>G	uc001hbw.2	-	11	2525	c.2461T>C	c.(2461-2463)TTC>CTC	p.F821L	DSTYK_uc001hbx.2_Missense_Mutation_p.F821L	NM_015375	NP_056190	Q6XUX3	DUSTY_HUMAN	receptor interacting protein kinase 5 isoform 1	821	Protein kinase.					cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1																		---	---	---	---
CTSE	1510	broad.mit.edu	37	1	206328829	206328829	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206328829A>G	uc001hdu.2	+	7	1014	c.896A>G	c.(895-897)AAC>AGC	p.N299S	CTSE_uc001hdv.2_Intron|CTSE_uc010prs.1_Intron	NM_001910	NP_001901	P14091	CATE_HUMAN	cathepsin E isoform a preproprotein	304					antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)															---	---	---	---
C1orf116	79098	broad.mit.edu	37	1	207196629	207196629	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207196629T>C	uc001hfd.2	-	4	739	c.480A>G	c.(478-480)GAA>GAG	p.E160E	C1orf116_uc009xcb.1_5'UTR	NM_023938	NP_076427	Q9BW04	SARG_HUMAN	specifically androgen-regulated protein isoform	160						cytoplasm|plasma membrane	receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4	Prostate(682;0.19)																	---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208205091	208205091	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208205091T>G	uc001hgz.2	-	29	5827	c.5069A>C	c.(5068-5070)AAG>ACG	p.K1690T	PLXNA2_uc001hgy.2_5'Flank	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	1690	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208269412	208269412	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208269412G>A	uc001hgz.2	-	8	2702	c.1944C>T	c.(1942-1944)AGC>AGT	p.S648S		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	648	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
HHAT	55733	broad.mit.edu	37	1	210686512	210686512	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210686512A>G	uc009xcx.2	+	9	1189	c.1023A>G	c.(1021-1023)GGA>GGG	p.G341G	HHAT_uc010psq.1_Silent_p.G204G|HHAT_uc001hhz.3_Silent_p.G341G|HHAT_uc010psr.1_Silent_p.G342G|HHAT_uc010pss.1_Silent_p.G296G|HHAT_uc009xcy.2_Silent_p.G276G|HHAT_uc010pst.1_Silent_p.G278G|HHAT_uc010psu.1_Silent_p.G276G|HHAT_uc001hia.3_Silent_p.G31G	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	341					multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)														---	---	---	---
RCOR3	55758	broad.mit.edu	37	1	211486764	211486764	+	Splice_Site	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211486764A>G	uc001hig.2	+	11	1313	c.1144_splice	c.e11-2	p.A382_splice	RCOR3_uc010psw.1_Splice_Site_p.A440_splice|RCOR3_uc001hif.2_Splice_Site_p.G359_splice|RCOR3_uc009xcz.2_Splice_Site	NM_018254	NP_060724			REST corepressor 3 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)														---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214557016	214557016	+	Missense_Mutation	SNP	G	A	A	rs143375730	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214557016G>A	uc001hkk.1	-	13	2453	c.2182C>T	c.(2182-2184)CGG>TGG	p.R728W	PTPN14_uc010pty.1_Missense_Mutation_p.R629W	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type	728					lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214575076	214575076	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214575076A>G	uc001hkk.1	-	7	892	c.621T>C	c.(619-621)AAT>AAC	p.N207N	PTPN14_uc010pty.1_Silent_p.N108N	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type	207	FERM.				lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216465672	216465672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216465672C>T	uc001hku.1	-	10	2072	c.1685G>A	c.(1684-1686)CGC>CAC	p.R562H	USH2A_uc001hkv.2_Missense_Mutation_p.R562H	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	562	Laminin EGF-like 1.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
LYPLAL1	127018	broad.mit.edu	37	1	219366532	219366532	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219366532G>A	uc001hlq.3	+	3	341	c.300G>A	c.(298-300)GTG>GTA	p.V100V	LYPLAL1_uc001hlr.3_Silent_p.V84V|LYPLAL1_uc001hls.3_Intron|LYPLAL1_uc001hlt.3_Intron|LYPLAL1_uc009xds.2_Intron	NM_138794	NP_620149	Q5VWZ2	LYPL1_HUMAN	lysophospholipase-like 1	100						cytoplasm	lysophospholipase activity				0				GBM - Glioblastoma multiforme(131;0.055)|all cancers(67;0.105)|OV - Ovarian serous cystadenocarcinoma(81;0.116)														---	---	---	---
IARS2	55699	broad.mit.edu	37	1	220279373	220279373	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220279373G>A	uc001hmc.2	+	9	1311	c.1207G>A	c.(1207-1209)GGT>AGT	p.G403S		NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase	403					isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)													---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220364615	220364615	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220364615C>T	uc010puk.1	-	14	1446	c.1282G>A	c.(1282-1284)GCA>ACA	p.A428T	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Missense_Mutation_p.A8T	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	428					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
HLX	3142	broad.mit.edu	37	1	221057685	221057685	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221057685G>A	uc001hmv.3	+	4	1563	c.1106G>A	c.(1105-1107)CGT>CAT	p.R369H		NM_021958	NP_068777	Q14774	HLX_HUMAN	H2.0-like homeobox	369	Ser-rich.				cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				GBM - Glioblastoma multiforme(131;0.00914)														---	---	---	---
C1orf65	164127	broad.mit.edu	37	1	223567946	223567946	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223567946C>T	uc001hoa.2	+	1	1232	c.1129C>T	c.(1129-1131)CGG>TGG	p.R377W		NM_152610	NP_689823	Q8N715	CA065_HUMAN	hypothetical protein LOC164127	377	Potential.									central_nervous_system(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0704)														---	---	---	---
TMEM63A	9725	broad.mit.edu	37	1	226037670	226037670	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226037670A>G	uc001hpm.1	-	21	2264	c.2014T>C	c.(2014-2016)TTG>CTG	p.L672L		NM_014698	NP_055513	O94886	TM63A_HUMAN	transmembrane protein 63A	672	Helical; (Potential).					integral to membrane|lysosomal membrane	nucleotide binding			ovary(1)|breast(1)	2	Breast(184;0.197)																	---	---	---	---
TMEM63A	9725	broad.mit.edu	37	1	226053597	226053597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226053597C>T	uc001hpm.1	-	10	996	c.746G>A	c.(745-747)CGG>CAG	p.R249Q		NM_014698	NP_055513	O94886	TM63A_HUMAN	transmembrane protein 63A	249						integral to membrane|lysosomal membrane	nucleotide binding			ovary(1)|breast(1)	2	Breast(184;0.197)																	---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228401921	228401921	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228401921C>T	uc009xez.1	+	4	1349	c.1305C>T	c.(1303-1305)GGC>GGT	p.G435G	OBSCN_uc001hsn.2_Silent_p.G435G|uc001hsm.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	435	Ig-like 5.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228462128	228462128	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228462128C>T	uc009xez.1	+	19	5710	c.5666C>T	c.(5665-5667)GCG>GTG	p.A1889V	OBSCN_uc001hsn.2_Missense_Mutation_p.A1889V	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1889	Ig-like 18.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
TAF5L	27097	broad.mit.edu	37	1	229737984	229737984	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229737984G>A	uc001htq.2	-	4	1096	c.930C>T	c.(928-930)GAC>GAT	p.D310D	TAF5L_uc001htr.2_Silent_p.D310D	NM_014409	NP_055224	O75529	TAF5L_HUMAN	PCAF associated factor 65 beta isoform a	310					histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
AGT	183	broad.mit.edu	37	1	230846080	230846080	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230846080A>G	uc001hty.3	-	2	1025	c.517T>C	c.(517-519)TCC>CCC	p.S173P	AGT_uc009xfe.2_Missense_Mutation_p.S173P|AGT_uc009xff.2_Missense_Mutation_p.S145P	NM_000029	NP_000020	P01019	ANGT_HUMAN	angiotensinogen preproprotein	173					activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|blood vessel remodeling|cell-cell signaling|cellular lipid metabolic process|G-protein signaling, coupled to cGMP nucleotide second messenger|kidney development|low-density lipoprotein particle remodeling|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of activation of JAK2 kinase activity|positive regulation of apoptosis|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of cardiac muscle hypertrophy|positive regulation of cholesterol esterification|positive regulation of cytokine production|positive regulation of endothelial cell migration|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of NAD(P)H oxidase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein tyrosine kinase activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription, DNA-dependent|regulation of proteolysis|regulation of renal output by angiotensin|regulation of renal sodium excretion|regulation of vasoconstriction|renin-angiotensin regulation of aldosterone production|response to muscle activity involved in regulation of muscle adaptation	extracellular space|soluble fraction	acetyltransferase activator activity|growth factor activity|hormone activity|serine-type endopeptidase inhibitor activity|type 1 angiotensin receptor binding|type 2 angiotensin receptor binding				0	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	Aliskiren(DB01258)|Atorvastatin(DB01076)|Cilazapril(DB01340)|Irbesartan(DB01029)|Lisinopril(DB00722)|Ouabain(DB01092)|Simvastatin(DB00641)													---	---	---	---
LYST	1130	broad.mit.edu	37	1	235909731	235909731	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235909731A>G	uc001hxj.2	-	29	8052	c.7877T>C	c.(7876-7878)ATG>ACG	p.M2626T	LYST_uc009xga.1_Missense_Mutation_p.M262T	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	2626					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											Chediak-Higashi_syndrome				---	---	---	---
HEATR1	55127	broad.mit.edu	37	1	236730088	236730088	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236730088T>C	uc001hyd.1	-	30	4291	c.4166A>G	c.(4165-4167)CAC>CGC	p.H1389R	HEATR1_uc009xgh.1_Missense_Mutation_p.H551R	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	1389					rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236906269	236906269	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236906269G>A	uc001hyf.2	+	11	1385	c.1181G>A	c.(1180-1182)CGG>CAG	p.R394Q	ACTN2_uc001hyg.2_Missense_Mutation_p.R186Q|ACTN2_uc009xgi.1_Missense_Mutation_p.R394Q|ACTN2_uc010pxu.1_Missense_Mutation_p.R83Q|ACTN2_uc001hyh.2_Missense_Mutation_p.R82Q	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	394					focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237947929	237947929	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237947929T>C	uc001hyl.1	+	90	13037	c.12917T>C	c.(12916-12918)TTC>TCC	p.F4306S	RYR2_uc010pya.1_Missense_Mutation_p.F721S	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4306	Helical; Name=M4; (Potential).				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
GREM2	64388	broad.mit.edu	37	1	240656299	240656299	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240656299G>A	uc001hys.2	-	2	757	c.477C>T	c.(475-477)TCC>TCT	p.S159S		NM_022469	NP_071914	Q9H772	GREM2_HUMAN	gremlin 2 precursor	159	CTCK.				BMP signaling pathway	extracellular space	cytokine activity				0		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)															---	---	---	---
FH	2271	broad.mit.edu	37	1	241680541	241680541	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241680541C>T	uc001hyx.2	-	2	240	c.208G>A	c.(208-210)GCC>ACC	p.A70T		NM_000143	NP_000134	P07954	FUMH_HUMAN	fumarate hydratase precursor	70					fumarate metabolic process|tricarboxylic acid cycle	cell junction|mitochondrial matrix|tricarboxylic acid cycle enzyme complex	fumarate hydratase activity			lung(3)|ovary(1)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)				Mis|N|F			lieomyomatosis|renal			Hereditary_Leiomyomatosis_and_Renal_Cell_Cancer				---	---	---	---
CNST	163882	broad.mit.edu	37	1	246797842	246797842	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246797842T>C	uc001ibp.2	+	6	1149	c.771T>C	c.(769-771)AAT>AAC	p.N257N	CNST_uc001ibo.3_Silent_p.N257N	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	257					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0																		---	---	---	---
OR2T6	254879	broad.mit.edu	37	1	248550915	248550915	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248550915T>C	uc001iei.1	+	1	6	c.6T>C	c.(4-6)AAT>AAC	p.N2N		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	2	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)															---	---	---	---
OR2T1	26696	broad.mit.edu	37	1	248569514	248569514	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248569514C>T	uc010pzm.1	+	1	219	c.219C>T	c.(217-219)ACC>ACT	p.T73T		NM_030904	NP_112166	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T,	73	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)															---	---	---	---
ACP1	52	broad.mit.edu	37	2	272122	272122	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:272122G>A	uc002qwg.2	+						ACP1_uc002qwd.2_Missense_Mutation_p.G68D|ACP1_uc002qwe.3_Intron|ACP1_uc002qwh.2_Intron|ACP1_uc002qwf.2_Missense_Mutation_p.G68D	NM_007099	NP_009030			acid phosphatase 1, soluble isoform b							cytoplasm|internal side of plasma membrane|nucleus|soluble fraction	acid phosphatase activity|identical protein binding|non-membrane spanning protein tyrosine phosphatase activity			skin(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1094066	1094066	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1094066G>A	uc002qwq.2	+	4	423	c.295G>A	c.(295-297)GTC>ATC	p.V99I	SNTG2_uc002qwp.2_RNA|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	99	PDZ.				central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1653372	1653372	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1653372C>T	uc002qxa.2	-	17	2244	c.2180G>A	c.(2179-2181)CGG>CAG	p.R727Q		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	727					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
ATP6V1C2	245973	broad.mit.edu	37	2	10923322	10923322	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10923322T>C	uc002ras.2	+	14	1326	c.1217T>C	c.(1216-1218)CTG>CCG	p.L406P	ATP6V1C2_uc002rat.2_Missense_Mutation_p.L360P	NM_001039362	NP_001034451	Q8NEY4	VATC2_HUMAN	vacuolar H+ ATPase C2 isoform a	406					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)														---	---	---	---
ROCK2	9475	broad.mit.edu	37	2	11334477	11334477	+	Intron	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11334477A>T	uc002rbd.1	-							NM_004850	NP_004841			Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)														---	---	---	---
RAD51AP2	729475	broad.mit.edu	37	2	17697058	17697058	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17697058T>C	uc002rcl.1	-	1	2649	c.2625A>G	c.(2623-2625)TCA>TCG	p.S875S	RAD51AP2_uc010exn.1_Silent_p.S866S	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	875										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26203671	26203671	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26203671G>A	uc002rgu.2	-	1	1773	c.1116C>T	c.(1114-1116)AAC>AAT	p.N372N	KIF3C_uc010eyj.1_RNA|KIF3C_uc010ykr.1_Silent_p.N372N	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	372	Kinesin-motor.				blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26684636	26684636	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26684636C>T	uc002rhk.2	-	43	5588	c.5461G>A	c.(5461-5463)GAG>AAG	p.E1821K	OTOF_uc010yla.1_Missense_Mutation_p.E551K|OTOF_uc002rhh.2_Missense_Mutation_p.E1054K|OTOF_uc002rhi.2_Missense_Mutation_p.E1131K|OTOF_uc002rhj.2_Missense_Mutation_p.E1054K	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1821	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf18	54978	broad.mit.edu	37	2	27001127	27001127	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27001127C>T	uc002rhp.1	+	6	940	c.864C>T	c.(862-864)AGC>AGT	p.S288S	C2orf18_uc002rhq.1_Silent_p.S205S|C2orf18_uc010eyo.1_Silent_p.S235S|C2orf18_uc010ylc.1_Silent_p.S141S	NM_017877	NP_060347	Q8N357	CB018_HUMAN	ANT2-binding protein precursor	288						integral to membrane|lysosomal membrane					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
EMILIN1	11117	broad.mit.edu	37	2	27305128	27305128	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27305128G>A	uc002rii.3	+	4	1117	c.689G>A	c.(688-690)CGC>CAC	p.R230H	EMILIN1_uc010eyq.1_Missense_Mutation_p.R230H|EMILIN1_uc002rik.3_5'Flank	NM_007046	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1 precursor	230	Potential.				cell adhesion	collagen				pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
CAD	790	broad.mit.edu	37	2	27458193	27458193	+	Silent	SNP	C	T	T	rs150732650		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27458193C>T	uc002rji.2	+	24	4029	c.3867C>T	c.(3865-3867)GCC>GCT	p.A1289A	CAD_uc010eyw.2_Silent_p.A1226A	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	1289	CPSase B.|CPSase (Carbamoyl-phosphate synthase).				'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)													---	---	---	---
CAD	790	broad.mit.edu	37	2	27460609	27460609	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27460609C>T	uc002rji.2	+	29	4749	c.4587C>T	c.(4585-4587)TGC>TGT	p.C1529C	CAD_uc010eyw.2_Silent_p.C1466C	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	1529	DHOase (dihydroorotase).				'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)													---	---	---	---
TRIM54	57159	broad.mit.edu	37	2	27505617	27505617	+	Silent	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27505617T>G	uc002rjo.2	+	1	18	c.18T>G	c.(16-18)GGT>GGG	p.G6G	TRIM54_uc002rjn.2_Silent_p.G6G	NM_187841	NP_912730	Q9BYV2	TRI54_HUMAN	ring finger protein 30 isoform 2	6					cell differentiation|microtubule-based process|multicellular organismal development|negative regulation of microtubule depolymerization	microtubule|sarcomere	signal transducer activity|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ZNF513	130557	broad.mit.edu	37	2	27601032	27601032	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27601032A>G	uc002rkk.2	-	4	1206	c.1006T>C	c.(1006-1008)TGT>CGT	p.C336R	ZNF513_uc002rkj.2_Missense_Mutation_p.C274R	NM_144631	NP_653232	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	336					regulation of transcription, DNA-dependent|response to stimulus|retina development in camera-type eye|transcription, DNA-dependent|visual perception	nucleus	transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KRTCAP3	200634	broad.mit.edu	37	2	27665636	27665636	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27665636C>T	uc002rks.2	+						KRTCAP3_uc010ylr.1_Intron|KRTCAP3_uc002rkt.2_Intron	NM_173853	NP_776252			keratinocyte associated protein 3							integral to membrane					0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SRD5A2	6716	broad.mit.edu	37	2	31805786	31805786	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31805786G>A	uc002rnw.1	-	2	256	c.185C>T	c.(184-186)GCG>GTG	p.A62V		NM_000348	NP_000339	P31213	S5A2_HUMAN	3-oxo-5 alpha-steroid 4-dehydrogenase 2	62					androgen biosynthetic process|cell differentiation|cell-cell signaling|male gonad development	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|sterol 5-alpha reductase activity				0	Acute lymphoblastic leukemia(172;0.155)				Azelaic Acid(DB00548)|Dutasteride(DB01126)													---	---	---	---
YIPF4	84272	broad.mit.edu	37	2	32526480	32526480	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32526480A>G	uc002rok.2	+	5	780	c.513A>G	c.(511-513)ATA>ATG	p.I171M		NM_032312	NP_115688	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4	171	Helical; (Potential).					endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32626574	32626574	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32626574T>C	uc010ezu.2	+	8	1435	c.1301T>C	c.(1300-1302)GTA>GCA	p.V434A		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	434					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37255949	37255949	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37255949C>T	uc002rpp.1	-	23	3572	c.3476G>A	c.(3475-3477)CGG>CAG	p.R1159Q		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1159							binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
DHX57	90957	broad.mit.edu	37	2	39053105	39053105	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39053105G>A	uc002rrf.2	-	16	2997	c.2898C>T	c.(2896-2898)GGC>GGT	p.G966G	DHX57_uc002rrd.3_Silent_p.G350G|DHX57_uc002rre.2_Silent_p.G399G	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	966	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)																---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40392055	40392055	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40392055C>T	uc002rrx.2	-	7	2132	c.2108G>A	c.(2107-2109)CGC>CAC	p.R703H	uc002rrw.2_Intron|SLC8A1_uc002rry.2_Missense_Mutation_p.R698H|SLC8A1_uc002rrz.2_Missense_Mutation_p.R690H|SLC8A1_uc002rsa.2_Missense_Mutation_p.R667H|SLC8A1_uc002rsd.3_Missense_Mutation_p.R667H	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	703	Cytoplasmic (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
KCNG3	170850	broad.mit.edu	37	2	42720441	42720441	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42720441C>A	uc002rsn.2	-	1	797	c.201G>T	c.(199-201)TCG>TCT	p.S67S	MTA3_uc002rso.1_5'Flank|KCNG3_uc002rsm.2_Silent_p.S67S	NM_133329	NP_579875	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G,	67	Cytoplasmic (Potential).					endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1																		---	---	---	---
THADA	63892	broad.mit.edu	37	2	43458106	43458106	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43458106C>A	uc002rsw.3	-	38	6195	c.5843G>T	c.(5842-5844)AGA>ATA	p.R1948I	THADA_uc010far.2_Missense_Mutation_p.R1143I|THADA_uc002rsx.3_Missense_Mutation_p.R1948I|THADA_uc002rsy.3_RNA	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1948							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
PREPL	9581	broad.mit.edu	37	2	44548581	44548581	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44548581T>C	uc002ruf.2	-	14	2133	c.2098A>G	c.(2098-2100)ACA>GCA	p.T700A	PREPL_uc002rug.2_Missense_Mutation_p.T634A|PREPL_uc002ruh.2_Missense_Mutation_p.T638A|PREPL_uc010fax.2_Missense_Mutation_p.T700A|PREPL_uc002rui.3_Missense_Mutation_p.T611A|PREPL_uc002ruj.1_Missense_Mutation_p.T611A|PREPL_uc002ruk.1_Missense_Mutation_p.T700A	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C	700					proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
EPAS1	2034	broad.mit.edu	37	2	46596995	46596995	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46596995A>C	uc002ruv.2	+	7	1297	c.809A>C	c.(808-810)GAG>GCG	p.E270A		NM_001430	NP_001421	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	270	PAS 2.				angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding			ovary(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
FBXO11	80204	broad.mit.edu	37	2	48046210	48046210	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48046210T>C	uc010fbl.2	-	15	1667	c.1553A>G	c.(1552-1554)AAG>AGG	p.K518R	FBXO11_uc002rwe.2_Missense_Mutation_p.K518R|FBXO11_uc002rwf.2_Missense_Mutation_p.K518R|FBXO11_uc002rwg.1_Missense_Mutation_p.K518R|FBXO11_uc010fbk.2_Missense_Mutation_p.K26R	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1	602	PbH1 10.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55544493	55544493	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55544493G>A	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc002ryu.2_Intron|CCDC88A_uc002rys.2_Intron|CCDC88A_uc002ryw.2_Intron|CCDC88A_uc010fby.1_Intron	NM_001135597	NP_001129069			coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4																		---	---	---	---
BCL11A	53335	broad.mit.edu	37	2	60688143	60688143	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60688143C>T	uc002sae.1	-	4	2132	c.1904G>A	c.(1903-1905)CGC>CAC	p.R635H	BCL11A_uc002sab.2_Missense_Mutation_p.R635H|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Missense_Mutation_p.R304H|BCL11A_uc010ypj.1_Missense_Mutation_p.R601H|BCL11A_uc002sad.1_Missense_Mutation_p.R483H|BCL11A_uc002saf.1_Missense_Mutation_p.R601H	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	635					negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)					T	IGH@	B-CLL								---	---	---	---
PUS10	150962	broad.mit.edu	37	2	61175289	61175289	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61175289C>T	uc010fci.2	-	16	1400	c.1340G>A	c.(1339-1341)CGC>CAC	p.R447H	PUS10_uc002sao.2_Missense_Mutation_p.R447H|PUS10_uc010ypk.1_Missense_Mutation_p.R224H	NM_144709	NP_653310	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	447	RNA binding thumb loop (Potential).				pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61456674	61456674	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61456674A>G	uc002sbe.2	-						USP34_uc002sbf.2_Intron	NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
GKN2	200504	broad.mit.edu	37	2	69173591	69173591	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69173591G>A	uc002sfa.2	-	5	426	c.317C>T	c.(316-318)GCT>GTT	p.A106V	GKN2_uc002sfb.3_Missense_Mutation_p.A106V	NM_182536	NP_872342	Q86XP6	GKN2_HUMAN	trefoil factor interactions(z) 1 precursor	106	BRICHOS.					extracellular region					0																		---	---	---	---
ASPRV1	151516	broad.mit.edu	37	2	70187970	70187970	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70187970A>G	uc002sfz.3	-	1	1428	c.851T>C	c.(850-852)ATT>ACT	p.I284T		NM_152792	NP_690005	Q53RT3	APRV1_HUMAN	aspartic peptidase, retroviral-like 1 precursor	284	Peptidase A2.|Extracellular (Potential).				protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1																		---	---	---	---
ADD2	119	broad.mit.edu	37	2	70890743	70890743	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70890743G>A	uc002sgz.2	-	16	2460	c.1995C>T	c.(1993-1995)GGC>GGT	p.G665G	ADD2_uc010fds.1_RNA|ADD2_uc002sgy.2_3'UTR|ADD2_uc002sha.2_Silent_p.G359G|ADD2_uc002sgx.2_3'UTR	NM_001617	NP_001608	P35612	ADDB_HUMAN	adducin 2 isoform a	665					actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3																		---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73762058	73762058	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73762058G>A	uc002sje.1	+	14	10003	c.9892G>A	c.(9892-9894)GTT>ATT	p.V3298I	ALMS1_uc002sjf.1_Missense_Mutation_p.V3254I|ALMS1_uc002sjg.2_Missense_Mutation_p.V2684I|ALMS1_uc002sjh.1_Missense_Mutation_p.V2684I|ALMS1_uc010fev.1_Missense_Mutation_p.V113I	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3296					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
ACTG2	72	broad.mit.edu	37	2	74140773	74140773	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74140773G>T	uc002sjw.2	+	6	735	c.613G>T	c.(613-615)GCT>TCT	p.A205S	ACTG2_uc010fey.2_Missense_Mutation_p.A205S|ACTG2_uc010yrn.1_Missense_Mutation_p.A162S	NM_001615	NP_001606	P63267	ACTH_HUMAN	actin, gamma 2 propeptide	205					muscle contraction	cytoskeleton|cytosol	ATP binding				0																		---	---	---	---
HTRA2	27429	broad.mit.edu	37	2	74758134	74758134	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74758134A>G	uc002smi.1	+	3	1410	c.808A>G	c.(808-810)ATC>GTC	p.I270V	AUP1_uc002sme.2_5'Flank|AUP1_uc002smf.2_5'Flank|AUP1_uc002smg.2_5'Flank|AUP1_uc002smh.2_5'Flank|AUP1_uc010yrx.1_5'Flank|AUP1_uc010yry.1_5'Flank|HTRA2_uc002smj.1_Intron|HTRA2_uc002smk.1_Missense_Mutation_p.I270V|HTRA2_uc002sml.1_Missense_Mutation_p.I270V|HTRA2_uc002smm.1_Missense_Mutation_p.I11V|HTRA2_uc002smn.1_Missense_Mutation_p.I11V|HTRA2_uc010ffl.2_Missense_Mutation_p.I11V	NM_013247	NP_037379	O43464	HTRA2_HUMAN	HtrA serine peptidase 2 isoform 1 preproprotein	270	Serine protease.				apoptosis|proteolysis|response to stress	CD40 receptor complex|endoplasmic reticulum membrane|internal side of plasma membrane|mitochondrial intermembrane space|mitochondrial membrane|nucleus	serine-type endopeptidase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75917175	75917175	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75917175C>T	uc002sno.2	-	9	1389	c.1259G>A	c.(1258-1260)GGG>GAG	p.G420E	C2orf3_uc010ffs.2_5'UTR|C2orf3_uc002snn.2_Missense_Mutation_p.G251E|C2orf3_uc010fft.2_Missense_Mutation_p.G95E	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936	420					negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75921541	75921541	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75921541T>C	uc002sno.2	-	6	976	c.846A>G	c.(844-846)CTA>CTG	p.L282L	C2orf3_uc010ffs.2_5'UTR|C2orf3_uc002snn.2_Silent_p.L113L|C2orf3_uc010fft.2_5'UTR	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936	282	Potential.				negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80085151	80085151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80085151G>A	uc010ysh.1	+	3	316	c.311G>A	c.(310-312)CGG>CAG	p.R104Q	CTNNA2_uc010yse.1_Missense_Mutation_p.R104Q|CTNNA2_uc010ysf.1_Missense_Mutation_p.R104Q|CTNNA2_uc010ysg.1_Missense_Mutation_p.R104Q	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	104					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
SUCLG1	8802	broad.mit.edu	37	2	84658722	84658722	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84658722G>A	uc002son.2	-	7	928	c.735C>T	c.(733-735)AAC>AAT	p.N245N		NM_003849	NP_003840	P53597	SUCA_HUMAN	succinate-CoA ligase, GDP-forming alpha subunit	245					tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)													---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84780090	84780090	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84780090A>G	uc010fgb.2	+	10	1671	c.1534A>G	c.(1534-1536)ATG>GTG	p.M512V	DNAH6_uc002soo.2_Missense_Mutation_p.M91V|DNAH6_uc002sop.2_Missense_Mutation_p.M91V	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	512	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
MRPL35	51318	broad.mit.edu	37	2	86433347	86433347	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86433347T>C	uc002srg.3	+	2	220	c.162T>C	c.(160-162)GTT>GTC	p.V54V	MRPL35_uc002srf.3_Silent_p.V54V	NM_016622	NP_057706	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35 isoform a	54					translation	mitochondrial ribosome	structural constituent of ribosome				0																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87000484	87000484	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87000484T>C	uc010ytm.1	+	9	1503	c.1126T>C	c.(1126-1128)TAC>CAC	p.Y376H	RMND5A_uc002srs.3_Intron|RMND5A_uc002srr.2_Missense_Mutation_p.Y376H	NM_022780	NP_073617	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog	376										ovary(1)|skin(1)	2																		---	---	---	---
CD8A	925	broad.mit.edu	37	2	87017507	87017507	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87017507G>A	uc002srt.2	-	2	1236	c.347C>T	c.(346-348)TCG>TTG	p.S116L	RMND5A_uc002srs.3_Intron|CD8A_uc002srv.2_Missense_Mutation_p.S116L|CD8A_uc010ytn.1_Missense_Mutation_p.S157L|CD8A_uc002sru.2_Missense_Mutation_p.S116L	NM_001768	NP_001759	P01732	CD8A_HUMAN	CD8 antigen alpha polypeptide isoform 1	116	Ig-like V-type.|Extracellular (Potential).				antigen processing and presentation|regulation of immune response|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane|T cell receptor complex	coreceptor activity|MHC class I protein binding			ovary(1)	1																		---	---	---	---
SMYD1	150572	broad.mit.edu	37	2	88409944	88409944	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88409944C>A	uc002ssr.2	+	10	1388	c.1386C>A	c.(1384-1386)CGC>CGA	p.R462R	SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_Silent_p.R158R	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	462					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
EIF2AK3	9451	broad.mit.edu	37	2	88857427	88857427	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88857427G>T	uc002stc.3	-	17	3380	c.3178C>A	c.(3178-3180)CCA>ACA	p.P1060T		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	1060	Cytoplasmic (Potential).|Protein kinase.				activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	89266235	89266235	+	RNA	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89266235T>C	uc010ytr.1	-	94		c.7457A>G			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90044327	90044327	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90044327T>C	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
ZAP70	7535	broad.mit.edu	37	2	98351887	98351887	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98351887C>T	uc002syd.1	+	10	1464	c.1257C>T	c.(1255-1257)GGC>GGT	p.G419G	ZAP70_uc010yvf.1_3'UTR|ZAP70_uc002sye.1_Silent_p.G309G|ZAP70_uc002syf.1_Silent_p.G112G	NM_001079	NP_001070	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	419	Protein kinase.				immune response|intracellular protein kinase cascade|positive thymic T cell selection|T cell receptor signaling pathway	cytosol|T cell receptor complex	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98928817	98928817	+	3'UTR	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98928817G>A	uc002syo.2	+	28					VWA3B_uc002syr.1_3'UTR|VWA3B_uc002sys.2_RNA	NM_144992	NP_659429			von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99688331	99688331	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99688331A>G	uc002szg.3	-	12	1573	c.945T>C	c.(943-945)TGT>TGC	p.C315C	TSGA10_uc002szh.3_Silent_p.C315C|TSGA10_uc002szi.3_Silent_p.C315C|TSGA10_uc010fin.1_Silent_p.C315C|TSGA10_uc010yvn.1_Missense_Mutation_p.Y297H	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10	315					spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101554312	101554312	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101554312T>C	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509			neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101587538	101587538	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101587538T>C	uc002tap.1	+	12	1426	c.1140_splice	c.e12+2	p.K380_splice	NPAS2_uc010yvt.1_Splice_Site_p.K445_splice	NM_002518	NP_002509			neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101591353	101591353	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101591353C>T	uc002tap.1	+	13	1515	c.1229C>T	c.(1228-1230)GCG>GTG	p.A410V	NPAS2_uc010yvt.1_Missense_Mutation_p.A475V|NPAS2_uc010fit.1_5'UTR	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	410					central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
IL1R2	7850	broad.mit.edu	37	2	102636284	102636284	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102636284T>C	uc002tbm.2	+						IL1R2_uc002tbn.2_Intron|IL1R2_uc002tbo.1_Intron	NM_004633	NP_004624			interleukin 1 receptor, type II precursor						immune response	integral to membrane|plasma membrane	interleukin-1, Type II, blocking receptor activity			ovary(1)|breast(1)	2					Anakinra(DB00026)													---	---	---	---
MRPS9	64965	broad.mit.edu	37	2	105709992	105709992	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105709992A>C	uc002tcn.3	+	9	893	c.825A>C	c.(823-825)AAA>AAC	p.K275N		NM_182640	NP_872578	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9 precursor	275					DNA damage response, detection of DNA damage|translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0																		---	---	---	---
MALL	7851	broad.mit.edu	37	2	110849314	110849314	+	Missense_Mutation	SNP	C	T	T	rs141817647		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110849314C>T	uc002tfk.2	-	2	913	c.139G>A	c.(139-141)GCC>ACC	p.A47T	MALL_uc010fju.2_Intron	NM_005434	NP_005425	Q13021	MALL_HUMAN	mal, T-cell differentiation protein-like	47	MARVEL.				cholesterol homeostasis	clathrin-coated vesicle|Golgi membrane|integral to membrane|membrane raft|plasma membrane	protein binding			ovary(1)|skin(1)	2				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)														---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112779029	112779029	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112779029G>A	uc002thk.1	+	17	2342	c.2220G>A	c.(2218-2220)GCG>GCA	p.A740A	MERTK_uc002thl.1_Silent_p.A564A	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor	740	Protein kinase.|Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9																		---	---	---	---
IL1F10	84639	broad.mit.edu	37	2	113831989	113831989	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113831989C>T	uc002tiu.2	+	3	191	c.116C>T	c.(115-117)GCA>GTA	p.A39V	IL1F10_uc002tiv.2_Missense_Mutation_p.A39V|IL1F10_uc002tiw.2_5'Flank	NM_173161	NP_775184	Q8WWZ1	IL1FA_HUMAN	interleukin 1 family, member 10	39						extracellular space	cytokine activity|interleukin-1 receptor antagonist activity			ovary(1)	1																		---	---	---	---
STEAP3	55240	broad.mit.edu	37	2	120012379	120012379	+	Silent	SNP	G	A	A	rs144510346		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120012379G>A	uc002tlp.2	+	5	1297	c.1140G>A	c.(1138-1140)CCG>CCA	p.P380P	STEAP3_uc002tlq.2_Silent_p.P390P|STEAP3_uc002tlr.2_Silent_p.P380P|STEAP3_uc010fle.2_Silent_p.P380P	NM_018234	NP_060704	Q658P3	STEA3_HUMAN	dudulin 2 isoform b	380	Ferric oxidoreductase.|Cytoplasmic (Potential).				apoptosis|cell cycle|cellular iron ion homeostasis|protein secretion|transferrin transport|transmembrane transport	endosome membrane|integral to membrane|multivesicular body	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122165438	122165438	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122165438G>T	uc002tnc.2	-						CLASP1_uc010yyv.1_Intron|CLASP1_uc002tmz.2_Intron|CLASP1_uc002tna.2_Intron|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
ERCC3	2071	broad.mit.edu	37	2	128030479	128030479	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128030479T>A	uc002toh.1	-	11	1884	c.1789A>T	c.(1789-1791)AAG>TAG	p.K597*	ERCC3_uc002toe.1_Nonsense_Mutation_p.K352*|ERCC3_uc002tof.1_Nonsense_Mutation_p.K533*|ERCC3_uc002tog.1_Nonsense_Mutation_p.K533*	NM_000122	NP_000113	P19447	ERCC3_HUMAN	excision repair cross-complementing rodent	597	Helicase C-terminal.				cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding			ovary(2)|lung(2)|breast(2)|kidney(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)				Mis|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128480887	128480887	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128480887T>C	uc002tpg.1	-	12	1414	c.1231A>G	c.(1231-1233)ATG>GTG	p.M411V		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	411	WD 7.				postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
SAP130	79595	broad.mit.edu	37	2	128707456	128707456	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128707456G>A	uc002tpp.2	-	17	2889	c.2757C>T	c.(2755-2757)GAC>GAT	p.D919D	SAP130_uc002tpn.2_Silent_p.D679D|SAP130_uc002tpo.2_Silent_p.D699D|SAP130_uc010fmd.2_Silent_p.D954D	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	919	Interactions with SIN3A and HDAC1.				histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)														---	---	---	---
SAP130	79595	broad.mit.edu	37	2	128707900	128707900	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128707900T>C	uc002tpp.2	-	16	2610	c.2478A>G	c.(2476-2478)CTA>CTG	p.L826L	SAP130_uc002tpn.2_Silent_p.L586L|SAP130_uc002tpo.2_Silent_p.L606L|SAP130_uc010fmd.2_Silent_p.L861L	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	826	Pro-rich.				histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)														---	---	---	---
UGGT1	56886	broad.mit.edu	37	2	128930143	128930143	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128930143T>G	uc002tps.2	+						UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505			UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
CCDC74A	90557	broad.mit.edu	37	2	132285715	132285715	+	Nonsense_Mutation	SNP	C	T	T	rs146378866		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132285715C>T	uc002tta.2	+	1	224	c.172C>T	c.(172-174)CAG>TAG	p.Q58*	CCDC74A_uc010fnb.1_Nonsense_Mutation_p.Q58*|CCDC74A_uc002ttb.2_Nonsense_Mutation_p.Q58*	NM_138770	NP_620125	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	58	Potential.									skin(1)	1																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133531439	133531439	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133531439T>A	uc002ttp.2	-	16	5452	c.5078A>T	c.(5077-5079)GAG>GTG	p.E1693V	NCKAP5_uc002ttq.2_Missense_Mutation_p.E374V	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	1693							protein binding				0																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133542288	133542288	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133542288T>A	uc002ttp.2	-	14	2470	c.2096A>T	c.(2095-2097)AAT>ATT	p.N699I	NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	699							protein binding				0																		---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136393667	136393667	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136393667C>T	uc002tuo.2	+	11	1187	c.817C>T	c.(817-819)CGT>TGT	p.R273C	R3HDM1_uc010fni.2_Missense_Mutation_p.R271C|R3HDM1_uc002tup.2_Missense_Mutation_p.R217C|R3HDM1_uc010zbh.1_Missense_Mutation_p.R105C	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	273							nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138378192	138378192	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138378192A>C	uc002tva.1	+	19	3608	c.3608A>C	c.(3607-3609)AAG>ACG	p.K1203T	THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
ZEB2	9839	broad.mit.edu	37	2	145147143	145147143	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145147143T>C	uc002tvu.2	-	10	4000	c.3520A>G	c.(3520-3522)ACG>GCG	p.T1174A	ZEB2_uc002tvv.2_Missense_Mutation_p.T1168A|ZEB2_uc010zbm.1_Missense_Mutation_p.T1145A|ZEB2_uc010fnp.2_Intron	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	1174	Glu-rich (acidic).					cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
ZEB2	9839	broad.mit.edu	37	2	145157490	145157490	+	Missense_Mutation	SNP	C	T	T	rs141793065	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145157490C>T	uc002tvu.2	-	8	1744	c.1264G>A	c.(1264-1266)GCC>ACC	p.A422T	ZEB2_uc002tvv.2_Missense_Mutation_p.A416T|ZEB2_uc010zbm.1_Missense_Mutation_p.A393T|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Missense_Mutation_p.A451T	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	422						cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152410392	152410392	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152410392C>T	uc010fnx.2	-	98	14664	c.14473G>A	c.(14473-14475)GAC>AAC	p.D4825N	NEB_uc002txr.2_Missense_Mutation_p.D1248N	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	4825	Nebulin 132.				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)														---	---	---	---
STAM2	10254	broad.mit.edu	37	2	153004561	153004561	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153004561C>G	uc002tyc.3	-	4	627	c.277G>C	c.(277-279)GTA>CTA	p.V93L	STAM2_uc010foa.1_Missense_Mutation_p.V93L|STAM2_uc002tyd.2_Missense_Mutation_p.V93L	NM_005843	NP_005834	O75886	STAM2_HUMAN	signal transducing adaptor molecule 2	93	VHS.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.22)														---	---	---	---
NR4A2	4929	broad.mit.edu	37	2	157182788	157182788	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157182788T>A	uc002tyz.3	-	7	1836	c.1414A>T	c.(1414-1416)AGG>TGG	p.R472W	NR4A2_uc002tyx.3_Missense_Mutation_p.R409W|NR4A2_uc010zcf.1_Missense_Mutation_p.R472W|NR4A2_uc010zcg.1_Intron	NM_006186	NP_006177	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	472					cellular response to extracellular stimulus|dopaminergic neuron differentiation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus	nucleoplasm	sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
GALNT5	11227	broad.mit.edu	37	2	158115241	158115241	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158115241T>C	uc002tzg.2	+	1	902	c.647T>C	c.(646-648)TTG>TCG	p.L216S	GALNT5_uc010zci.1_RNA	NM_014568	NP_055383	Q7Z7M9	GALT5_HUMAN	N-acetylgalactosaminyltransferase 5	216	Lumenal (Potential).				glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)|skin(1)	4																		---	---	---	---
GALNT5	11227	broad.mit.edu	37	2	158152294	158152294	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158152294A>G	uc002tzg.2	+	4	2116	c.1861A>G	c.(1861-1863)AAT>GAT	p.N621D	GALNT5_uc010zci.1_RNA	NM_014568	NP_055383	Q7Z7M9	GALT5_HUMAN	N-acetylgalactosaminyltransferase 5	621	Lumenal (Potential).				glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)|skin(1)	4																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160086950	160086950	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160086950C>T	uc002uag.2	+	27	5287	c.5013C>T	c.(5011-5013)AGC>AGT	p.S1671S	TANC1_uc010zcm.1_3'UTR|TANC1_uc010fon.2_Silent_p.S515S	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1671	Ser-rich.					cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160252270	160252270	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160252270A>G	uc002uao.2	-						BAZ2B_uc002uap.2_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160295518	160295518	+	Splice_Site	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160295518A>G	uc002uao.2	-	7	1252	c.900_splice	c.e7+1	p.Q300_splice	BAZ2B_uc002uap.2_Splice_Site_p.Q298_splice|BAZ2B_uc002uas.1_Splice_Site_p.Q237_splice|BAZ2B_uc002uau.1_Splice_Site_p.Q298_splice|BAZ2B_uc002uaq.1_Splice_Site_p.Q228_splice|BAZ2B_uc002uat.3_Missense_Mutation_p.V238A|BAZ2B_uc010fop.1_Splice_Site_p.Q298_splice	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
SLC4A10	57282	broad.mit.edu	37	2	162719492	162719492	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162719492T>G	uc002ubx.3	+	6	870	c.686T>G	c.(685-687)CTC>CGC	p.L229R	SLC4A10_uc010fpa.1_Missense_Mutation_p.L241R|SLC4A10_uc010zcr.1_RNA|SLC4A10_uc002uby.3_Missense_Mutation_p.L229R|SLC4A10_uc010zcs.1_Missense_Mutation_p.L240R	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	229	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5																		---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	165984367	165984367	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165984367T>C	uc002ucx.2	-	18	3659	c.3167A>G	c.(3166-3168)GAA>GGA	p.E1056G	SCN3A_uc002ucy.2_Missense_Mutation_p.E1007G|SCN3A_uc002ucz.2_Missense_Mutation_p.E1007G|SCN3A_uc002uda.1_Missense_Mutation_p.E876G|SCN3A_uc002udb.1_Missense_Mutation_p.E876G	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1056						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168100923	168100923	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168100923A>C	uc002udx.2	+	8	3039	c.3021A>C	c.(3019-3021)GAA>GAC	p.E1007D	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.E832D|XIRP2_uc010fpq.2_Missense_Mutation_p.E785D|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	832					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168114632	168114632	+	3'UTR	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168114632T>C	uc002udx.2	+	10					XIRP2_uc010fpn.2_Silent_p.L559L|XIRP2_uc010fpo.2_Silent_p.L526L|XIRP2_uc010fpp.2_Silent_p.L526L|XIRP2_uc010fpq.2_3'UTR|XIRP2_uc010fpr.2_Silent_p.L304L	NM_152381	NP_689594			xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
GORASP2	26003	broad.mit.edu	37	2	171806085	171806085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171806085G>A	uc002ugk.2	+	3	321	c.181G>A	c.(181-183)GCA>ACA	p.A61T	GORASP2_uc002ugj.2_5'UTR|GORASP2_uc010zdl.1_Missense_Mutation_p.A73T|GORASP2_uc010zdm.1_Missense_Mutation_p.A17T|GORASP2_uc002ugl.2_5'UTR	NM_015530	NP_056345	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2	61	PDZ.					Golgi membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
DLX1	1745	broad.mit.edu	37	2	172952935	172952935	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172952935T>C	uc002uhl.2	+	3	916	c.718T>C	c.(718-720)TGG>CGG	p.W240R	DLX1_uc002uhm.2_3'UTR	NM_178120	NP_835221	P56177	DLX1_HUMAN	distal-less homeobox 1 isoform 1	240						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
CHRNA1	1134	broad.mit.edu	37	2	175613330	175613330	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175613330T>G	uc002ujd.2	-	9	1373	c.1295A>C	c.(1294-1296)AAG>ACG	p.K432T	uc002uiw.2_Intron|CHRNA1_uc002uje.2_Missense_Mutation_p.K407T	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a	432	Cytoplasmic.				muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)|skin(1)	4																OREG0015079	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HOXD13	3239	broad.mit.edu	37	2	176957879	176957879	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176957879G>A	uc002ukf.1	+	1	348	c.261G>A	c.(259-261)TCG>TCA	p.S87S		NM_000523	NP_000514	P35453	HXD13_HUMAN	homeobox D13	87	Poly-Ser.				skeletal system development|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0526)|READ - Rectum adenocarcinoma(9;0.0678)				T	NUP98	AML*								---	---	---	---
HOXD1	3231	broad.mit.edu	37	2	177054070	177054070	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177054070G>A	uc002ukv.3	+	1	764	c.541G>A	c.(541-543)GCA>ACA	p.A181T	HOXD1_uc010fqy.2_Missense_Mutation_p.A181T|HOXD1_uc010zez.1_Missense_Mutation_p.A181T	NM_024501	NP_078777	Q9GZZ0	HXD1_HUMAN	homeobox D1	181						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)														---	---	---	---
MTX2	10651	broad.mit.edu	37	2	177161579	177161579	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177161579T>C	uc002ukx.2	+						MTX2_uc002ukw.2_Intron	NM_006554	NP_006545			metaxin 2						protein targeting to mitochondrion	mitochondrial outer membrane				ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00365)|Epithelial(96;0.0654)|all cancers(119;0.181)															---	---	---	---
TTC30B	150737	broad.mit.edu	37	2	178415909	178415909	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178415909T>C	uc002uln.2	-	1	1616	c.1583A>G	c.(1582-1584)GAA>GGA	p.E528G	TTC30B_uc010zfc.1_Missense_Mutation_p.E300G	NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	528	Potential.				cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)															---	---	---	---
RBM45	129831	broad.mit.edu	37	2	178985972	178985972	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178985972C>T	uc002ulv.2	+	5	831	c.739C>T	c.(739-741)CGC>TGC	p.R247C		NM_152945	NP_694453	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	249					cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179396497	179396497	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179396497G>A	uc010zfg.1	-	307	97365	c.97141C>T	c.(97141-97143)CGC>TGC	p.R32381C	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R26076C|TTN_uc010zfi.1_Missense_Mutation_p.R26009C|TTN_uc010zfj.1_Missense_Mutation_p.R25884C|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33308							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179403902	179403902	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179403902C>T	uc010zfg.1	-	302	91280	c.91056G>A	c.(91054-91056)CGG>CGA	p.R30352R	uc002umo.2_RNA|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.R24047R|TTN_uc010zfi.1_Silent_p.R23980R|TTN_uc010zfj.1_Silent_p.R23855R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	31279							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179436451	179436451	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179436451A>C	uc010zfg.1	-	275	66928	c.66704T>G	c.(66703-66705)GTT>GGT	p.V22235G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V15930G|TTN_uc010zfi.1_Missense_Mutation_p.V15863G|TTN_uc010zfj.1_Missense_Mutation_p.V15738G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23162							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179436480	179436480	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179436480T>C	uc010zfg.1	-	275	66899	c.66675A>G	c.(66673-66675)TCA>TCG	p.S22225S	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.S15920S|TTN_uc010zfi.1_Silent_p.S15853S|TTN_uc010zfj.1_Silent_p.S15728S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23152							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179462439	179462439	+	Missense_Mutation	SNP	C	T	T	rs142841000	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179462439C>T	uc010zfg.1	-	243	49890	c.49666G>A	c.(49666-49668)GTC>ATC	p.V16556I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V10251I|TTN_uc010zfi.1_Missense_Mutation_p.V10184I|TTN_uc010zfj.1_Missense_Mutation_p.V10059I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17483							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179484765	179484765	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179484765T>C	uc010zfg.1	-	198	38899	c.38675A>G	c.(38674-38676)TAT>TGT	p.Y12892C	TTN_uc010zfh.1_Missense_Mutation_p.Y6587C|TTN_uc010zfi.1_Missense_Mutation_p.Y6520C|TTN_uc010zfj.1_Missense_Mutation_p.Y6395C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13819							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179485466	179485466	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179485466T>C	uc010zfg.1	-	196	38391	c.38167A>G	c.(38167-38169)AGT>GGT	p.S12723G	TTN_uc010zfh.1_Missense_Mutation_p.S6418G|TTN_uc010zfi.1_Missense_Mutation_p.S6351G|TTN_uc010zfj.1_Missense_Mutation_p.S6226G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13650							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179532356	179532356	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179532356G>A	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_Intron	NM_133378	NP_596869			titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179604130	179604130	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179604130T>C	uc010zfh.1	-	46	13541	c.13317A>G	c.(13315-13317)ACA>ACG	p.T4439T	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Silent_p.T4372T|TTN_uc010zfj.1_Silent_p.T4247T|TTN_uc002umz.1_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179640650	179640650	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179640650T>C	uc010zfg.1	-	28	6165	c.5941A>G	c.(5941-5943)AGG>GGG	p.R1981G	TTN_uc010zfh.1_Missense_Mutation_p.R1935G|TTN_uc010zfi.1_Missense_Mutation_p.R1935G|TTN_uc010zfj.1_Missense_Mutation_p.R1935G|TTN_uc002unb.2_Missense_Mutation_p.R1981G|uc002unc.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1981							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
DNAJC10	54431	broad.mit.edu	37	2	183601076	183601076	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183601076G>C	uc002uow.1	+	11	1365	c.950G>C	c.(949-951)GGA>GCA	p.G317A	DNAJC10_uc002uox.1_RNA|DNAJC10_uc002uoy.1_RNA|DNAJC10_uc002uoz.1_Intron|DNAJC10_uc010fro.1_Intron	NM_018981	NP_061854	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	317					apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)															---	---	---	---
CALCRL	10203	broad.mit.edu	37	2	188211132	188211132	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188211132A>G	uc002upv.3	-						CALCRL_uc010frt.2_Intron	NM_005795	NP_005786			calcitonin receptor-like precursor							integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)															---	---	---	---
MFSD6	54842	broad.mit.edu	37	2	191362251	191362251	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191362251G>A	uc002urz.2	+	7	2302	c.1978G>A	c.(1978-1980)GAT>AAT	p.D660N	MFSD6_uc010zge.1_Missense_Mutation_p.D122N	NM_017694	NP_060164	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing	660					transmembrane transport	integral to membrane				ovary(2)	2																		---	---	---	---
GLS	2744	broad.mit.edu	37	2	191819482	191819482	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191819482T>C	uc002usf.2	+	17	2055	c.1791T>C	c.(1789-1791)GGT>GGC	p.G597G	GLS_uc002ush.2_Silent_p.G258G|GLS_uc010zgi.1_Missense_Mutation_p.S200P|GLS_uc010zgj.1_Silent_p.G102G	NM_014905	NP_055720	O94925	GLSK_HUMAN	glutaminase precursor	597	ANK.				cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197990131	197990131	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197990131C>T	uc002uuc.2	-	6	691	c.524G>A	c.(523-525)CGT>CAT	p.R175H	ANKRD44_uc002utz.3_5'Flank|ANKRD44_uc002uua.1_Missense_Mutation_p.R150H|ANKRD44_uc002uub.2_Missense_Mutation_p.R175H|ANKRD44_uc010zgw.1_Missense_Mutation_p.R103H	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	175	ANK 6.						protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
SGOL2	151246	broad.mit.edu	37	2	201438699	201438699	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201438699A>G	uc002uvw.2	+	7	3743	c.3630A>G	c.(3628-3630)ATA>ATG	p.I1210M	SGOL2_uc010zhd.1_Missense_Mutation_p.I1210M|SGOL2_uc010zhe.1_Missense_Mutation_p.I1210M	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2 isoform 1	1210					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)|skin(2)	4																		---	---	---	---
NRP2	8828	broad.mit.edu	37	2	206592625	206592625	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206592625G>A	uc002vaw.2	+	7	1792	c.1001G>A	c.(1000-1002)CGC>CAC	p.R334H	NRP2_uc002vat.2_Missense_Mutation_p.R334H|NRP2_uc002vau.2_Missense_Mutation_p.R334H|NRP2_uc002vav.2_Missense_Mutation_p.R334H|NRP2_uc002vax.2_Missense_Mutation_p.R334H|NRP2_uc002vay.2_Missense_Mutation_p.R334H|NRP2_uc010fud.2_Missense_Mutation_p.R334H	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	334	Extracellular (Potential).|F5/8 type C 1.				angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
C2orf80	389073	broad.mit.edu	37	2	209049730	209049730	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209049730C>T	uc002vcr.2	-	3	240	c.68G>A	c.(67-69)CGG>CAG	p.R23Q		NM_001099334	NP_001092804	Q0P641	CB080_HUMAN	hypothetical protein LOC389073	23										skin(1)	1																		---	---	---	---
LANCL1	10314	broad.mit.edu	37	2	211336712	211336712	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211336712C>T	uc010zjh.1	-	3	245	c.170G>A	c.(169-171)CGG>CAG	p.R57Q	LANCL1_uc002ved.2_Missense_Mutation_p.R57Q|LANCL1_uc010fuq.2_Missense_Mutation_p.R57Q	NM_001136574	NP_001130046	O43813	LANC1_HUMAN	lanthionine synthetase C-like protein 1	57						cytoplasm|integral to plasma membrane|microtubule cytoskeleton|nucleus	catalytic activity|G-protein coupled receptor activity|glutathione binding|low-density lipoprotein particle receptor binding|SH3 domain binding|zinc ion binding				0				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)														---	---	---	---
FN1	2335	broad.mit.edu	37	2	216272919	216272919	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216272919C>T	uc002vfa.2	-	17	2696	c.2430G>A	c.(2428-2430)GCG>GCA	p.A810A	FN1_uc002vfb.2_Silent_p.A810A|FN1_uc002vfc.2_Silent_p.A810A|FN1_uc002vfd.2_Silent_p.A810A|FN1_uc002vfe.2_Silent_p.A810A|FN1_uc002vff.2_Silent_p.A810A|FN1_uc002vfg.2_Silent_p.A810A|FN1_uc002vfh.2_Silent_p.A810A|FN1_uc002vfi.2_Silent_p.A810A|FN1_uc002vfj.2_Silent_p.A810A	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	810					acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
FN1	2335	broad.mit.edu	37	2	216288950	216288950	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216288950G>A	uc002vfa.2	-	8	1401	c.1135C>T	c.(1135-1137)CGA>TGA	p.R379*	FN1_uc002vfb.2_Nonsense_Mutation_p.R379*|FN1_uc002vfc.2_Nonsense_Mutation_p.R379*|FN1_uc002vfd.2_Nonsense_Mutation_p.R379*|FN1_uc002vfe.2_Nonsense_Mutation_p.R379*|FN1_uc002vff.2_Nonsense_Mutation_p.R379*|FN1_uc002vfg.2_Nonsense_Mutation_p.R379*|FN1_uc002vfh.2_Nonsense_Mutation_p.R379*|FN1_uc002vfi.2_Nonsense_Mutation_p.R379*|FN1_uc002vfj.2_Nonsense_Mutation_p.R379*|FN1_uc002vfl.2_Nonsense_Mutation_p.R379*	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	379	Fibronectin type-II 1.|Collagen-binding.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
VIL1	7429	broad.mit.edu	37	2	219294217	219294217	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219294217G>A	uc002via.2	+						VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Intron|VIL1_uc002vic.1_Intron	NM_007127	NP_009058			villin 1						actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
DES	1674	broad.mit.edu	37	2	220283174	220283174	+	5'UTR	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220283174G>A	uc002vll.2	+	1						NM_001927	NP_001918			desmin						cytoskeleton organization|muscle filament sliding|regulation of heart contraction	cytosol|Z disc	protein binding|structural constituent of cytoskeleton			central_nervous_system(2)	2		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)												OREG0003984	type=REGULATORY REGION|Gene=DES|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
ACCN4	55515	broad.mit.edu	37	2	220401863	220401863	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220401863C>T	uc002vma.2	+	6	1643	c.1629C>T	c.(1627-1629)GGC>GGT	p.G543G	ACCN4_uc002vlz.2_Silent_p.G562G|ACCN4_uc002vmb.2_Silent_p.G216G	NM_182847	NP_878267	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 2	543	Extracellular (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)														---	---	---	---
SERPINE2	5270	broad.mit.edu	37	2	224866464	224866464	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224866464C>T	uc002vnu.2	-	2	397	c.154G>A	c.(154-156)GTG>ATG	p.V52M	SERPINE2_uc002vnt.2_Missense_Mutation_p.V52M|SERPINE2_uc010zlr.1_Missense_Mutation_p.V64M|SERPINE2_uc002vnv.2_Missense_Mutation_p.V52M	NM_006216	NP_006207	P07093	GDN_HUMAN	plasminogen activator inhibitor type 1, member 2	52					negative regulation of blood coagulation|negative regulation of plasminogen activation|negative regulation of platelet aggregation|positive regulation of astrocyte differentiation|regulation of cell migration	cytosol|extracellular matrix|extracellular space|extrinsic to external side of plasma membrane|neuromuscular junction|platelet alpha granule	heparin binding|receptor binding|serine-type endopeptidase inhibitor activity			breast(2)|ovary(1)|central_nervous_system(1)	4		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225729333	225729333	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225729333T>G	uc010fwz.1	-	13	1778	c.1539A>C	c.(1537-1539)AAA>AAC	p.K513N	DOCK10_uc002vob.2_Missense_Mutation_p.K507N|DOCK10_uc002vod.1_Missense_Mutation_p.K513N	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	513							GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
WDR69	164781	broad.mit.edu	37	2	228755966	228755966	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228755966T>C	uc002vpn.1	+						WDR69_uc010zlw.1_Intron|WDR69_uc002vpo.1_Intron	NM_178821	NP_849143			WD repeat domain 69											breast(1)	1		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;1.22e-10)|all cancers(144;8.11e-08)|Lung(261;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0148)														---	---	---	---
DNER	92737	broad.mit.edu	37	2	230312192	230312192	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230312192G>A	uc002vpv.2	-	8	1473	c.1326C>T	c.(1324-1326)AAC>AAT	p.N442N	DNER_uc010zly.1_Silent_p.N170N	NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing	442	Extracellular (Potential).|EGF-like 6.				central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
C2orf57	165100	broad.mit.edu	37	2	232457920	232457920	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232457920A>G	uc002vrz.2	+	1	309	c.258A>G	c.(256-258)ACA>ACG	p.T86T		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	86										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)														---	---	---	---
MIR1244	100302285	broad.mit.edu	37	2	232578077	232578077	+	RNA	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232578077T>C	hsa-mir-1244-1|MI0006379	+			c.54T>C			PTMA_uc002vsb.3_3'UTR|PTMA_uc002vsc.3_3'UTR|PTMA_uc010zmf.1_RNA																	0																		---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	232894801	232894801	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232894801T>C	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vsn.1_Intron|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596			DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)														---	---	---	---
CHRNG	1146	broad.mit.edu	37	2	233408082	233408082	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233408082G>A	uc002vsx.1	+	8	924	c.903G>A	c.(901-903)GCG>GCA	p.A301A	CHRNG_uc010fye.1_Silent_p.A249A	NM_005199	NP_005190	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma	301					muscle contraction	cell junction|postsynaptic membrane	acetylcholine receptor activity				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233748147	233748147	+	Missense_Mutation	SNP	G	A	A	rs141871026	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233748147G>A	uc002vts.2	-	12	1879	c.1631C>T	c.(1630-1632)CCG>CTG	p.P544L	NGEF_uc010zmm.1_Missense_Mutation_p.P267L|NGEF_uc010fyg.1_Missense_Mutation_p.P452L	NM_019850	NP_062824	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	544	PH.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233759467	233759467	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233759467G>A	uc002vts.2	-	6	1236	c.988C>T	c.(988-990)CGG>TGG	p.R330W	NGEF_uc010zmm.1_Missense_Mutation_p.R53W|NGEF_uc010fyg.1_Missense_Mutation_p.R238W|NGEF_uc002vtt.2_Missense_Mutation_p.R238W	NM_019850	NP_062824	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	330	DH.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233785159	233785159	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233785159C>T	uc002vts.2	-	5	911	c.663G>A	c.(661-663)GAG>GAA	p.E221E	NGEF_uc010fyg.1_Silent_p.E129E|NGEF_uc002vtt.2_Silent_p.E129E	NM_019850	NP_062824	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	221	Poly-Glu.|Regulatory region; modulates activity toward RHOA, RAC1 and CDC42 (By similarity).				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
UGT1A1	54658	broad.mit.edu	37	2	234668959	234668959	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234668959G>A	uc002vvb.2	+	1	41	c.26G>A	c.(25-27)CGC>CAC	p.R9H	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A5_uc002vuw.2_Intron|UGT1A4_uc010zna.1_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Intron|UGT1A3_uc002vuy.2_Intron|UGT1A9_uc002vva.2_Intron|UGT1A1_uc010znc.1_Missense_Mutation_p.R9H	NM_000463	NP_000454	P22309	UD11_HUMAN	UDP glycosyltransferase 1 family, polypeptide A1	9					bilirubin conjugation|digestion|estrogen metabolic process|flavone metabolic process|heme catabolic process	endoplasmic reticulum membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding|steroid binding			central_nervous_system(1)|skin(1)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Adenine(DB00173)|Diclofenac(DB00586)|Estradiol(DB00783)|Ezetimibe(DB00973)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Rifampin(DB01045)|Troglitazone(DB00197)											OREG0003837	type=REGULATORY REGION|Gene=UGT1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
HJURP	55355	broad.mit.edu	37	2	234749838	234749838	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234749838T>C	uc002vvg.2	-	8	1654	c.1588A>G	c.(1588-1590)ACA>GCA	p.T530A	HJURP_uc010znd.1_Missense_Mutation_p.T469A|HJURP_uc010zne.1_Missense_Mutation_p.T438A	NM_018410	NP_060880	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	530					cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238287272	238287272	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238287272G>A	uc002vwl.2	-						COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwq.2_Intron|COL6A3_uc002vwr.2_Intron|COL6A3_uc010znk.1_Intron	NM_004369	NP_004360			alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
ANKMY1	51281	broad.mit.edu	37	2	241439944	241439944	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241439944C>A	uc002vyz.1	-	13	2527	c.2298G>T	c.(2296-2298)AAG>AAT	p.K766N	ANKMY1_uc002vza.1_Missense_Mutation_p.K542N|ANKMY1_uc010fzd.1_Missense_Mutation_p.K855N|ANKMY1_uc002vzb.1_Missense_Mutation_p.K527N|ANKMY1_uc002vzc.1_Missense_Mutation_p.K545N|ANKMY1_uc002vzd.1_Missense_Mutation_p.K589N	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	766	ANK 7.						zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242076435	242076435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242076435G>A	uc002wao.1	-	7	1213	c.1121C>T	c.(1120-1122)ACG>ATG	p.T374M	PASK_uc010zol.1_Missense_Mutation_p.T188M|PASK_uc010zom.1_Missense_Mutation_p.T339M|PASK_uc010fzl.1_Missense_Mutation_p.T374M|PASK_uc010zon.1_Missense_Mutation_p.T155M|PASK_uc002wap.2_5'Flank|PASK_uc002waq.2_Missense_Mutation_p.T374M	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	374	PAS 2.				regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
THAP4	51078	broad.mit.edu	37	2	242524055	242524055	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242524055T>C	uc002wbt.2	-	6	1923	c.1700A>G	c.(1699-1701)CAT>CGT	p.H567R	THAP4_uc002wbs.2_Missense_Mutation_p.H155R	NM_015963	NP_057047	Q8WY91	THAP4_HUMAN	THAP domain containing 4 isoform 1	567		Iron (heme axial ligand).					DNA binding|metal ion binding				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)														---	---	---	---
GAL3ST2	64090	broad.mit.edu	37	2	242741320	242741320	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242741320G>A	uc002wcj.1	+	3	375	c.244G>A	c.(244-246)GTG>ATG	p.V82M		NM_022134	NP_071417	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	82	Lumenal (Potential).				biosynthetic process	Golgi cisterna membrane|integral to membrane	galactosylceramide sulfotransferase activity				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)														---	---	---	---
TRNT1	51095	broad.mit.edu	37	3	3189636	3189636	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3189636A>G	uc003bpp.3	+	8	1205	c.1103A>G	c.(1102-1104)TAC>TGC	p.Y368C	TRNT1_uc010hbv.2_Missense_Mutation_p.Y348C|TRNT1_uc003bpm.2_RNA	NM_182916	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	368					protein targeting to mitochondrion|tRNA 3'-end processing	mitochondrion	ATP binding|tRNA adenylyltransferase activity|tRNA binding				0				Epithelial(13;0.00226)|OV - Ovarian serous cystadenocarcinoma(96;0.00592)|all cancers(10;0.011)														---	---	---	---
GRM7	2917	broad.mit.edu	37	3	6903533	6903533	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6903533T>C	uc003bqm.2	+	1	732	c.458T>C	c.(457-459)GTG>GCG	p.V153A	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Missense_Mutation_p.V153A|GRM7_uc003bql.2_Missense_Mutation_p.V153A	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	153	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7621037	7621037	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7621037C>T	uc003bqm.2	+	8	2718	c.2444C>T	c.(2443-2445)GCG>GTG	p.A815V	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Missense_Mutation_p.A815V|GRM7_uc003bql.2_Missense_Mutation_p.A815V|GRM7_uc003bqn.1_Missense_Mutation_p.A398V|GRM7_uc010hch.1_Missense_Mutation_p.A326V	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	815	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9488921	9488921	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9488921T>G	uc003brt.2	+	14	2147	c.1712T>G	c.(1711-1713)GTT>GGT	p.V571G	SETD5_uc003brs.1_Missense_Mutation_p.V552G|SETD5_uc003bru.2_Missense_Mutation_p.V473G|SETD5_uc003brv.2_Missense_Mutation_p.V460G|SETD5_uc010hck.2_Missense_Mutation_p.V53G|SETD5_uc003brx.2_Missense_Mutation_p.V240G	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	571										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10886039	10886039	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10886039G>A	uc003bvz.2	+							NM_014229	NP_055044			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
SLC6A1	6529	broad.mit.edu	37	3	11059010	11059010	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11059010C>T	uc010hdq.2	+	3	524	c.113C>T	c.(112-114)GCG>GTG	p.A38V		NM_003042	NP_003033	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter	38	Cytoplasmic (Potential).				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)|skin(1)	2		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Cocaine(DB00907)|Tiagabine(DB00906)													---	---	---	---
ATG7	10533	broad.mit.edu	37	3	11389392	11389392	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11389392G>T	uc003bwc.2	+	12	1284	c.1167G>T	c.(1165-1167)AAG>AAT	p.K389N	ATG7_uc003bwd.2_Missense_Mutation_p.K389N|ATG7_uc011aum.1_Missense_Mutation_p.K350N	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a	389					autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1																		---	---	---	---
CAND2	23066	broad.mit.edu	37	3	12858373	12858373	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12858373C>T	uc003bxk.2	+	10	1991	c.1942C>T	c.(1942-1944)CCC>TCC	p.P648S	CAND2_uc003bxj.2_Missense_Mutation_p.P555S	NM_001162499	NP_001155971	O75155	CAND2_HUMAN	TBP-interacting protein isoform 1	648	HEAT 14.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			skin(3)|pancreas(1)	4																		---	---	---	---
TMEM43	79188	broad.mit.edu	37	3	14175298	14175298	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14175298T>C	uc003byk.2	+	7	826	c.572T>C	c.(571-573)TTC>TCC	p.F191S	TMEM43_uc003byl.1_Missense_Mutation_p.F71S	NM_024334	NP_077310	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	191	Lumenal (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|nuclear inner membrane				ovary(1)	1																		---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18391030	18391030	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18391030G>A	uc003cbh.2	-	11	3659	c.1924C>T	c.(1924-1926)CGA>TGA	p.R642*	SATB1_uc003cbi.2_Nonsense_Mutation_p.R674*|SATB1_uc003cbj.2_Nonsense_Mutation_p.R642*	NM_002971	NP_002962	Q01826	SATB1_HUMAN	special AT-rich sequence binding protein 1	642					cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18436246	18436246	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18436246G>T	uc003cbh.2	-	7	2649	c.914C>A	c.(913-915)CCT>CAT	p.P305H	SATB1_uc003cbi.2_Missense_Mutation_p.P305H|SATB1_uc003cbj.2_Missense_Mutation_p.P305H	NM_002971	NP_002962	Q01826	SATB1_HUMAN	special AT-rich sequence binding protein 1	305					cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
SGOL1	151648	broad.mit.edu	37	3	20225109	20225109	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20225109T>C	uc003cbs.2	-	3	517	c.330A>G	c.(328-330)GAA>GAG	p.E110E	SGOL1_uc003cbr.2_Silent_p.E110E|SGOL1_uc010hfa.2_Silent_p.E110E|SGOL1_uc003cbt.2_Silent_p.E110E|SGOL1_uc003cbu.2_Silent_p.E110E|SGOL1_uc003cbv.2_Silent_p.E110E|SGOL1_uc003cbw.2_Silent_p.E110E|SGOL1_uc003cbx.2_Silent_p.E110E|SGOL1_uc003cby.2_Silent_p.E110E|SGOL1_uc003cbz.2_Silent_p.E110E|SGOL1_uc003cca.2_Silent_p.E110E|SGOL1_uc003ccb.2_Silent_p.E110E|SGOL1_uc003ccc.2_Silent_p.E110E	NM_001012410	NP_001012410	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 isoform A2	110	Necessary for interaction with PPP2CA and PPP2R1A.				attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase	centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole	protein binding				0																		---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29781233	29781233	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29781233A>G	uc003cel.2	+	5	652	c.422A>G	c.(421-423)AAC>AGC	p.N141S	RBMS3_uc003cek.2_Missense_Mutation_p.N141S|RBMS3_uc010hfq.2_Missense_Mutation_p.N141S|RBMS3_uc003cem.2_Missense_Mutation_p.N140S|RBMS3_uc010hfr.2_Missense_Mutation_p.N141S	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting	141	RRM 2.					cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
TRIM71	131405	broad.mit.edu	37	3	32915308	32915308	+	Splice_Site	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32915308A>G	uc003cff.2	+	2	916	c.853_splice	c.e2-2	p.V285_splice		NM_001039111	NP_001034200			tripartite motif-containing 71						multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
STAC	6769	broad.mit.edu	37	3	36484874	36484874	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36484874T>G	uc003cgh.1	+	2	169	c.130T>G	c.(130-132)TCA>GCA	p.S44A	STAC_uc010hgd.1_RNA|STAC_uc011aya.1_Missense_Mutation_p.S44A	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	44					intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
STAC	6769	broad.mit.edu	37	3	36484922	36484922	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36484922T>G	uc003cgh.1	+	2	217	c.178T>G	c.(178-180)TTC>GTC	p.F60V	STAC_uc010hgd.1_RNA|STAC_uc011aya.1_Missense_Mutation_p.F60V	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	60					intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
DLEC1	9940	broad.mit.edu	37	3	38163883	38163883	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38163883A>G	uc003cho.1	+	37	5269	c.5248A>G	c.(5248-5250)ATG>GTG	p.M1750V	DLEC1_uc003chp.1_Silent_p.T1708T|DLEC1_uc010hgv.1_Missense_Mutation_p.M1753V|DLEC1_uc003chr.1_Missense_Mutation_p.M821V|DLEC1_uc003chs.1_Silent_p.T265T	NM_007335	NP_031361	Q9Y238	DLEC1_HUMAN	deleted in lung and esophageal cancer 1 isoform	1750					negative regulation of cell proliferation	cytoplasm				ovary(2)|pancreas(2)|central_nervous_system(2)|skin(2)|breast(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)														---	---	---	---
SLC22A14	9389	broad.mit.edu	37	3	38357177	38357177	+	Missense_Mutation	SNP	G	A	A	rs114657493	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38357177G>A	uc010hhc.1	+	9	1549	c.1507G>A	c.(1507-1509)GCT>ACT	p.A503T	SLC22A14_uc003cib.2_Missense_Mutation_p.A503T|SLC22A14_uc011ayo.1_RNA	NM_004803	NP_004794	Q9Y267	S22AE_HUMAN	organic cation transporter like 4	503	Helical; (Potential).					integral to plasma membrane	organic cation transmembrane transporter activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)														---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38651314	38651314	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38651314C>T	uc003cio.2	-	7	1039	c.845G>A	c.(844-846)CGC>CAC	p.R282H	SCN5A_uc003cin.2_Missense_Mutation_p.R282H|SCN5A_uc003cil.3_Missense_Mutation_p.R282H|SCN5A_uc010hhi.2_Missense_Mutation_p.R282H|SCN5A_uc010hhk.2_Missense_Mutation_p.R282H|SCN5A_uc011ayr.1_Missense_Mutation_p.R282H|SCN5A_uc010hhl.1_Missense_Mutation_p.R105H	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	282			R -> H (in BRS1).		blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)													---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38888742	38888742	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38888742A>C	uc011ays.1	-	26	5018	c.4819T>G	c.(4819-4821)TTC>GTC	p.F1607V		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	1607					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38962583	38962583	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38962583A>G	uc011ays.1	-	6	1075	c.876T>C	c.(874-876)AGT>AGC	p.S292S		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	292	I.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
XIRP1	165904	broad.mit.edu	37	3	39230437	39230437	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39230437T>G	uc003cjk.1	-	2	721	c.500A>C	c.(499-501)GAG>GCG	p.E167A	XIRP1_uc003cji.2_Missense_Mutation_p.E167A|XIRP1_uc003cjj.2_Intron	NM_194293	NP_919269	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	167							actin binding			ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41746635	41746635	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41746635C>T	uc003ckv.3	-	27	2896	c.2695G>A	c.(2695-2697)GCA>ACA	p.A899T		NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	899							ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
SEC22C	9117	broad.mit.edu	37	3	42594846	42594846	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42594846A>G	uc003clj.2	-	7	924	c.806T>C	c.(805-807)CTG>CCG	p.L269P	SEC22C_uc003clh.2_Intron|SEC22C_uc011azo.1_Intron|SEC22C_uc010hic.2_Intron|SEC22C_uc003cli.2_Intron	NM_032970	NP_116752	Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C	269	Helical; (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.222)														---	---	---	---
ZBTB47	92999	broad.mit.edu	37	3	42700986	42700986	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42700986G>T	uc003clu.1	+	1	113	c.11G>T	c.(10-12)CGG>CTG	p.R4L		NM_145166	NP_660149	Q9UFB7	ZBT47_HUMAN	zinc finger protein 651	4					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.216)														---	---	---	---
CLEC3B	7123	broad.mit.edu	37	3	45067848	45067848	+	5'UTR	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45067848C>T	uc003cok.3	+	1						NM_003278	NP_003269			C-type lectin domain family 3, member B						skeletal system development	extracellular space	protein binding|sugar binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00863)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LTF	4057	broad.mit.edu	37	3	46497793	46497793	+	Silent	SNP	G	A	A	rs145234336		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46497793G>A	uc003cpq.2	-	3	341	c.303C>T	c.(301-303)TAC>TAT	p.Y101Y	LTF_uc003fzr.2_Silent_p.Y57Y|LTF_uc010hjh.2_Silent_p.Y101Y|LTF_uc003cpr.2_Silent_p.Y88Y	NM_002343	NP_002334	P02788	TRFL_HUMAN	lactotransferrin precursor	101	Transferrin-like 1.				cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)													---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47030358	47030358	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47030358C>T	uc003cqp.2	+	3	346	c.167C>T	c.(166-168)CCG>CTG	p.P56L	NBEAL2_uc003cqq.1_Missense_Mutation_p.P49L	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	56							binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)														---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47045470	47045470	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47045470C>T	uc003cqp.2	+						NBEAL2_uc010hjm.1_Intron|NBEAL2_uc010hjn.1_Intron|NBEAL2_uc010hjo.1_5'Flank	NM_015175	NP_055990			neurobeachin-like 2								binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)														---	---	---	---
SCAP	22937	broad.mit.edu	37	3	47466983	47466983	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47466983G>A	uc003crh.1	-	8	1284	c.1029C>T	c.(1027-1029)CTC>CTT	p.L343L	SCAP_uc011baz.1_Silent_p.L88L|SCAP_uc003crg.2_Intron	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein	343	Lumenal (By similarity).|SSD.				cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48620089	48620089	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48620089G>A	uc003ctz.2	-							NM_000094	NP_000085			alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
UQCRC1	7384	broad.mit.edu	37	3	48638477	48638477	+	Silent	SNP	C	T	T	rs141289289		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48638477C>T	uc003cub.1	-	8	942	c.897G>A	c.(895-897)CCG>CCA	p.P299P	UQCRC1_uc003cua.1_Silent_p.P184P|UQCRC1_uc003cuc.1_Silent_p.P300P|UQCRC1_uc003cud.1_Silent_p.P299P	NM_003365	NP_003356	P31930	QCR1_HUMAN	ubiquinol-cytochrome c reductase core protein I	299					aerobic respiration|proteolysis		metalloendopeptidase activity|ubiquinol-cytochrome-c reductase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	Atovaquone(DB01117)													---	---	---	---
P4HTM	54681	broad.mit.edu	37	3	49042575	49042575	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49042575T>C	uc003cvg.2	+						P4HTM_uc003cvh.2_Missense_Mutation_p.M390T|WDR6_uc011bbx.1_5'Flank|WDR6_uc003cvj.2_5'Flank|WDR6_uc011bby.1_5'Flank|WDR6_uc010hkn.2_5'Flank|WDR6_uc011bbz.1_5'Flank	NM_177939	NP_808808			hypoxia-inducible factor prolyl 4-hydroxylase							endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)|pancreas(1)	2					Vitamin C(DB00126)													---	---	---	---
USP19	10869	broad.mit.edu	37	3	49149205	49149205	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49149205C>T	uc003cwd.1	-	20	2797	c.2636G>A	c.(2635-2637)CGC>CAC	p.R879H	USP19_uc003cwa.2_Missense_Mutation_p.R687H|USP19_uc003cvz.3_Missense_Mutation_p.R982H|USP19_uc011bcg.1_Missense_Mutation_p.R970H|USP19_uc003cwb.2_Intron|USP19_uc003cwc.1_Missense_Mutation_p.R637H|USP19_uc011bch.1_Missense_Mutation_p.R980H	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	879	Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
LAMB2	3913	broad.mit.edu	37	3	49167318	49167318	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49167318A>C	uc003cwe.2	-	10	1658	c.1359T>G	c.(1357-1359)CGT>CGG	p.R453R	LAMB2_uc003cwf.1_Silent_p.R453R	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	453	Laminin EGF-like 3.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
LAMB2	3913	broad.mit.edu	37	3	49168877	49168877	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49168877T>C	uc003cwe.2	-	6	948	c.649_splice	c.e6-1	p.V217_splice	LAMB2_uc003cwf.1_Splice_Site_p.V217_splice	NM_002292	NP_002283			laminin, beta 2 precursor						cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
BSN	8927	broad.mit.edu	37	3	49699821	49699821	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49699821C>A	uc003cxe.3	+	6	10657	c.10543C>A	c.(10543-10545)CGC>AGC	p.R3515S		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	3515					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)														---	---	---	---
MON1A	84315	broad.mit.edu	37	3	49949267	49949267	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49949267G>A	uc003cxz.2	-	3	722	c.596C>T	c.(595-597)ACG>ATG	p.T199M	MON1A_uc003cya.2_Intron|MON1A_uc003cyb.2_Intron	NM_032355	NP_115731	Q86VX9	MON1A_HUMAN	MON1 homolog A isoform a	102							protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50211525	50211525	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50211525T>C	uc003cyj.2	+	4	512	c.314T>C	c.(313-315)GTG>GCG	p.V105A	SEMA3F_uc003cyk.2_Missense_Mutation_p.V105A	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	105	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50219807	50219807	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50219807C>T	uc003cyj.2	+	8	932	c.734C>T	c.(733-735)ACG>ATG	p.T245M	SEMA3F_uc003cyk.2_Missense_Mutation_p.T214M	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	245	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
GNAI2	2771	broad.mit.edu	37	3	50289879	50289879	+	Missense_Mutation	SNP	C	T	T	rs138213627		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50289879C>T	uc003cyq.1	+	3	333	c.212C>T	c.(211-213)GCG>GTG	p.A71V	GNAI2_uc003cyo.1_Missense_Mutation_p.A55V|GNAI2_uc003cyp.1_Missense_Mutation_p.A55V|GNAI2_uc010hlg.1_5'UTR|GNAI2_uc011bdn.1_Missense_Mutation_p.A34V|GNAI2_uc003cyr.1_5'UTR	NM_002070	NP_002061	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein),	71					adenosine receptor signaling pathway|cell cycle|cell division|gamma-aminobutyric acid signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|platelet activation|response to nutrient|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)														---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50418494	50418494	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50418494C>T	uc003daq.2	-	7	754	c.716G>A	c.(715-717)CGC>CAC	p.R239H	CACNA2D2_uc003dap.2_Missense_Mutation_p.R239H	NM_006030	NP_006021	Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha	239	Extracellular (Potential).				energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)													---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51669660	51669660	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51669660C>T	uc011bdt.1	+	9	1319	c.1194C>T	c.(1192-1194)GGC>GGT	p.G398G	RAD54L2_uc003dbh.2_5'UTR|RAD54L2_uc011bdu.1_Silent_p.G92G|RAD54L2_uc003dbj.2_5'UTR	NM_015106	NP_055921	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2	398	Helicase ATP-binding.					nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)														---	---	---	---
GRM2	2912	broad.mit.edu	37	3	51746690	51746690	+	Missense_Mutation	SNP	G	A	A	rs143196180		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51746690G>A	uc010hlv.2	+	3	891	c.652G>A	c.(652-654)GAG>AAG	p.E218K	GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_RNA	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	218	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
PCBP4	57060	broad.mit.edu	37	3	51994171	51994171	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51994171G>A	uc003dcd.1	-						PCBP4_uc003dcb.1_Intron|PCBP4_uc003dcc.1_Missense_Mutation_p.R107W|PCBP4_uc003dce.1_Intron|PCBP4_uc003dcf.1_Intron|PCBP4_uc003dcg.1_Intron|PCBP4_uc003dch.1_Intron|PCBP4_uc003dci.1_Intron|PCBP4_uc003dcj.1_Intron|PCBP4_uc003dck.1_Intron|PCBP4_uc003dcl.1_Intron	NM_033010	NP_127503			poly(rC) binding protein 4 isoform c							cytoplasm|ribonucleoprotein complex	DNA binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
PCBP4	57060	broad.mit.edu	37	3	51994571	51994571	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51994571C>T	uc003dcd.1	-	4	622	c.226G>A	c.(226-228)GTC>ATC	p.V76I	PCBP4_uc003dcb.1_Missense_Mutation_p.V42I|PCBP4_uc003dcc.1_Missense_Mutation_p.V42I|PCBP4_uc003dce.1_Missense_Mutation_p.V76I|PCBP4_uc003dcf.1_Missense_Mutation_p.V76I|PCBP4_uc003dcg.1_Missense_Mutation_p.V42I|PCBP4_uc003dch.1_Missense_Mutation_p.V76I|PCBP4_uc003dci.1_5'UTR|PCBP4_uc003dcj.1_Missense_Mutation_p.V76I|PCBP4_uc003dck.1_Missense_Mutation_p.V76I|PCBP4_uc003dcl.1_Missense_Mutation_p.V76I	NM_033010	NP_127503	P57723	PCBP4_HUMAN	poly(rC) binding protein 4 isoform c	76						cytoplasm|ribonucleoprotein complex	DNA binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
ABHD14B	84836	broad.mit.edu	37	3	52004061	52004061	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52004061G>T	uc003dcm.2	-	3	1239	c.351C>A	c.(349-351)TCC>TCA	p.S117S	PCBP4_uc003dch.1_5'Flank|PCBP4_uc003dci.1_5'Flank|PCBP4_uc003dcj.1_5'Flank|PCBP4_uc003dck.1_5'Flank|ABHD14B_uc010hly.2_Intron|ABHD14B_uc011bdy.1_Silent_p.S117S|ABHD14B_uc003dcn.2_Silent_p.S117S|ABHD14B_uc011bdz.1_Silent_p.S117S	NM_032750	NP_116139	Q96IU4	ABHEB_HUMAN	abhydrolase domain containing 14B	117						cytoplasm|nucleus	hydrolase activity				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000548)|KIRC - Kidney renal clear cell carcinoma(197;0.00072)														---	---	---	---
ALAS1	211	broad.mit.edu	37	3	52245348	52245348	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52245348G>T	uc003dcy.1	+	10	1717	c.1380G>T	c.(1378-1380)CTG>CTT	p.L460L	ALAS1_uc003dcz.1_Silent_p.L460L|ALAS1_uc011bec.1_Silent_p.L477L	NM_000688	NP_000679	P13196	HEM1_HUMAN	5-aminolevulinate synthase 1 precursor	460					heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
WDR82	80335	broad.mit.edu	37	3	52294398	52294398	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52294398T>C	uc003ddl.2	-						WDR82_uc003ddk.2_Intron	NM_025222	NP_079498			WD repeat domain 82						histone H3-K4 methylation	chromatin|PTW/PP1 phosphatase complex|Set1C/COMPASS complex	protein binding				0				BRCA - Breast invasive adenocarcinoma(193;2.67e-05)|Kidney(197;0.00198)|KIRC - Kidney renal clear cell carcinoma(197;0.00223)|OV - Ovarian serous cystadenocarcinoma(275;0.246)														---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52379598	52379598	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52379598C>T	uc011bef.1	+	10	1793	c.1532C>T	c.(1531-1533)ACG>ATG	p.T511M	DNAH1_uc003ddt.1_Missense_Mutation_p.T511M	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	511	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
GNL3	26354	broad.mit.edu	37	3	52720100	52720100	+	5'UTR	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52720100A>C	uc003dfd.2	+	1					PBRM1_uc003dey.2_5'Flank|GNL3_uc011beh.1_RNA|GNL3_uc003dfe.2_5'UTR|GNL3_uc003dff.2_Intron	NM_014366	NP_055181			guanine nucleotide binding protein-like 3						regulation of cell proliferation	nucleolus	GTP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53781379	53781379	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53781379G>A	uc003dgv.3	+	26	3381	c.3218G>A	c.(3217-3219)CGT>CAT	p.R1073H	CACNA1D_uc003dgu.3_Missense_Mutation_p.R1093H|CACNA1D_uc003dgy.3_Missense_Mutation_p.R1073H|CACNA1D_uc003dgw.3_Missense_Mutation_p.R740H|CACNA1D_uc003dgx.1_Missense_Mutation_p.R221H	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1073	Extracellular (Potential).|III.				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58134519	58134519	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58134519G>A	uc003djj.2	+	36	6196	c.6031G>A	c.(6031-6033)GGC>AGC	p.G2011S	FLNB_uc010hne.2_Missense_Mutation_p.G2042S|FLNB_uc003djk.2_Missense_Mutation_p.G2000S|FLNB_uc010hnf.2_Missense_Mutation_p.G1987S|FLNB_uc003djl.2_Missense_Mutation_p.G1831S|FLNB_uc003djm.2_Missense_Mutation_p.G1818S|FLNB_uc010hng.1_5'Flank	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	2011	Filamin 19.|Interaction with the cytoplasmic tail of GP1BA.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
PDHB	5162	broad.mit.edu	37	3	58414198	58414198	+	Splice_Site	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58414198A>G	uc003dkf.3	-	9	963	c.934_splice	c.e9+1	p.G312_splice	PDHB_uc003dke.3_Splice_Site_p.G270_splice|PDHB_uc003dkg.3_Splice_Site_p.G294_splice|PDHB_uc010hnl.2_Silent_p.G294G|PDHB_uc011bff.1_Splice_Site_p.G294_splice	NM_000925	NP_000916			pyruvate dehydrogenase (lipoamide) beta						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate|tricarboxylic acid cycle	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	NADH(DB00157)|Pyruvic acid(DB00119)													---	---	---	---
LMOD3	56203	broad.mit.edu	37	3	69168508	69168508	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69168508C>T	uc003dns.2	-	2	1207	c.998G>A	c.(997-999)TGT>TAT	p.C333Y	LMOD3_uc003dnt.2_Missense_Mutation_p.C333Y	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	333						cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)														---	---	---	---
LMOD3	56203	broad.mit.edu	37	3	69171477	69171477	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69171477C>T	uc003dns.2	-	1	270	c.61G>A	c.(61-63)GAT>AAT	p.D21N	LMOD3_uc003dnt.2_Missense_Mutation_p.D21N	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	21	Potential.					cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)														---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77530243	77530243	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77530243T>G	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933			roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79174622	79174622	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79174622A>C	uc003dqe.2	-	3	364	c.156T>G	c.(154-156)AAT>AAG	p.N52K		NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	52	Extracellular (Potential).				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
NFKBIZ	64332	broad.mit.edu	37	3	101575980	101575980	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101575980C>T	uc003dvp.2	+	10	2003	c.1888C>T	c.(1888-1890)CGC>TGC	p.R630C	NFKBIZ_uc003dvo.2_Missense_Mutation_p.R530C|NFKBIZ_uc010hpo.2_Missense_Mutation_p.R530C|NFKBIZ_uc003dvq.2_Missense_Mutation_p.R508C	NM_031419	NP_113607	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene	630	Interaction with NFKB1/p50 (By similarity).|ANK 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2																		---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	102171933	102171933	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102171933A>T	uc003dvs.1	+	10	1159	c.277A>T	c.(277-279)ATT>TTT	p.I93F	ZPLD1_uc003dvt.1_Missense_Mutation_p.I109F|ZPLD1_uc011bhg.1_Missense_Mutation_p.I93F	NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	93	ZP.|Extracellular (Potential).					integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108220600	108220600	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108220600G>A	uc003dxa.1	-	4	415	c.358C>T	c.(358-360)CTG>TTG	p.L120L		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	120	Myosin head-like.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113128021	113128021	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113128021T>G	uc003eae.1	-	7	868	c.822A>C	c.(820-822)GAA>GAC	p.E274D		NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2	274	WD 2.									central_nervous_system(1)	1																		---	---	---	---
SIDT1	54847	broad.mit.edu	37	3	113327350	113327350	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113327350C>T	uc003eak.2	+	17	2338	c.1687C>T	c.(1687-1689)CAT>TAT	p.H563Y	SIDT1_uc011bif.1_RNA|SIDT1_uc003eaj.1_Missense_Mutation_p.H563Y|SIDT1_uc011big.1_Missense_Mutation_p.H316Y|SIDT1_uc011bih.1_RNA|SIDT1_uc011bii.1_Missense_Mutation_p.H16Y	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor	563	Extracellular (Potential).					integral to membrane				ovary(3)|pancreas(1)|skin(1)	5																		---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121416792	121416792	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121416792T>A	uc003eei.3	-	13	2689	c.2563A>T	c.(2563-2565)AGG>TGG	p.R855W	GOLGB1_uc010hrc.2_Missense_Mutation_p.R860W|GOLGB1_uc003eej.3_Missense_Mutation_p.R821W|GOLGB1_uc011bjm.1_Missense_Mutation_p.R741W|GOLGB1_uc010hrd.1_Missense_Mutation_p.R819W	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	855	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
HSPBAP1	79663	broad.mit.edu	37	3	122474162	122474162	+	Missense_Mutation	SNP	C	T	T	rs115965208	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122474162C>T	uc003efu.1	-	5	809	c.686G>A	c.(685-687)CGT>CAT	p.R229H	HSPBAP1_uc003efv.1_3'UTR	NM_024610	NP_078886	Q96EW2	HBAP1_HUMAN	Hspb associated protein 1	229	JmjC.					cytoplasm				ovary(1)|lung(1)	2				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124351289	124351289	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124351289C>T	uc003ehg.2	+	35	5326	c.5199C>T	c.(5197-5199)AGC>AGT	p.S1733S	KALRN_uc003ehi.2_Silent_p.S106S|KALRN_uc003ehk.2_Silent_p.S36S|KALRN_uc003ehj.2_Silent_p.S36S	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1733					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124413236	124413236	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124413236T>C	uc003ehg.2	+	53	7590	c.7463T>C	c.(7462-7464)GTG>GCG	p.V2488A	KALRN_uc003ehk.2_Missense_Mutation_p.V791A	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	2487	Ig-like C2-type.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125824741	125824741	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125824741G>T	uc003eim.1	-	22	2671	c.2481C>A	c.(2479-2481)GCC>GCA	p.A827A	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Silent_p.A726A|ALDH1L1_uc003ein.1_Silent_p.A362A	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	827	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)													---	---	---	---
CHST13	166012	broad.mit.edu	37	3	126261003	126261003	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126261003G>A	uc003eja.2	+	3	608	c.608G>A	c.(607-609)CGC>CAC	p.R203H		NM_152889	NP_690849	Q8NET6	CHSTD_HUMAN	carbohydrate sulfotransferase 13	203	Lumenal (Potential).				chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.151)														---	---	---	---
PODXL2	50512	broad.mit.edu	37	3	127379771	127379771	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127379771C>T	uc003ejq.2	+	3	924	c.900C>T	c.(898-900)CAC>CAT	p.H300H		NM_015720	NP_056535	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2 precursor	300	Extracellular (Potential).				leukocyte tethering or rolling	integral to plasma membrane	glycosaminoglycan binding|protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128344441	128344441	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128344441G>A	uc003ekr.1	-	8	1407	c.1331C>T	c.(1330-1332)GCG>GTG	p.A444V	RPN1_uc011bkq.1_Missense_Mutation_p.A272V	NM_002950	NP_002941	P04843	RPN1_HUMAN	ribophorin I precursor	444	Helical; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)				T	EVI1	AML								---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129231177	129231177	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129231177G>A	uc003emm.2	+	24	3115	c.2909G>A	c.(2908-2910)CGT>CAT	p.R970H	IFT122_uc003eml.2_Missense_Mutation_p.R1021H|IFT122_uc003emn.2_Missense_Mutation_p.R911H|IFT122_uc003emo.2_Missense_Mutation_p.R860H|IFT122_uc003emp.2_Missense_Mutation_p.R820H|IFT122_uc010htc.2_Missense_Mutation_p.R963H|IFT122_uc011bky.1_Missense_Mutation_p.R761H|IFT122_uc003emq.2_Missense_Mutation_p.R810H|IFT122_uc003emr.2_Missense_Mutation_p.R723H|IFT122_uc011bla.1_Missense_Mutation_p.R744H|IFT122_uc010hte.2_Missense_Mutation_p.R296H|IFT122_uc003ems.2_Missense_Mutation_p.R352H|IFT122_uc011bkx.1_Missense_Mutation_p.R811H	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2	970					camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134920469	134920469	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134920469G>A	uc003eqt.2	+	12	2504	c.2284G>A	c.(2284-2286)GAC>AAC	p.D762N	EPHB1_uc003equ.2_Missense_Mutation_p.D323N	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	762	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134967254	134967254	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134967254C>T	uc003eqt.2	+	14	2813	c.2593C>T	c.(2593-2595)CGG>TGG	p.R865W	EPHB1_uc003equ.2_Missense_Mutation_p.R426W	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	865	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
ATP1B3	483	broad.mit.edu	37	3	141622486	141622486	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141622486T>C	uc003eug.1	+	2	308	c.134T>C	c.(133-135)GTT>GCT	p.V45A	ATP1B3_uc011bne.1_RNA|ATP1B3_uc003euh.1_Missense_Mutation_p.V31A	NM_001679	NP_001670	P54709	AT1B3_HUMAN	Na+/K+ -ATPase beta 3 subunit	45	Helical; Signal-anchor for type II membrane protein; (Potential).				ATP biosynthetic process|blood coagulation|leukocyte migration	melanosome|sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity				0																		---	---	---	---
PLSCR1	5359	broad.mit.edu	37	3	146246494	146246494	+	Silent	SNP	T	C	C	rs147509085	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146246494T>C	uc003evx.3	-	4	607	c.219A>G	c.(217-219)GTA>GTG	p.V73V	PLSCR1_uc003evy.3_Silent_p.V66V|PLSCR1_uc011bnn.1_Intron|PLSCR1_uc003evz.3_Intron|PLSCR1_uc003ewa.2_Silent_p.V73V	NM_021105	NP_066928	O15162	PLS1_HUMAN	phospholipid scramblase 1	73	Cytoplasmic.				phospholipid scrambling|platelet activation|response to virus	integral to membrane|plasma membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding			ovary(2)	2																		---	---	---	---
ZIC4	84107	broad.mit.edu	37	3	147108745	147108745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147108745G>A	uc003ewd.1	-	4	1250	c.977C>T	c.(976-978)GCG>GTG	p.A326V	ZIC4_uc003ewc.1_Missense_Mutation_p.A256V|ZIC4_uc011bno.1_Missense_Mutation_p.A376V	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN	zinc finger protein of the cerebellum 4	326						nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2																		---	---	---	---
ZIC4	84107	broad.mit.edu	37	3	147113821	147113821	+	Missense_Mutation	SNP	G	A	A	rs62001026	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147113821G>A	uc003ewd.1	-	3	779	c.506C>T	c.(505-507)GCC>GTC	p.A169V	ZIC4_uc003ewc.1_Missense_Mutation_p.A99V|ZIC4_uc011bno.1_Missense_Mutation_p.A219V	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN	zinc finger protein of the cerebellum 4	169						nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2																		---	---	---	---
HLTF	6596	broad.mit.edu	37	3	148778424	148778424	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148778424A>G	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636			helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151082912	151082912	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151082912C>A	uc003eyp.2	+	20	3036	c.2998C>A	c.(2998-3000)CTC>ATC	p.L1000I	MED12L_uc011bnz.1_Missense_Mutation_p.L860I|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.L163I	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1000					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155210547	155210547	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155210547G>C	uc011bok.1	-	17	2519	c.2242C>G	c.(2242-2244)CCA>GCA	p.P748A	PLCH1_uc011boj.1_Missense_Mutation_p.P748A|PLCH1_uc011bol.1_Missense_Mutation_p.P730A	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	748	C2.				lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
VEPH1	79674	broad.mit.edu	37	3	157004431	157004431	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157004431T>G	uc003fbj.1	-	12	2360	c.2043A>C	c.(2041-2043)GAA>GAC	p.E681D	VEPH1_uc003fbk.1_Missense_Mutation_p.E681D|VEPH1_uc010hvu.1_Missense_Mutation_p.E636D	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1	681						plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)															---	---	---	---
SMC4	10051	broad.mit.edu	37	3	160135634	160135634	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160135634A>G	uc003fdh.2	+	11	1674	c.1561A>G	c.(1561-1563)ACT>GCT	p.T521A	IFT80_uc003fda.2_Intron|SMC4_uc010hwc.1_Missense_Mutation_p.T285A|SMC4_uc003fdi.2_Missense_Mutation_p.T496A|SMC4_uc003fdj.2_Missense_Mutation_p.T521A|SMC4_uc010hwd.2_Missense_Mutation_p.T521A|SMC4_uc003fdl.2_Missense_Mutation_p.T224A	NM_001002800	NP_001002800	Q9NTJ3	SMC4_HUMAN	SMC4 structural maintenance of chromosomes	521	Potential.				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
GOLIM4	27333	broad.mit.edu	37	3	167745560	167745560	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167745560G>A	uc003ffe.2	-	12	1923	c.1579C>T	c.(1579-1581)CGT>TGT	p.R527C	GOLIM4_uc011bpe.1_Missense_Mutation_p.R528C|GOLIM4_uc011bpf.1_Missense_Mutation_p.R500C|GOLIM4_uc011bpg.1_Missense_Mutation_p.R499C	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	527	Glu-rich.|Lumenal (Potential).				transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5																		---	---	---	---
LRRC31	79782	broad.mit.edu	37	3	169572672	169572672	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169572672A>G	uc003fgc.1	-	6	997	c.920T>C	c.(919-921)GTC>GCC	p.V307A	LRRC31_uc010hwp.1_Missense_Mutation_p.V251A	NM_024727	NP_079003	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	307										ovary(2)|skin(1)	3	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)															---	---	---	---
CLDN11	5010	broad.mit.edu	37	3	170140971	170140971	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170140971G>A	uc003fgx.2	+	2	449	c.247G>A	c.(247-249)GCC>ACC	p.A83T	CLDN11_uc011bpt.1_Missense_Mutation_p.A83T|CLDN11_uc003fgy.2_5'UTR	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11	83	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173322759	173322759	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173322759G>A	uc003fio.1	+	3	794	c.371G>A	c.(370-372)GGC>GAC	p.G124D	NLGN1_uc010hww.1_Missense_Mutation_p.G124D|NLGN1_uc003fip.1_Missense_Mutation_p.G124D	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	124	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
FXR1	8087	broad.mit.edu	37	3	180688129	180688129	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180688129T>C	uc003fkq.2	+	15	1608	c.1586T>C	c.(1585-1587)GTT>GCT	p.V529A	FXR1_uc003fkp.2_Missense_Mutation_p.V444A|FXR1_uc003fkr.2_Missense_Mutation_p.V529A|FXR1_uc011bqj.1_Missense_Mutation_p.V443A|FXR1_uc003fks.2_Missense_Mutation_p.V472A|FXR1_uc011bqk.1_Missense_Mutation_p.V480A|FXR1_uc011bql.1_Missense_Mutation_p.V516A	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1	529					apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183521871	183521871	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183521871G>A	uc003fly.2	+	27	3874	c.3679G>A	c.(3679-3681)GCT>ACT	p.A1227T	uc003fma.1_3'UTR	NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1227					histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
ECE2	9718	broad.mit.edu	37	3	184008885	184008885	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184008885C>T	uc003fni.3	+	17	2284	c.2246C>T	c.(2245-2247)GCA>GTA	p.A749V	ECE2_uc011brh.1_Missense_Mutation_p.A602V|ECE2_uc003fnl.3_Missense_Mutation_p.A677V|ECE2_uc003fnm.3_Missense_Mutation_p.A631V|ECE2_uc003fnk.3_Missense_Mutation_p.A602V|ECE2_uc011bri.1_Missense_Mutation_p.A664V|ECE2_uc010hxv.2_3'UTR	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	749	Lumenal (Potential).|Endothelin-converting enzyme 2 region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
PSMD2	5708	broad.mit.edu	37	3	184022156	184022156	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184022156G>A	uc003fnn.1	+	12	1549	c.1516G>A	c.(1516-1518)GGA>AGA	p.G506R	PSMD2_uc011brj.1_Missense_Mutation_p.G347R|PSMD2_uc011brk.1_Missense_Mutation_p.G376R	NM_002808	NP_002799	Q13200	PSMD2_HUMAN	proteasome 26S non-ATPase subunit 2	506	PC 3.				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|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding				0	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)													---	---	---	---
PSMD2	5708	broad.mit.edu	37	3	184025433	184025433	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184025433G>A	uc003fnn.1	+	18	2268	c.2235G>A	c.(2233-2235)CTG>CTA	p.L745L	PSMD2_uc011brj.1_Silent_p.L586L|PSMD2_uc011brk.1_Silent_p.L615L	NM_002808	NP_002799	Q13200	PSMD2_HUMAN	proteasome 26S non-ATPase subunit 2	745	PC 7.				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|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding				0	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)													---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184040475	184040475	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184040475T>C	uc003fnp.2	+	12	1950	c.1752T>C	c.(1750-1752)GCT>GCC	p.A584A	EIF4G1_uc003fno.1_Silent_p.A525A|EIF4G1_uc010hxw.1_Silent_p.A420A|EIF4G1_uc003fnt.2_Silent_p.A295A|EIF4G1_uc003fnq.2_Silent_p.A497A|EIF4G1_uc003fnr.2_Silent_p.A420A|EIF4G1_uc010hxx.2_Silent_p.A591A|EIF4G1_uc003fns.2_Silent_p.A544A|EIF4G1_uc010hxy.2_Silent_p.A591A|EIF4G1_uc003fnv.3_Silent_p.A584A|EIF4G1_uc003fnu.3_Silent_p.A584A|EIF4G1_uc003fnw.2_Silent_p.A591A|EIF4G1_uc003fnx.2_Silent_p.A388A|EIF4G1_uc003fny.3_Silent_p.A388A	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	584	MIF4G.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
EPHB3	2049	broad.mit.edu	37	3	184298195	184298195	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184298195C>A	uc003foz.2	+	12	2615	c.2178C>A	c.(2176-2178)AAC>AAA	p.N726K		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	726	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184542471	184542471	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184542471G>T	uc003fpb.1	+	2	222	c.51G>T	c.(49-51)AAG>AAT	p.K17N	VPS8_uc010hyd.1_Missense_Mutation_p.K17N|VPS8_uc003fpc.1_Missense_Mutation_p.K17N	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	17							zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184717545	184717545	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184717545G>T	uc003fpb.1	+	44	4063	c.3892G>T	c.(3892-3894)GGC>TGC	p.G1298C	VPS8_uc010hyd.1_Missense_Mutation_p.G1208C|VPS8_uc010hye.1_Missense_Mutation_p.G727C	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	1300	RING-type; atypical.						zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
C3orf70	285382	broad.mit.edu	37	3	184801181	184801181	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184801181A>G	uc003fpd.2	-	2	558	c.367T>C	c.(367-369)TAC>CAC	p.Y123H		NM_001025266	NP_001020437	A6NLC5	CC070_HUMAN	hypothetical protein LOC285382	123											0																		---	---	---	---
MIR1248	100302143	broad.mit.edu	37	3	186504535	186504535	+	RNA	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186504535G>A	hsa-mir-1248|MI0006383	+			c.75G>A			EIF4A2_uc003fqs.2_Intron|EIF4A2_uc003fqt.2_Intron|EIF4A2_uc003fqu.2_Intron|EIF4A2_uc003fqv.2_Intron|EIF4A2_uc003fqw.2_Intron|EIF4A2_uc011bsb.1_Intron|SNORA81_uc010hyv.1_RNA|SNORA63_uc010hyw.1_5'Flank|SNORA4_uc010hyx.1_5'Flank																	0																		---	---	---	---
BCL6	604	broad.mit.edu	37	3	187451439	187451439	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187451439C>T	uc003frp.3	-	3	500	c.43G>A	c.(43-45)GCC>ACC	p.A15T	BCL6_uc011bsf.1_Missense_Mutation_p.A15T|BCL6_uc010hza.2_5'UTR|BCL6_uc003frq.1_Missense_Mutation_p.A15T	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1	15					negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)				T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193048947	193048947	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193048947T>G	uc011bsq.1	-	12	1426	c.1426A>C	c.(1426-1428)ATG>CTG	p.M476L		NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5	476					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)														---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193361319	193361319	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193361319T>C	uc003ftm.2	+	13	1449	c.1215T>C	c.(1213-1215)ACT>ACC	p.T405T	OPA1_uc003ftg.2_Silent_p.T460T|OPA1_uc003fth.2_Silent_p.T424T|OPA1_uc003fti.2_Silent_p.T442T|OPA1_uc003ftj.2_Silent_p.T423T|OPA1_uc003ftk.2_Silent_p.T406T|OPA1_uc003ftl.2_Silent_p.T387T|OPA1_uc003ftn.2_Silent_p.T369T	NM_015560	NP_056375	O60313	OPA1_HUMAN	optic atrophy 1 isoform 1	405	Mitochondrial intermembrane (By similarity).				apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)														---	---	---	---
CPN2	1370	broad.mit.edu	37	3	194063301	194063301	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194063301G>A	uc003fts.2	-	2	221	c.131C>T	c.(130-132)CCA>CTA	p.P44L		NM_001080513	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	44	LRRNT.				protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)														---	---	---	---
PPP1R2	5504	broad.mit.edu	37	3	195256585	195256585	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195256585G>A	uc003fup.2	-						PPP1R2_uc003fuq.3_3'UTR	NM_006241	NP_006232			protein phosphatase 1, regulatory subunit 2						glycogen metabolic process|regulation of phosphoprotein phosphatase activity|regulation of signal transduction		protein binding|protein serine/threonine phosphatase inhibitor activity			urinary_tract(1)	1	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)		Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;9.55e-05)														---	---	---	---
TCTEX1D2	255758	broad.mit.edu	37	3	196018210	196018210	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196018210A>G	uc003fwi.2	-	5	553	c.417T>C	c.(415-417)TGT>TGC	p.C139C		NM_152773	NP_689986	Q8WW35	TC1D2_HUMAN	Tctex1 domain containing 2	139							protein binding			ovary(1)|breast(1)	2	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
GAK	2580	broad.mit.edu	37	4	876506	876506	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:876506G>A	uc003gbm.3	-	14	1705	c.1506C>T	c.(1504-1506)AAC>AAT	p.N502N	GAK_uc003gbn.3_Silent_p.N423N|GAK_uc010ibk.1_Silent_p.N396N|GAK_uc003gbl.3_Silent_p.N366N	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	502	Phosphatase tensin-type.				cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
TMEM175	84286	broad.mit.edu	37	4	951841	951841	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:951841G>T	uc003gbq.2	+	11	1170	c.1072G>T	c.(1072-1074)GCC>TCC	p.A358S	TMEM175_uc003gbr.2_Missense_Mutation_p.A276S|TMEM175_uc003gbu.2_Missense_Mutation_p.A276S|TMEM175_uc003gbs.2_Missense_Mutation_p.A241S|TMEM175_uc003gbt.2_Missense_Mutation_p.A241S|TMEM175_uc003gbv.2_Missense_Mutation_p.A241S|TMEM175_uc010ibm.2_Missense_Mutation_p.A174S	NM_032326	NP_115702	Q9BSA9	TM175_HUMAN	transmembrane protein 175	358	Helical; (Potential).					integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)															---	---	---	---
C4orf42	92070	broad.mit.edu	37	4	1244750	1244750	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1244750G>A	uc003gcz.1	+	1	574	c.389G>A	c.(388-390)CGC>CAC	p.R130H	CTBP1_uc003gcu.1_5'Flank|CTBP1_uc003gcv.1_5'Flank|C4orf42_uc003gcy.1_RNA	NM_052861	NP_443093			hypothetical protein LOC92070											ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0101)	Colorectal(103;0.188)														---	---	---	---
LETM1	3954	broad.mit.edu	37	4	1818606	1818606	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1818606A>C	uc003gdv.2	-	12	2076	c.1779T>G	c.(1777-1779)ACT>ACG	p.T593T		NM_012318	NP_036450	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane	593	Mitochondrial matrix (Potential).|Potential.				cristae formation	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			central_nervous_system(1)	1			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)															---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1955098	1955098	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1955098C>T	uc003gdz.3	+	12	2361	c.2185C>T	c.(2185-2187)CGC>TGC	p.R729C	WHSC1_uc003geb.3_Missense_Mutation_p.R729C|WHSC1_uc003gec.3_Missense_Mutation_p.R729C|WHSC1_uc003ged.3_Missense_Mutation_p.R729C|WHSC1_uc003gee.3_RNA|WHSC1_uc003gef.3_RNA|WHSC1_uc003gei.3_5'UTR|WHSC1_uc011bvh.1_5'UTR|WHSC1_uc010icf.2_Missense_Mutation_p.R77C	NM_001042424	NP_001035889	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1 protein	729	PHD-type 2.				anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
HTT	3064	broad.mit.edu	37	4	3107097	3107097	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3107097G>A	uc011bvq.1	+	6	693	c.548G>A	c.(547-549)CGG>CAG	p.R183Q		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	181					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
EVC	2121	broad.mit.edu	37	4	5754554	5754554	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5754554T>G	uc003gil.1	+						EVC_uc003gim.1_Intron|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928			Ellis van Creveld syndrome protein						muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
EVC	2121	broad.mit.edu	37	4	5754612	5754612	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5754612A>G	uc003gil.1	+	9	1332	c.1148A>G	c.(1147-1149)GAG>GGG	p.E383G	EVC_uc003gim.1_RNA|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	383					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5837754	5837754	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5837754T>G	uc003gip.2	-	12	1270	c.1169A>C	c.(1168-1170)AAG>ACG	p.K390T	CRMP1_uc003gin.1_Missense_Mutation_p.K302T|CRMP1_uc003giq.2_Missense_Mutation_p.K390T|CRMP1_uc003gir.2_Missense_Mutation_p.K385T|CRMP1_uc003gis.2_Missense_Mutation_p.K504T	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2	390					axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5838618	5838618	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5838618G>A	uc003gip.2	-	11	1085	c.984C>T	c.(982-984)GTC>GTT	p.V328V	CRMP1_uc003gin.1_Silent_p.V240V|CRMP1_uc003giq.2_Silent_p.V328V|CRMP1_uc003gir.2_Silent_p.V323V|CRMP1_uc003gis.2_Silent_p.V442V	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2	328					axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
PSAPL1	768239	broad.mit.edu	37	4	7435678	7435678	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7435678G>T	uc011bwj.1	-	1	1023	c.929C>A	c.(928-930)TCC>TAC	p.S310Y	SORCS2_uc003gkb.3_Intron|SORCS2_uc011bwi.1_Intron	NM_001085382	NP_001078851	Q6NUJ1	SAPL1_HUMAN	prosaposin-like protein 1	310	Saposin B-type 3.				sphingolipid metabolic process	extracellular region|lysosome					0																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7715973	7715973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7715973C>T	uc003gkb.3	+	16	1996	c.1996C>T	c.(1996-1998)CGC>TGC	p.R666C	SORCS2_uc011bwi.1_Missense_Mutation_p.R494C	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor	666	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13597501	13597501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13597501C>T	uc003gmz.1	-	12	8204	c.8087G>A	c.(8086-8088)GGA>GAA	p.G2696E		NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	2696							DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13603668	13603668	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13603668G>A	uc003gmz.1	-	10	4973	c.4856C>T	c.(4855-4857)GCT>GTT	p.A1619V	BOD1L_uc010idr.1_Missense_Mutation_p.A956V	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1619							DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
PACRGL	133015	broad.mit.edu	37	4	20709442	20709442	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20709442G>A	uc010iek.2	+	4	615	c.224G>A	c.(223-225)CGA>CAA	p.R75Q	PACRGL_uc003gpu.2_RNA|PACRGL_uc010iei.1_Missense_Mutation_p.R123Q|PACRGL_uc003gpz.2_Missense_Mutation_p.R75Q|PACRGL_uc011bxm.1_Intron|PACRGL_uc003gqa.2_Intron|PACRGL_uc003gpx.3_RNA|PACRGL_uc003gpv.2_Missense_Mutation_p.R75Q|PACRGL_uc003gpw.2_RNA|PACRGL_uc010iej.1_Intron|PACRGL_uc011bxn.1_Intron|PACRGL_uc003gpy.2_Intron	NM_145048	NP_659485	Q8N7B6	PACRL_HUMAN	PARK2 co-regulated-like isoform 1	75							binding				0																		---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22390136	22390136	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22390136A>C	uc003gqm.1	-	19	3423	c.3158T>G	c.(3157-3159)GTT>GGT	p.V1053G	GPR125_uc010ieo.1_Missense_Mutation_p.V909G|GPR125_uc003gql.1_Missense_Mutation_p.V180G	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	1053	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
DHX15	1665	broad.mit.edu	37	4	24541776	24541776	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24541776A>G	uc003gqx.2	-	10	1909	c.1741T>C	c.(1741-1743)TAC>CAC	p.Y581H	DHX15_uc003gqw.2_5'Flank	NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15	581					mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)																---	---	---	---
CCDC149	91050	broad.mit.edu	37	4	24854802	24854802	+	Splice_Site	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24854802C>A	uc011bxr.1	-	5	409	c.265_splice	c.e5-1	p.A89_splice	CCDC149_uc003grc.2_Splice_Site_p.A89_splice|CCDC149_uc003grb.2_Splice_Site|CCDC149_uc003grd.2_Splice_Site_p.A89_splice|CCDC149_uc003gre.2_Splice_Site_p.A34_splice|CCDC149_uc011bxq.1_Translation_Start_Site	NM_173463	NP_775734			coiled-coil domain containing 149 isoform 1												0		Breast(46;0.173)																---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36134893	36134893	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36134893C>T	uc003gsq.1	-	20	3720	c.3382G>A	c.(3382-3384)GTT>ATT	p.V1128I		NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1128	Rho-GAP.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
DCAF4L1	285429	broad.mit.edu	37	4	41984913	41984913	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41984913C>T	uc003gwk.2	+	1	1201	c.1104C>T	c.(1102-1104)TTC>TTT	p.F368F		NM_001029955	NP_001025126	Q3SXM0	DC4L1_HUMAN	WD repeat domain 21B	368										skin(1)	1																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47597894	47597894	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47597894A>G	uc003gxm.2	-	22	3066	c.2973T>C	c.(2971-2973)TGT>TGC	p.C991C	CORIN_uc011bzf.1_Silent_p.C852C|CORIN_uc011bzg.1_Silent_p.C924C	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	991	Extracellular (Potential).|Peptidase S1.				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625144	48625144	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625144T>C	uc003gyh.1	-	5	778	c.173A>G	c.(172-174)CAG>CGG	p.Q58R	FRYL_uc003gyk.2_Missense_Mutation_p.Q58R|FRYL_uc003gyl.1_Missense_Mutation_p.Q109R|FRYL_uc003gym.1_Missense_Mutation_p.Q58R	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	58					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
OCIAD1	54940	broad.mit.edu	37	4	48850469	48850469	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48850469T>C	uc003gyo.2	+						OCIAD1_uc011bzk.1_Intron|OCIAD1_uc003gyr.2_Intron|OCIAD1_uc003gyp.2_Intron|OCIAD1_uc003gys.2_Intron|OCIAD1_uc003gyq.2_Intron|OCIAD1_uc010igk.2_Intron	NM_017830	NP_060300			OCIA domain containing 1 isoform 1							endosome	protein binding				0																		---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	55129887	55129887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55129887G>A	uc003han.3	+	4	752	c.421G>A	c.(421-423)GAG>AAG	p.E141K	PDGFRA_uc003haa.2_Intron|PDGFRA_uc003hal.2_Missense_Mutation_p.E141K|PDGFRA_uc010igq.1_Missense_Mutation_p.E35K|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	141	Extracellular (Potential).|Ig-like C2-type 2.				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	55139866	55139866	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55139866T>C	uc003han.3	+	10	1858	c.1527T>C	c.(1525-1527)GCT>GCC	p.A509A	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Silent_p.A403A|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	509	Ig-like C2-type 5.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity	p.A509D(1)		soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
KIT	3815	broad.mit.edu	37	4	55603434	55603434	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55603434G>C	uc010igr.2	+	20	2877	c.2790G>C	c.(2788-2790)GAG>GAC	p.E930D	KIT_uc010igs.2_Missense_Mutation_p.E926D	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral	930	Protein kinase.|Cytoplasmic (Potential).				male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62761492	62761492	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62761492T>C	uc010ihh.2	+	8	1796	c.1623T>C	c.(1621-1623)GAT>GAC	p.D541D	LPHN3_uc003hcq.3_Silent_p.D541D|LPHN3_uc003hcs.1_Silent_p.D370D	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	541	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
C4orf40	401137	broad.mit.edu	37	4	71024227	71024227	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71024227T>C	uc003hfa.3	+	4	331	c.258T>C	c.(256-258)TAT>TAC	p.Y86Y	C4orf40_uc003hfb.3_Silent_p.Y86Y	NM_214711	NP_999876	Q6MZM9	CD040_HUMAN	hypothetical protein LOC401137 precursor	86						extracellular region					0																		---	---	---	---
BTC	685	broad.mit.edu	37	4	75681147	75681147	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75681147C>A	uc003hig.2	-	3	550	c.203G>T	c.(202-204)AGG>ATG	p.R68M		NM_001729	NP_001720	P35070	BTC_HUMAN	betacellulin precursor	68	Extracellular (Potential).|EGF-like.				positive regulation of cell division|positive regulation of cell proliferation	extracellular space|integral to membrane|plasma membrane|soluble fraction	epidermal growth factor receptor binding|growth factor activity			central_nervous_system(1)|skin(1)	2			Lung(101;0.219)															---	---	---	---
NAA11	84779	broad.mit.edu	37	4	80246728	80246728	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80246728A>T	uc003hlt.3	-	1	444	c.304T>A	c.(304-306)TTT>ATT	p.F102I		NM_032693	NP_116082	Q9BSU3	NAA11_HUMAN	alpha-N-acetyltransferase 1B	102	N-acetyltransferase.					cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85600249	85600249	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85600249T>C	uc003hpd.2	-	65	10378	c.9970A>G	c.(9970-9972)ACT>GCT	p.T3324A	WDFY3_uc003hpc.2_Missense_Mutation_p.T79A	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	3324						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87685814	87685814	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87685814G>A	uc003hpz.2	+	25	4566	c.4086G>A	c.(4084-4086)AAG>AAA	p.K1362K	PTPN13_uc003hpy.2_Silent_p.K1362K|PTPN13_uc003hqa.2_Silent_p.K1343K|PTPN13_uc003hqb.2_Silent_p.K1171K	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1362				KP -> RS (in Ref. 5; CAA56124).		cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
KLHL8	57563	broad.mit.edu	37	4	88116486	88116486	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88116486A>G	uc011cdb.1	-	2	591	c.206T>C	c.(205-207)GTC>GCC	p.V69A	KLHL8_uc003hql.1_Missense_Mutation_p.V69A|KLHL8_uc003hqm.1_Missense_Mutation_p.V69A|KLHL8_uc003hqn.1_Missense_Mutation_p.V69A|KLHL8_uc010ikj.1_5'UTR	NM_020803	NP_065854	Q9P2G9	KLHL8_HUMAN	kelch-like 8	69	BTB.										0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89389505	89389505	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89389505A>G	uc003hrt.2	+	8	1219	c.1066A>G	c.(1066-1068)ACC>GCC	p.T356A	HERC5_uc011cdm.1_Translation_Start_Site	NM_016323	NP_057407	Q9UII4	HERC5_HUMAN	hect domain and RLD 5	356	RCC1 5.				innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96166150	96166150	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96166150T>C	uc003htp.1	-	6	1075	c.921A>G	c.(919-921)ATA>ATG	p.I307M	UNC5C_uc010ilc.1_Missense_Mutation_p.I307M|UNC5C_uc003htq.2_Missense_Mutation_p.I307M	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor	307	Extracellular (Potential).|TSP type-1 1.				apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)														---	---	---	---
ADH4	127	broad.mit.edu	37	4	100052797	100052797	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100052797T>G	uc003hun.2	-	6	777	c.701A>C	c.(700-702)AAG>ACG	p.K234T	uc003hum.1_Intron|ADH4_uc011ced.1_Missense_Mutation_p.K253T	NM_000670	NP_000661	P08319	ADH4_HUMAN	class II alcohol dehydrogenase, pi subunit	234		NAD.			alcohol catabolic process|cellular aldehyde metabolic process|ethanol oxidation|quinone cofactor metabolic process|retinol metabolic process|xenobiotic metabolic process	cytosol|microtubule cytoskeleton	alcohol dehydrogenase activity, zinc-dependent|all-trans retinal binding|benzaldehyde dehydrogenase activity|NAD binding|NADPH:quinone reductase activity|retinol binding|retinol dehydrogenase activity|zinc ion binding			skin(2)	2				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)	NADH(DB00157)													---	---	---	---
ADH1A	124	broad.mit.edu	37	4	100201419	100201419	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100201419A>G	uc003hur.1	-	7	917	c.846T>C	c.(844-846)TGT>TGC	p.C282C	uc003hum.1_Intron|ADH1A_uc011ceg.1_Silent_p.C282C	NM_000667	NP_000658	P07327	ADH1A_HUMAN	class I alcohol dehydrogenase, alpha subunit	282					ethanol oxidation|transcription, DNA-dependent|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|protein binding|zinc ion binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Fomepizole(DB01213)|NADH(DB00157)													---	---	---	---
MTTP	4547	broad.mit.edu	37	4	100515985	100515985	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100515985C>T	uc003hvc.3	+	8	1110	c.854C>T	c.(853-855)ACG>ATG	p.T285M	MTTP_uc011cej.1_Missense_Mutation_p.T312M	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large	285	Vitellogenin.				lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)													---	---	---	---
NHEDC1	150159	broad.mit.edu	37	4	103822407	103822407	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103822407A>T	uc003hww.2	-	12	1537	c.1415T>A	c.(1414-1416)GTA>GAA	p.V472E	NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Missense_Mutation_p.V245E	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1	472	Helical; (Potential).					integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)														---	---	---	---
NHEDC1	150159	broad.mit.edu	37	4	103870499	103870499	+	Missense_Mutation	SNP	G	T	T	rs78972166		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103870499G>T	uc003hww.2	-	4	419	c.297C>A	c.(295-297)TTC>TTA	p.F99L	NHEDC1_uc003hwu.2_Missense_Mutation_p.F99L|NHEDC1_uc010ilm.2_5'UTR|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1	99	Helical; (Potential).					integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)														---	---	---	---
NHEDC1	150159	broad.mit.edu	37	4	103870505	103870505	+	Silent	SNP	C	T	T	rs78695762		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103870505C>T	uc003hww.2	-	4	413	c.291G>A	c.(289-291)GGG>GGA	p.G97G	NHEDC1_uc003hwu.2_Silent_p.G97G|NHEDC1_uc010ilm.2_5'UTR|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1	97	Helical; (Potential).					integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)														---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107114826	107114826	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107114826G>A	uc010ilv.2	-	22	2364	c.1999C>T	c.(1999-2001)CGG>TGG	p.R667W	TBCK_uc003hyb.2_Missense_Mutation_p.R410W|TBCK_uc003hye.2_Missense_Mutation_p.R628W|TBCK_uc003hyc.2_Missense_Mutation_p.R604W|TBCK_uc003hyd.2_Missense_Mutation_p.R495W|TBCK_uc003hyf.2_Missense_Mutation_p.R667W	NM_001163435	NP_001156907	Q8TEA7	TBCK_HUMAN	TBC domain-containing protein kinase-like	667						intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
LEF1	51176	broad.mit.edu	37	4	108999372	108999372	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108999372T>G	uc003hyt.1	-						LEF1_uc011cfj.1_Intron|LEF1_uc011cfk.1_Intron|LEF1_uc003hyu.1_Intron|LEF1_uc003hyv.1_Intron|LEF1_uc010imb.1_Intron|LEF1_uc010ima.1_Intron|LEF1_uc003hyw.1_Intron	NM_016269	NP_057353			lymphoid enhancer-binding factor 1 isoform 1						canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)														---	---	---	---
LEF1	51176	broad.mit.edu	37	4	108999451	108999451	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108999451T>A	uc003hyt.1	-	8	1588	c.933A>T	c.(931-933)AAA>AAT	p.K311N	LEF1_uc011cfj.1_Missense_Mutation_p.K168N|LEF1_uc011cfk.1_Missense_Mutation_p.K215N|LEF1_uc003hyu.1_Missense_Mutation_p.K283N|LEF1_uc003hyv.1_Missense_Mutation_p.K283N|LEF1_uc010imb.1_RNA|LEF1_uc010ima.1_Translation_Start_Site|LEF1_uc003hyw.1_RNA	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	311	HMG box.				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)														---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	110223100	110223100	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110223100G>A	uc003hze.1	-	2	607	c.76C>T	c.(76-78)CAT>TAT	p.H26Y	COL25A1_uc003hzg.2_Missense_Mutation_p.H26Y|COL25A1_uc003hzh.1_Missense_Mutation_p.H26Y	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1	26	Cytoplasmic (Potential).					collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110416004	110416004	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110416004T>C	uc003hzk.2	+	6	1535	c.1480T>C	c.(1480-1482)TAT>CAT	p.Y494H	SEC24B_uc003hzl.2_Missense_Mutation_p.Y459H|SEC24B_uc011cfp.1_Missense_Mutation_p.Y525H|SEC24B_uc011cfq.1_Missense_Mutation_p.Y494H|SEC24B_uc011cfr.1_Missense_Mutation_p.Y459H	NM_006323	NP_006314	O95487	SC24B_HUMAN	SEC24 (S. cerevisiae) homolog B isoform a	494					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)														---	---	---	---
PLA2G12A	81579	broad.mit.edu	37	4	110638766	110638766	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110638766T>A	uc003hzp.2	-	3	666	c.389A>T	c.(388-390)TAT>TTT	p.Y130F	PLA2G12A_uc010img.2_Missense_Mutation_p.Y128F	NM_030821	NP_110448	Q9BZM1	PG12A_HUMAN	phospholipase A2, group XIIA precursor	130					lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity				0				OV - Ovarian serous cystadenocarcinoma(123;0.000268)														---	---	---	---
EGF	1950	broad.mit.edu	37	4	110885671	110885671	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110885671A>T	uc003hzy.3	+	10	2005	c.1553A>T	c.(1552-1554)GAT>GTT	p.D518V	EGF_uc011cfu.1_Missense_Mutation_p.D476V|EGF_uc011cfv.1_Missense_Mutation_p.D518V	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor	518	LDL-receptor class B 5.|Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)													---	---	---	---
ANK2	287	broad.mit.edu	37	4	114276333	114276333	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114276333T>C	uc003ibe.3	+	38	6659	c.6559T>C	c.(6559-6561)TTC>CTC	p.F2187L	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_5'Flank|ANK2_uc011cgb.1_Missense_Mutation_p.F2202L	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	2154					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
USP53	54532	broad.mit.edu	37	4	120189470	120189470	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120189470G>C	uc003ics.3	+	13	2249	c.1183G>C	c.(1183-1185)GGA>CGA	p.G395R	USP53_uc003icr.3_Missense_Mutation_p.G395R|USP53_uc003icu.3_Missense_Mutation_p.G18R|USP53_uc003ict.2_Missense_Mutation_p.G18R	NM_019050	NP_061923	Q70EK8	UBP53_HUMAN	ubiquitin specific protease 53	395					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			ovary(1)|breast(1)|kidney(1)|skin(1)	4																		---	---	---	---
PRDM5	11107	broad.mit.edu	37	4	121774675	121774675	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121774675T>G	uc003idn.2	-	3	448	c.198A>C	c.(196-198)GAA>GAC	p.E66D	PRDM5_uc003ido.2_Missense_Mutation_p.E66D|PRDM5_uc010ine.2_Missense_Mutation_p.E66D|PRDM5_uc010inf.2_Missense_Mutation_p.E66D|PRDM5_uc003idp.1_Missense_Mutation_p.E66D	NM_018699	NP_061169	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	66	SET.				histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
IL21	59067	broad.mit.edu	37	4	123542048	123542048	+	Missense_Mutation	SNP	C	T	T	rs141748932	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123542048C>T	uc003ies.2	-	1	164	c.119G>A	c.(118-120)CGT>CAT	p.R40H	uc003iet.2_RNA|IL21_uc010int.2_Missense_Mutation_p.R33H	NM_021803	NP_068575	Q9HBE4	IL21_HUMAN	interleukin 21	33					cell maturation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-17 production|positive regulation of T cell proliferation|signal transduction	extracellular space	cytokine activity|interleukin-2 receptor binding				0																		---	---	---	---
ANKRD50	57182	broad.mit.edu	37	4	125591259	125591259	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125591259A>T	uc003ifg.3	-	3	3439	c.3173T>A	c.(3172-3174)ATT>AAT	p.I1058N	ANKRD50_uc011cgo.1_Missense_Mutation_p.I879N|ANKRD50_uc010inw.2_Missense_Mutation_p.I1058N	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1058	ANK 18.									central_nervous_system(1)	1																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126238232	126238232	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126238232G>A	uc003ifj.3	+	1	666	c.666G>A	c.(664-666)GTG>GTA	p.V222V		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	222	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MFSD8	256471	broad.mit.edu	37	4	128864930	128864930	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128864930C>T	uc003ifp.2	-	5	579	c.416G>A	c.(415-417)CGT>CAT	p.R139H	MFSD8_uc011cgu.1_Missense_Mutation_p.R94H|MFSD8_uc011cgv.1_Missense_Mutation_p.R139H|MFSD8_uc011cgw.1_RNA|MFSD8_uc011cgx.1_Missense_Mutation_p.R94H	NM_152778	NP_689991	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing	139	Helical; (Potential).		R -> H (in CLN7).		cell death|transmembrane transport	integral to membrane|lysosomal membrane				ovary(1)|liver(1)	2																		---	---	---	---
SCLT1	132320	broad.mit.edu	37	4	129812269	129812269	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129812269A>C	uc003igp.2	-	19	2359	c.1853T>G	c.(1852-1854)CTT>CGT	p.L618R	SCLT1_uc003ign.2_Missense_Mutation_p.L282R|SCLT1_uc003igo.2_Missense_Mutation_p.L228R|SCLT1_uc003igq.2_Missense_Mutation_p.L237R|SCLT1_uc010iob.1_Missense_Mutation_p.L105R	NM_144643	NP_653244	Q96NL6	SCLT1_HUMAN	sodium channel associated protein 1	618	Potential.					centrosome				ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
ELF2	1998	broad.mit.edu	37	4	139980201	139980201	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139980201G>A	uc003ihp.1	-	9	1888	c.1682C>T	c.(1681-1683)GCG>GTG	p.A561V	ELF2_uc003ihm.1_Missense_Mutation_p.A513V|ELF2_uc003ihn.1_Missense_Mutation_p.A501V|ELF2_uc003iho.1_Missense_Mutation_p.A484V|ELF2_uc011chc.1_Missense_Mutation_p.A376V	NM_201999	NP_973728	Q15723	ELF2_HUMAN	E74-like factor 2 (ets domain transcription	573					negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
MMAA	166785	broad.mit.edu	37	4	146572253	146572253	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146572253A>G	uc003ikh.3	+	5	858	c.773A>G	c.(772-774)GAC>GGC	p.D258G	MMAA_uc010iow.2_Intron	NM_172250	NP_758454	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria type A precursor	258						mitochondrion	GTP binding|nucleoside-triphosphatase activity			ovary(1)	1	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
TMEM184C	55751	broad.mit.edu	37	4	148554111	148554111	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148554111G>A	uc003ila.3	+	8	1406	c.837G>A	c.(835-837)ACG>ACA	p.T279T		NM_018241	NP_060711	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	279						integral to membrane					0																		---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149075852	149075852	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149075852C>T	uc003ilj.3	-	5	2549	c.2215G>A	c.(2215-2217)GTT>ATT	p.V739I	NR3C2_uc003ilk.3_Intron|NR3C2_uc010iph.2_Intron	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	739	Steroid-binding.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
LRBA	987	broad.mit.edu	37	4	151765907	151765907	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151765907C>T	uc010ipj.2	-	27	4838	c.4364G>A	c.(4363-4365)TGC>TAC	p.C1455Y	LRBA_uc003ilt.3_Missense_Mutation_p.C114Y|LRBA_uc003ilu.3_Missense_Mutation_p.C1455Y	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1455						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
DCHS2	54798	broad.mit.edu	37	4	155157153	155157153	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155157153T>C	uc003inw.2	-	25	7286	c.7286A>G	c.(7285-7287)CAG>CGG	p.Q2429R		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	2429	Cadherin 22.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)														---	---	---	---
DCHS2	54798	broad.mit.edu	37	4	155243493	155243493	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155243493A>C	uc003inw.2	-	13	2801	c.2801T>G	c.(2800-2802)GTT>GGT	p.V934G		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	934	Cadherin 7.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)														---	---	---	---
DCHS2	54798	broad.mit.edu	37	4	155254317	155254317	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155254317G>A	uc003inw.2	-	9	1546	c.1546C>T	c.(1546-1548)CGG>TGG	p.R516W	DCHS2_uc003inx.2_Missense_Mutation_p.R1015W	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	516	Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)														---	---	---	---
FGG	2266	broad.mit.edu	37	4	155526190	155526190	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155526190A>G	uc003ioj.2	-	9	1299	c.1158T>C	c.(1156-1158)CCT>CCC	p.P386P	FGG_uc003iog.2_Silent_p.P386P|FGG_uc003ioh.2_Silent_p.P394P|FGG_uc010ipx.2_Silent_p.P214P|FGG_uc010ipy.2_Silent_p.P97P|FGG_uc003ioi.2_Silent_p.P97P|FGG_uc003iok.2_Silent_p.P394P	NM_021870	NP_068656	P02679	FIBG_HUMAN	fibrinogen, gamma chain isoform gamma-B	386	Fibrinogen C-terminal.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)													---	---	---	---
RBM46	166863	broad.mit.edu	37	4	155749070	155749070	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155749070A>G	uc003ioo.2	+	5	1626	c.1453A>G	c.(1453-1455)ACC>GCC	p.T485A	RBM46_uc011cim.1_3'UTR|RBM46_uc003iop.1_3'UTR	NM_144979	NP_659416	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	485							nucleotide binding|RNA binding			central_nervous_system(1)|skin(1)	2	all_hematologic(180;0.24)	Renal(120;0.0854)																---	---	---	---
MAP9	79884	broad.mit.edu	37	4	156281312	156281312	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156281312A>G	uc003ios.2	-						MAP9_uc011cin.1_Intron|MAP9_uc010iqa.1_Intron|MAP9_uc003iot.1_Intron	NM_001039580	NP_001034669			aster-associated protein						cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)														---	---	---	---
GUCY1A3	2982	broad.mit.edu	37	4	156618181	156618181	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156618181C>A	uc003iov.2	+	4	698	c.162C>A	c.(160-162)AAC>AAA	p.N54K	GUCY1A3_uc003iou.2_Missense_Mutation_p.N54K|GUCY1A3_uc010iqc.2_Missense_Mutation_p.N54K|GUCY1A3_uc003iow.2_Missense_Mutation_p.N54K|GUCY1A3_uc010iqd.2_Missense_Mutation_p.N54K|GUCY1A3_uc003iox.2_Missense_Mutation_p.N54K|GUCY1A3_uc003ioz.2_5'UTR|GUCY1A3_uc003ioy.2_Missense_Mutation_p.N54K|GUCY1A3_uc010iqe.2_5'UTR|GUCY1A3_uc003ipa.2_RNA|GUCY1A3_uc003ipb.2_Missense_Mutation_p.N54K	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	54					blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)														---	---	---	---
TDO2	6999	broad.mit.edu	37	4	156832687	156832687	+	Silent	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156832687A>T	uc003ipf.1	+	7	721	c.657A>T	c.(655-657)GGA>GGT	p.G219G		NM_005651	NP_005642	P48775	T23O_HUMAN	tryptophan 2,3-dioxygenase	219					tryptophan catabolic process to kynurenine	cytosol	tryptophan 2,3-dioxygenase activity				0	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)	L-Tryptophan(DB00150)													---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160260432	160260432	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160260432T>C	uc003iqg.3	+	13	2287	c.1977T>C	c.(1975-1977)CCT>CCC	p.P659P		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	659	Ras-associating.				cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170076730	170076730	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170076730A>C	uc003isa.1	-						SH3RF1_uc010irc.1_Intron	NM_020870	NP_065921			SH3 domain containing ring finger 1							Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)														---	---	---	---
NEIL3	55247	broad.mit.edu	37	4	178272681	178272681	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178272681T>C	uc003iut.2	+	7	1134	c.1017T>C	c.(1015-1017)GCT>GCC	p.A339A	NEIL3_uc010irs.2_Intron	NM_018248	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3	339	RanBP2-type.				base-excision repair|nucleotide-excision repair	nucleus	bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding			lung(2)|ovary(1)|central_nervous_system(1)	4		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)									BER_DNA_glycosylases					---	---	---	---
IRF2	3660	broad.mit.edu	37	4	185340688	185340688	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185340688G>A	uc003iwf.3	-	3	322	c.122C>T	c.(121-123)GCG>GTG	p.A41V		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	41	IRF tryptophan pentad repeat.				blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)														---	---	---	---
MLF1IP	79682	broad.mit.edu	37	4	185637662	185637662	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185637662C>T	uc003iwq.2	-	6	577	c.507G>A	c.(505-507)GCG>GCA	p.A169A	MLF1IP_uc003iwp.2_RNA|MLF1IP_uc003iwr.1_Silent_p.A169A	NM_024629	NP_078905	Q71F23	CENPU_HUMAN	MLF1 interacting protein	169					CenH3-containing nucleosome assembly at centromere|interspecies interaction between organisms|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|condensed chromosome kinetochore|cytosol|nucleoplasm					0		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)														---	---	---	---
ACSL1	2180	broad.mit.edu	37	4	185678331	185678331	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185678331C>A	uc003iww.2	-	21	2339	c.2045G>T	c.(2044-2046)CGG>CTG	p.R682L	ACSL1_uc011ckm.1_Missense_Mutation_p.R511L|ACSL1_uc003iwt.1_Missense_Mutation_p.R682L|ACSL1_uc003iwu.1_Missense_Mutation_p.R682L|ACSL1_uc011ckn.1_Missense_Mutation_p.R648L|ACSL1_uc003iws.1_Missense_Mutation_p.R242L	NM_001995	NP_001986	P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	682	Cytoplasmic (Potential).				digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(2)	2		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
SLC25A4	291	broad.mit.edu	37	4	186068023	186068023	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186068023A>G	uc003ixd.2	+	4	924	c.795A>G	c.(793-795)GAA>GAG	p.E265E	SLC25A4_uc003ixe.2_RNA	NM_001151	NP_001142	P12235	ADT1_HUMAN	adenine nucleotide translocator 1	265	Solcar 3.				energy reserve metabolic process|interspecies interaction between organisms|mitochondrial genome maintenance|negative regulation of necrotic cell death|regulation of insulin secretion|viral reproduction	integral to plasma membrane|mitochondrial inner membrane	adenine transmembrane transporter activity|protein binding			ovary(1)	1		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;4.48e-44)|Epithelial(43;2.1e-41)|all cancers(43;1.37e-36)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)	Adenosine triphosphate(DB00171)|Clodronate(DB00720)													---	---	---	---
FAM149A	25854	broad.mit.edu	37	4	187084649	187084649	+	Missense_Mutation	SNP	G	A	A	rs139445329	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187084649G>A	uc003iyt.3	+	10	1484	c.905G>A	c.(904-906)CGG>CAG	p.R302Q	FAM149A_uc011cla.1_Missense_Mutation_p.R302Q|FAM149A_uc003iyu.3_Missense_Mutation_p.R302Q|FAM149A_uc010isl.2_Missense_Mutation_p.R302Q|FAM149A_uc011clb.1_Missense_Mutation_p.R302Q	NM_015398	NP_056213	A5PLN7	F149A_HUMAN	hypothetical protein LOC25854	593										breast(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)														---	---	---	---
TRIML2	205860	broad.mit.edu	37	4	189013068	189013068	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189013068G>T	uc003izl.2	-	7	659	c.623C>A	c.(622-624)GCT>GAT	p.A208D	TRIML2_uc003izj.1_Missense_Mutation_p.A36D|TRIML2_uc003izk.1_Missense_Mutation_p.A16D|TRIML2_uc011cle.1_Missense_Mutation_p.A283D	NM_173553	NP_775824	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	208	B30.2/SPRY.						ligase activity			central_nervous_system(2)	2		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)														---	---	---	---
CCDC127	133957	broad.mit.edu	37	5	206059	206059	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:206059T>C	uc003jam.1	-	3	236	c.136A>G	c.(136-138)AGG>GGG	p.R46G		NM_145265	NP_660308	Q96BQ5	CC127_HUMAN	coiled-coil domain containing 127	46											0			all cancers(22;0.0236)|Lung(60;0.113)															---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1073892	1073892	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1073892G>A	uc003jbu.2	-	17	2163	c.2097C>T	c.(2095-2097)AAC>AAT	p.N699N		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	699					potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)													---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5462178	5462178	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5462178A>G	uc003jdm.3	+	13	2953	c.2731A>G	c.(2731-2733)ACA>GCA	p.T911A		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	911										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5464615	5464615	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5464615A>G	uc003jdm.3	+	13	5390	c.5168A>G	c.(5167-5169)CAC>CGC	p.H1723R		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	1723	Pro-rich.									ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14497134	14497134	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14497134C>T	uc003jff.2	+						TRIO_uc003jfg.2_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)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14498254	14498254	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14498254G>A	uc003jff.2	+	52	8110	c.8104G>A	c.(8104-8106)GTT>ATT	p.V2702I	TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2702	Ig-like C2-type.				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)																	---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15936943	15936943	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15936943G>A	uc003jfn.1	+	4	1605	c.1124G>A	c.(1123-1125)TGC>TAC	p.C375Y		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	375	LRR 8.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
ZNF622	90441	broad.mit.edu	37	5	16465449	16465449	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16465449A>G	uc003jfq.2	-	1	446	c.326T>C	c.(325-327)ATG>ACG	p.M109T		NM_033414	NP_219482	Q969S3	ZN622_HUMAN	zinc finger protein 622	109						cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21802401	21802401	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21802401G>A	uc010iuc.2	-	7	1589	c.1131C>T	c.(1129-1131)GAC>GAT	p.D377D	CDH12_uc011cno.1_Silent_p.D337D|CDH12_uc003jgk.2_Silent_p.D377D	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	377	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24493022	24493022	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24493022T>G	uc003jgr.1	-	10	1860	c.1528A>C	c.(1528-1530)ATA>CTA	p.I510L	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	510	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31534401	31534401	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31534401C>T	uc003jhj.3	+	2	231	c.104C>T	c.(103-105)GCC>GTC	p.A35V	RNASEN_uc003jhh.2_5'Flank|RNASEN_uc003jhg.2_5'Flank|RNASEN_uc003jhi.2_5'Flank|C5orf22_uc011cnw.1_RNA|C5orf22_uc003jhk.3_5'UTR	NM_018356	NP_060826	Q49AR2	CE022_HUMAN	hypothetical protein LOC55322	35										ovary(2)	2																		---	---	---	---
ZFR	51663	broad.mit.edu	37	5	32417836	32417836	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32417836T>A	uc003jhr.1	-	4	562	c.482A>T	c.(481-483)TAC>TTC	p.Y161F	ZFR_uc010iun.1_Missense_Mutation_p.Y161F	NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	161	Ala-rich.				multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)														---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33658358	33658358	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33658358C>T	uc003jia.1	-	7	1284	c.1121G>A	c.(1120-1122)CGC>CAC	p.R374H	ADAMTS12_uc010iuq.1_Missense_Mutation_p.R374H	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	374	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
C1QTNF3	114899	broad.mit.edu	37	5	34043119	34043119	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34043119C>T	uc003jin.2	-						C1QTNF3_uc003jio.2_Missense_Mutation_p.A38T	NM_030945	NP_112207			C1q and tumor necrosis factor related protein 3							collagen					0	all_lung(31;0.0207)																	---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35646909	35646909	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35646909A>C	uc003jjo.2	+	5	837	c.726A>C	c.(724-726)GAA>GAC	p.E242D	SPEF2_uc003jjn.1_Missense_Mutation_p.E242D|SPEF2_uc003jjq.3_Missense_Mutation_p.E242D	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	242	Potential.				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35807348	35807348	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35807348A>G	uc003jjo.2	+	36	5483	c.5372A>G	c.(5371-5373)AAG>AGG	p.K1791R	SPEF2_uc003jjp.1_Missense_Mutation_p.K1277R|SPEF2_uc003jjr.2_Missense_Mutation_p.K846R	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	1791					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
C9	735	broad.mit.edu	37	5	39288948	39288948	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39288948T>C	uc003jlv.3	-	10	1611	c.1522A>G	c.(1522-1524)AGA>GGA	p.R508G		NM_001737	NP_001728	P02748	CO9_HUMAN	complement component 9 precursor	508	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis|hemolysis by symbiont of host erythrocytes	extracellular region|membrane attack complex					0	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)															---	---	---	---
C9	735	broad.mit.edu	37	5	39316123	39316123	+	Silent	SNP	G	A	A	rs139000312	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39316123G>A	uc003jlv.3	-	6	713	c.624C>T	c.(622-624)GGC>GGT	p.G208G		NM_001737	NP_001728	P02748	CO9_HUMAN	complement component 9 precursor	208	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis|hemolysis by symbiont of host erythrocytes	extracellular region|membrane attack complex					0	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)															---	---	---	---
C6	729	broad.mit.edu	37	5	41201782	41201782	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41201782A>T	uc003jmk.2	-	3	388	c.178T>A	c.(178-180)TTT>ATT	p.F60I	C6_uc003jml.1_Missense_Mutation_p.F60I	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	60	TSP type-1 1.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)																---	---	---	---
SNX18	112574	broad.mit.edu	37	5	53814454	53814454	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53814454C>A	uc003jpj.3	+	1	862	c.672C>A	c.(670-672)ACC>ACA	p.T224T	SNX18_uc011cqg.1_Silent_p.T224T|SNX18_uc003jpi.3_Silent_p.T224T	NM_052870	NP_443102	Q96RF0	SNX18_HUMAN	sorting nexin 18 isoform b	224					cell communication|endocytosis|positive regulation of GTPase activity|protein transport	endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane	phosphatidylinositol binding|protein binding				0		Lung NSC(810;3.46e-05)|Breast(144;0.102)																---	---	---	---
IL6ST	3572	broad.mit.edu	37	5	55247857	55247857	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55247857G>A	uc003jqq.2	-	13	1854	c.1599C>T	c.(1597-1599)AAC>AAT	p.N533N	IL6ST_uc010iwb.2_Silent_p.N472N|IL6ST_uc010iwc.2_Intron|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_Silent_p.N244N|IL6ST_uc003jqr.2_3'UTR|IL6ST_uc010iwe.1_5'Flank	NM_002184	NP_002175	P40189	IL6RB_HUMAN	interleukin 6 signal transducer isoform 1	533	Extracellular (Potential).|Fibronectin type-III 5.				interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)						O		hepatocellular ca								---	---	---	---
C5orf35	133383	broad.mit.edu	37	5	56209799	56209799	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56209799T>C	uc003jqx.2	+	4	1062	c.689T>C	c.(688-690)GTC>GCC	p.V230A	C5orf35_uc003jqy.2_RNA	NM_153706	NP_714917	Q8NE22	CE035_HUMAN	hypothetical protein LOC133383	230										ovary(1)	1		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.173)		OV - Ovarian serous cystadenocarcinoma(10;2.58e-39)														---	---	---	---
HTR1A	3350	broad.mit.edu	37	5	63257304	63257304	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63257304G>A	uc011cqt.1	-	1	243	c.243C>T	c.(241-243)ACC>ACT	p.T81T		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	81	Helical; Name=2; (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)													---	---	---	---
OCLN	4950	broad.mit.edu	37	5	68805114	68805114	+	Missense_Mutation	SNP	G	A	A	rs116363086	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68805114G>A	uc003jwu.2	+	3	633	c.197G>A	c.(196-198)CGG>CAG	p.R66Q	OCLN_uc003jwv.3_Missense_Mutation_p.R66Q	NM_002538	NP_002529			occludin												0		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
UTP15	84135	broad.mit.edu	37	5	72872794	72872794	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72872794G>A	uc003kcw.1	+	8	1050	c.827G>A	c.(826-828)AGC>AAC	p.S276N	UTP15_uc011cso.1_Missense_Mutation_p.S257N|UTP15_uc011csp.1_Missense_Mutation_p.S86N|UTP15_uc010ize.1_Missense_Mutation_p.S276N	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,	276	WD 6.				rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)														---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74130280	74130280	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74130280G>A	uc003kdm.2	-	5	504	c.461C>T	c.(460-462)GCC>GTC	p.A154V	FAM169A_uc010izm.2_Missense_Mutation_p.A154V|FAM169A_uc003kdl.2_Intron	NM_015566	NP_056381	Q9Y6X4	F169A_HUMAN	hypothetical protein LOC26049	154											0																		---	---	---	---
HMGCR	3156	broad.mit.edu	37	5	74643075	74643075	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74643075C>T	uc003kdp.2	+	6	653	c.497C>T	c.(496-498)CCT>CTT	p.P166L	HMGCR_uc011cst.1_Missense_Mutation_p.P186L|HMGCR_uc003kdq.2_Missense_Mutation_p.P166L|HMGCR_uc010izn.1_Missense_Mutation_p.P6L	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	166	Helical; (Potential).				cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)													---	---	---	---
WDR41	55255	broad.mit.edu	37	5	76785281	76785281	+	Splice_Site	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76785281C>T	uc003kff.1	-	2	454	c.167_splice	c.e2+1	p.R56_splice	WDR41_uc011csy.1_Splice_Site_p.R56_splice|WDR41_uc011csz.1_Intron|WDR41_uc011cta.1_Splice_Site|WDR41_uc011ctb.1_Splice_Site	NM_018268	NP_060738			WD repeat domain 41												0		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79027504	79027504	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79027504C>T	uc003kgc.2	+	2	2988	c.2916C>T	c.(2914-2916)TGC>TGT	p.C972C		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	972						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82833689	82833689	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82833689A>G	uc003kii.3	+	8	5223	c.4867A>G	c.(4867-4869)ACT>GCT	p.T1623A	VCAN_uc003kij.3_Missense_Mutation_p.T636A|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.T287A	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	1623	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
ERAP1	51752	broad.mit.edu	37	5	96139461	96139461	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96139461A>G	uc003kmm.2	-	2	516	c.169T>C	c.(169-171)TAC>CAC	p.Y57H	ERAP1_uc003kml.2_Missense_Mutation_p.Y57H|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_Missense_Mutation_p.Y57H	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding	57	Lumenal (Potential).				angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)														---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107700605	107700605	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107700605C>T	uc011cvc.1	-	3	1615	c.1208G>A	c.(1207-1209)GGC>GAC	p.G403D	FBXL17_uc003kon.3_Missense_Mutation_p.G5D	NM_001163315	NP_001156787	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17	403											0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
WDR36	134430	broad.mit.edu	37	5	110439999	110439999	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110439999T>G	uc003kpd.2	+	8	1139	c.1022T>G	c.(1021-1023)TTT>TGT	p.F341C	WDR36_uc010jbu.2_RNA	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	341	WD 4.				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)														---	---	---	---
APC	324	broad.mit.edu	37	5	112164562	112164562	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112164562A>G	uc010jby.2	+	14	2016	c.1636A>G	c.(1636-1638)AGT>GGT	p.S546G	APC_uc011cvt.1_Missense_Mutation_p.S528G|APC_uc003kpz.3_Missense_Mutation_p.S546G|APC_uc003kpy.3_Missense_Mutation_p.S546G|APC_uc010jbz.2_Missense_Mutation_p.S263G|APC_uc010jca.2_Intron	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	546	ARM 2.|Leu-rich.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.?(1)		large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)			12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			---	---	---	---
MCC	4163	broad.mit.edu	37	5	112379243	112379243	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112379243T>C	uc003kqj.3	-	15	2700	c.2170A>G	c.(2170-2172)ACC>GCC	p.T724A	MCC_uc003kqk.3_RNA|MCC_uc003kql.3_Missense_Mutation_p.T914A	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2	724					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)												OREG0016728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TSSK1B	83942	broad.mit.edu	37	5	112769928	112769928	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112769928G>A	uc003kqm.2	-	1	801	c.609C>T	c.(607-609)GGC>GGT	p.G203G	MCC_uc003kql.3_Intron	NM_032028	NP_114417	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1	203	Protein kinase.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|skin(2)|stomach(1)	5		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)														---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118433795	118433795	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118433795G>A	uc003ksd.2	+	2	390	c.209G>A	c.(208-210)GGC>GAC	p.G70D	DMXL1_uc010jcl.1_Missense_Mutation_p.G70D|DMXL1_uc003ksc.1_Missense_Mutation_p.G70D	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	70										ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)														---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118451940	118451940	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118451940C>A	uc003ksd.2	+	7	833	c.652C>A	c.(652-654)CAA>AAA	p.Q218K	DMXL1_uc010jcl.1_Missense_Mutation_p.Q218K|DMXL1_uc003ksc.1_Missense_Mutation_p.Q218K	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	218										ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)														---	---	---	---
ADAMTS19	171019	broad.mit.edu	37	5	129072766	129072766	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129072766T>G	uc003kvb.1	+	23	3479	c.3479T>G	c.(3478-3480)CTG>CGG	p.L1160R	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1160	PLAC.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131080362	131080362	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131080362A>G	uc003kvp.1	-	2	256	c.114T>C	c.(112-114)GAT>GAC	p.D38D	FNIP1_uc003kvs.1_Silent_p.D38D|FNIP1_uc003kvt.1_Silent_p.D38D|FNIP1_uc010jdm.1_Silent_p.D38D|FNIP1_uc003kvu.2_Silent_p.D38D	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	Error:Variant_position_missing_in_Q8TEU7_after_alignment					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)														---	---	---	---
TCF7	6932	broad.mit.edu	37	5	133478495	133478495	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133478495T>C	uc003kyt.2	+	7	1035	c.839T>C	c.(838-840)ATG>ACG	p.M280T	TCF7_uc003kyu.1_Missense_Mutation_p.M165T|TCF7_uc003kyv.2_Missense_Mutation_p.M165T|TCF7_uc003kyw.2_Missense_Mutation_p.M165T|TCF7_uc003kyx.2_Missense_Mutation_p.M78T|TCF7_uc003kyy.2_Missense_Mutation_p.M165T|TCF7_uc003kyz.2_Missense_Mutation_p.M165T|TCF7_uc003kza.2_Missense_Mutation_p.M165T|TCF7_uc003kzb.2_Missense_Mutation_p.M94T|TCF7_uc010jdu.2_5'Flank	NM_003202	NP_003193	P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific,	280	HMG box.				cellular response to interleukin-4|immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription regulatory region DNA binding				0		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
CATSPER3	347732	broad.mit.edu	37	5	134305635	134305635	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134305635C>T	uc003lag.2	+	2	173	c.105C>T	c.(103-105)AAC>AAT	p.N35N		NM_178019	NP_821138	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	35	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
CATSPER3	347732	broad.mit.edu	37	5	134332192	134332192	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134332192A>G	uc003lag.2	+	3	550	c.482A>G	c.(481-483)CAG>CGG	p.Q161R		NM_178019	NP_821138	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	161	Helical; Name=Segment S4; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KIF20A	10112	broad.mit.edu	37	5	137517429	137517429	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137517429A>G	uc003lcj.2	+						KIF20A_uc011cyo.1_Intron	NM_005733	NP_005724			kinesin family member 20A						cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
KIF20A	10112	broad.mit.edu	37	5	137519724	137519724	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137519724G>T	uc003lcj.2	+	11	1778	c.1282G>T	c.(1282-1284)GGA>TGA	p.G428*	KIF20A_uc011cyo.1_Nonsense_Mutation_p.G410*	NM_005733	NP_005724	O95235	KI20A_HUMAN	kinesin family member 20A	428	Kinesin-motor.				cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
CDC23	8697	broad.mit.edu	37	5	137525405	137525405	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137525405G>A	uc003lcl.2	-	15	1571	c.1540C>T	c.(1540-1542)CGC>TGC	p.R514C		NM_004661	NP_004652	Q9UJX2	CDC23_HUMAN	cell division cycle protein 23	514					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|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 K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137710881	137710881	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137710881T>C	uc003lcy.1	+	3	660	c.460T>C	c.(460-462)TTG>CTG	p.L154L	KDM3B_uc010jew.1_5'UTR	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	154					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
HSPA9	3313	broad.mit.edu	37	5	137893599	137893599	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137893599T>C	uc003ldf.2	-	13	1700	c.1592A>G	c.(1591-1593)CAT>CGT	p.H531R	HSPA9_uc003lde.2_5'Flank|HSPA9_uc011cyw.1_Intron	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor	531					anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
CTNNA1	1495	broad.mit.edu	37	5	138268334	138268334	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138268334A>G	uc003ldh.2	+	17	2461	c.2366A>G	c.(2365-2367)CAG>CGG	p.Q789R	CTNNA1_uc011cyx.1_Missense_Mutation_p.Q686R|CTNNA1_uc011cyy.1_Missense_Mutation_p.Q666R|CTNNA1_uc003ldi.2_Missense_Mutation_p.Q487R|CTNNA1_uc003ldj.2_Missense_Mutation_p.Q789R|CTNNA1_uc003ldl.2_Missense_Mutation_p.Q419R	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1	789				Q -> H (in Ref. 1; BAA03530).	adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
UBE2D2	7322	broad.mit.edu	37	5	139002941	139002941	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139002941T>C	uc003ler.2	+						UBE2D2_uc003leq.2_Intron	NM_003339	NP_003330			ubiquitin-conjugating enzyme E2D 2 isoform 1						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|protein binding|ubiquitin-protein ligase activity			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
APBB3	10307	broad.mit.edu	37	5	139941778	139941778	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139941778G>A	uc003lgd.1	-	6	892	c.533C>T	c.(532-534)GCC>GTC	p.A178V	APBB3_uc003lgb.1_5'UTR|APBB3_uc003lgc.1_5'UTR|APBB3_uc003lge.1_Missense_Mutation_p.A178V|APBB3_uc003lgf.1_RNA|APBB3_uc010jfp.1_RNA|APBB3_uc011czi.1_5'UTR|APBB3_uc010jfq.1_5'Flank|SLC35A4_uc003lgg.1_5'Flank|SLC35A4_uc003lgh.1_5'Flank	NM_133172	NP_573418	O95704	APBB3_HUMAN	amyloid beta precursor protein-binding, family	178	PID 1.					actin cytoskeleton|cytoplasm				ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
TMCO6	55374	broad.mit.edu	37	5	140023147	140023147	+	Splice_Site	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140023147A>G	uc003lgl.2	+	8	908	c.807_splice	c.e8-2	p.S269_splice	TMCO6_uc003lgm.2_Splice_Site_p.S275_splice|TMCO6_uc010jft.2_Splice_Site_p.S29_splice|TMCO6_uc003lgn.2_Splice_Site_p.S160_splice|TMCO6_uc003lgo.2_Splice_Site_p.S29_splice	NM_018502	NP_060972			transmembrane and coiled-coil domains 6						protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
TMCO6	55374	broad.mit.edu	37	5	140023674	140023674	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140023674T>C	uc003lgl.2	+						TMCO6_uc003lgm.2_Intron|TMCO6_uc010jft.2_Intron|TMCO6_uc003lgn.2_Intron|TMCO6_uc003lgo.2_Intron	NM_018502	NP_060972			transmembrane and coiled-coil domains 6						protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140188686	140188686	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188686C>T	uc003lhi.2	+	1	2015	c.1914C>T	c.(1912-1914)GAC>GAT	p.D638D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.D638D|PCDHA4_uc011daa.1_Silent_p.D638D	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	638	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA5	56143	broad.mit.edu	37	5	140202575	140202575	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140202575G>A	uc003lhl.2	+	1	1215	c.1215G>A	c.(1213-1215)TCG>TCA	p.S405S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Silent_p.S405S|PCDHA5_uc003lhj.1_Silent_p.S405S	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	405	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA8	56140	broad.mit.edu	37	5	140221176	140221176	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140221176C>T	uc003lhs.2	+	1	270	c.270C>T	c.(268-270)ATC>ATT	p.I90I	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Silent_p.I90I	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	90	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA10	56139	broad.mit.edu	37	5	140235929	140235929	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140235929T>C	uc003lhx.2	+	1	296	c.296T>C	c.(295-297)GTG>GCG	p.V99A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Missense_Mutation_p.V99A|PCDHA10_uc011dad.1_Missense_Mutation_p.V99A	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	99	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA12	56137	broad.mit.edu	37	5	140257241	140257241	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140257241C>T	uc003lic.2	+	1	2311	c.2184C>T	c.(2182-2184)ACC>ACT	p.T728T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc011daf.1_Silent_p.T728T	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	728	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB4	56131	broad.mit.edu	37	5	140503797	140503797	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140503797C>T	uc003lip.1	+	1	2217	c.2217C>T	c.(2215-2217)AGC>AGT	p.S739S		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	739	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB8	56128	broad.mit.edu	37	5	140559636	140559636	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140559636T>C	uc011dai.1	+	1	2207	c.2021T>C	c.(2020-2022)CTT>CCT	p.L674P	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	674	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB16	57717	broad.mit.edu	37	5	140562237	140562237	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140562237G>A	uc003liv.2	+	1	1258	c.103G>A	c.(103-105)GTA>ATA	p.V35I	PCDHB16_uc010jfw.1_Intron	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	35	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB11	56125	broad.mit.edu	37	5	140580848	140580848	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140580848G>A	uc003liy.2	+	1	1501	c.1501G>A	c.(1501-1503)GCC>ACC	p.A501T	PCDHB11_uc011daj.1_Missense_Mutation_p.A136T	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	501	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626735	140626735	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626735G>A	uc003lje.2	+	1	1589	c.1589G>A	c.(1588-1590)CGC>CAC	p.R530H		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	530	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
SLC25A2	83884	broad.mit.edu	37	5	140683099	140683099	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140683099C>T	uc003ljf.2	-	1	514	c.334G>A	c.(334-336)GCG>ACG	p.A112T		NM_031947	NP_114153	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 member 2	112	Helical; Name=3; (Potential).|Solcar 2.				mitochondrial ornithine transport|urea cycle	integral to membrane|mitochondrial inner membrane	L-ornithine transmembrane transporter activity			ovary(1)	1		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)													---	---	---	---
PCDHGA6	56109	broad.mit.edu	37	5	140756049	140756049	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140756049C>T	uc003ljy.1	+	1	2399	c.2399C>T	c.(2398-2400)ACG>ATG	p.T800M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Missense_Mutation_p.T800M	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	800	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGB5	56101	broad.mit.edu	37	5	140779417	140779417	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140779417C>T	uc003lkf.1	+	1	1723	c.1723C>T	c.(1723-1725)CCG>TCG	p.P575S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc011daw.1_Missense_Mutation_p.P575S	NM_018925	NP_061748	Q9Y5G0	PCDGH_HUMAN	protocadherin gamma subfamily B, 5 isoform 1	575	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA12	26025	broad.mit.edu	37	5	140811041	140811041	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140811041G>A	uc003lkt.1	+	1	884	c.715G>A	c.(715-717)GCA>ACA	p.A239T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc011dba.1_Missense_Mutation_p.A239T	NM_003735	NP_003726	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12 isoform 1	239	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDH1	5097	broad.mit.edu	37	5	141243692	141243692	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141243692G>A	uc003llq.2	-	3	2321	c.2204C>T	c.(2203-2205)ACG>ATG	p.T735M	PCDH1_uc003llp.2_Missense_Mutation_p.T735M|PCDH1_uc011dbf.1_Missense_Mutation_p.T713M	NM_002587	NP_002578	Q08174	PCDH1_HUMAN	protocadherin 1 isoform 1 precursor	735	Extracellular (Potential).|Cadherin 7.				cell-cell signaling|homophilic cell adhesion|nervous system development	cell-cell junction|integral to plasma membrane	calcium ion binding			ovary(5)	5		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)														---	---	---	---
RBM27	54439	broad.mit.edu	37	5	145650551	145650551	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145650551T>G	uc003lnz.3	+	18	2892	c.2726T>G	c.(2725-2727)CTC>CGC	p.L909R		NM_018989	NP_061862	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	909					mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148386495	148386495	+	Nonsense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148386495G>C	uc003lpu.2	-	16	3776	c.3624C>G	c.(3622-3624)TAC>TAG	p.Y1208*	SH3TC2_uc003lpp.1_RNA|SH3TC2_uc010jgw.2_Nonsense_Mutation_p.Y852*|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_Nonsense_Mutation_p.Y755*|SH3TC2_uc010jgx.2_Nonsense_Mutation_p.Y1201*	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1208							binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ARSI	340075	broad.mit.edu	37	5	149677000	149677000	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149677000T>C	uc003lrv.2	-	2	2076	c.1487A>G	c.(1486-1488)AAC>AGC	p.N496S		NM_001012301	NP_001012301	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I precursor	496						endoplasmic reticulum|extracellular region	arylsulfatase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
TCOF1	6949	broad.mit.edu	37	5	149776323	149776323	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149776323G>A	uc003lry.2	+	24	4368	c.4260G>A	c.(4258-4260)GAG>GAA	p.E1420E	TCOF1_uc011dch.1_Silent_p.E1383E|TCOF1_uc003lrz.2_Silent_p.E1382E|TCOF1_uc003lrx.2_Silent_p.E1344E|TCOF1_uc003lsa.2_Silent_p.E1343E	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1420					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
NDST1	3340	broad.mit.edu	37	5	149901204	149901204	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149901204C>T	uc003lsk.3	+	2	890	c.388C>T	c.(388-390)CGT>TGT	p.R130C	NDST1_uc011dcj.1_Missense_Mutation_p.R130C|NDST1_uc003lsl.2_Missense_Mutation_p.R130C	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	130	Heparan sulfate N-deacetylase 1.|Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
NDST1	3340	broad.mit.edu	37	5	149921174	149921174	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149921174G>A	uc003lsk.3	+	9	2294	c.1792G>A	c.(1792-1794)GAG>AAG	p.E598K	NDST1_uc011dcj.1_Missense_Mutation_p.E598K	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	598	Heparan sulfate N-deacetylase 1.|Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150946762	150946762	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150946762C>T	uc003lue.3	-	1	1744	c.1731G>A	c.(1729-1731)TGG>TGA	p.W577*	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Nonsense_Mutation_p.W577*	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	577	Extracellular (Potential).|Cadherin 5.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150948282	150948282	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150948282A>G	uc003lue.3	-	1	224	c.211T>C	c.(211-213)TAC>CAC	p.Y71H	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Missense_Mutation_p.Y71H	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	71	Extracellular (Potential).|Cadherin 1.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151179453	151179453	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151179453C>T	uc003lun.2	+	9	1018	c.847C>T	c.(847-849)CGT>TGT	p.R283C	G3BP1_uc003lum.2_Missense_Mutation_p.R283C|G3BP1_uc011dcu.1_Missense_Mutation_p.R101C|G3BP1_uc010jhz.2_Missense_Mutation_p.R101C|G3BP1_uc003luq.2_Intron	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	283					Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)															---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	153026477	153026477	+	Intron	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153026477T>A	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_Intron|GRIA1_uc011dcy.1_Intron|GRIA1_uc011dcz.1_Intron|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655			glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	153029894	153029894	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153029894A>G	uc003lva.3	+	4	830	c.465A>G	c.(463-465)TTA>TTG	p.L155L	GRIA1_uc003luy.3_Silent_p.L155L|GRIA1_uc003luz.3_Silent_p.L60L|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Silent_p.L75L|GRIA1_uc011dcx.1_Silent_p.L86L|GRIA1_uc011dcy.1_Silent_p.L165L|GRIA1_uc011dcz.1_Silent_p.L165L|GRIA1_uc010jia.1_Silent_p.L135L	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	155	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
GEMIN5	25929	broad.mit.edu	37	5	154284999	154284999	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154284999T>C	uc003lvx.3	-	17	2516	c.2433A>G	c.(2431-2433)TCA>TCG	p.S811S	GEMIN5_uc011ddk.1_Silent_p.S810S	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	811					ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding	p.S811L(1)		skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
KIF4B	285643	broad.mit.edu	37	5	154395130	154395130	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154395130C>T	uc010jih.1	+	1	1871	c.1711C>T	c.(1711-1713)CTG>TTG	p.L571L		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	571	Potential.				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
FAM71B	153745	broad.mit.edu	37	5	156592737	156592737	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156592737C>T	uc003lwn.2	-	1	543	c.443G>A	c.(442-444)CGT>CAT	p.R148H		NM_130899	NP_570969	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	148						nucleus				ovary(4)|pancreas(1)|skin(1)	6	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
ADAM19	8728	broad.mit.edu	37	5	156964960	156964960	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156964960A>C	uc003lwz.2	-	4	355	c.291T>G	c.(289-291)ACT>ACG	p.T97T	ADAM19_uc003lww.1_5'UTR|ADAM19_uc011ddr.1_Silent_p.T28T	NM_033274	NP_150377	Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19 preproprotein	97					proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
THG1L	54974	broad.mit.edu	37	5	157164949	157164949	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157164949T>C	uc003lxd.2	+	5	808	c.682T>C	c.(682-684)TAT>CAT	p.Y228H	THG1L_uc011ddu.1_Missense_Mutation_p.Y96H	NM_017872	NP_060342	Q9NWX6	THG1_HUMAN	interphase cytoplasmic foci protein 45	228					protein homotetramerization|tRNA modification	mitochondrion	GTP binding|metal ion binding|tRNA guanylyltransferase activity				0	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
C1QTNF2	114898	broad.mit.edu	37	5	159781796	159781796	+	Missense_Mutation	SNP	G	A	A	rs115558158	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159781796G>A	uc003lyd.2	-	2	362	c.358C>T	c.(358-360)CGG>TGG	p.R120W		NM_031908	NP_114114	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	75	Collagen-like.					collagen				skin(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
C1QTNF2	114898	broad.mit.edu	37	5	159781937	159781937	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159781937G>A	uc003lyd.2	-	2	221	c.217C>T	c.(217-219)CGG>TGG	p.R73W		NM_031908	NP_114114	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	28						collagen				skin(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160076199	160076199	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160076199A>T	uc003lym.1	-	8	1587	c.740T>A	c.(739-741)CTC>CAC	p.L247H	ATP10B_uc003lyp.2_Missense_Mutation_p.L247H|ATP10B_uc011deg.1_Missense_Mutation_p.L291H|ATP10B_uc003lyo.2_Missense_Mutation_p.L219H	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	247	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
GABRA1	2554	broad.mit.edu	37	5	161292772	161292772	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161292772G>T	uc010jiw.2	+	5	701	c.233G>T	c.(232-234)GGA>GTA	p.G78V	GABRA1_uc010jix.2_Missense_Mutation_p.G78V|GABRA1_uc010jiy.2_Missense_Mutation_p.G78V|GABRA1_uc003lyx.3_Missense_Mutation_p.G78V|GABRA1_uc010jiz.2_Missense_Mutation_p.G78V|GABRA1_uc010jja.2_Missense_Mutation_p.G78V|GABRA1_uc010jjb.2_Missense_Mutation_p.G78V	NM_000806	NP_000797	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	78	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|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)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)													---	---	---	---
GABRG2	2566	broad.mit.edu	37	5	161530885	161530885	+	Intron	SNP	C	G	G	rs144248417	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161530885C>G	uc003lyz.3	+						GABRG2_uc010jjc.2_Intron|GABRG2_uc003lyy.3_Intron|GABRG2_uc011dej.1_Intron	NM_000816	NP_000807			gamma-aminobutyric acid A receptor, gamma 2						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)														---	---	---	---
GABRG2	2566	broad.mit.edu	37	5	161530980	161530980	+	Missense_Mutation	SNP	A	T	T	rs78261481	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161530980A>T	uc003lyz.3	+	6	1075	c.717A>T	c.(715-717)CAA>CAT	p.Q239H	GABRG2_uc010jjc.2_Missense_Mutation_p.Q279H|GABRG2_uc003lyy.3_Missense_Mutation_p.Q239H|GABRG2_uc011dej.1_Missense_Mutation_p.Q144H	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	239	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)														---	---	---	---
NUDCD2	134492	broad.mit.edu	37	5	162887021	162887021	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162887021T>C	uc003lze.2	-	1	123	c.36A>G	c.(34-36)GTA>GTG	p.V12V	HMMR_uc003lzh.2_5'Flank|HMMR_uc003lzf.2_5'Flank|HMMR_uc003lzg.2_5'Flank|HMMR_uc011dem.1_5'Flank	NM_145266	NP_660309	Q8WVJ2	NUDC2_HUMAN	NudC domain containing 2	12						intracellular					0	Renal(175;0.000281)	Medulloblastoma(196;0.0207)|all_neural(177;0.0966)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0981)|OV - Ovarian serous cystadenocarcinoma(192;0.183)|Epithelial(171;0.247)														---	---	---	---
FBLL1	345630	broad.mit.edu	37	5	167957204	167957204	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167957204C>T	uc011dep.1	+	1	623	c.410C>T	c.(409-411)CCG>CTG	p.P137L		NR_024356				RecName: Full=rRNA/tRNA 2'-O-methyltransferase fibrillarin-like protein 1;          EC=2.1.1.-;												0																		---	---	---	---
CPEB4	80315	broad.mit.edu	37	5	173376500	173376500	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173376500T>C	uc003mcs.3	+						CPEB4_uc010jju.1_Intron|CPEB4_uc010jjv.2_Intron|CPEB4_uc011dfg.1_Intron|CPEB4_uc003mct.3_Intron|CPEB4_uc003mcu.3_Intron	NM_030627	NP_085130			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
CPEB4	80315	broad.mit.edu	37	5	173383109	173383109	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173383109G>A	uc003mcs.3	+	10	3565	c.2159G>A	c.(2158-2160)CGC>CAC	p.R720H	CPEB4_uc010jjv.2_Missense_Mutation_p.R703H|CPEB4_uc011dfg.1_Missense_Mutation_p.R695H|CPEB4_uc003mct.3_Missense_Mutation_p.R330H|CPEB4_uc003mcu.3_Missense_Mutation_p.R313H	NM_030627	NP_085130	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding	720							nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
SFXN1	94081	broad.mit.edu	37	5	174937167	174937167	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174937167G>A	uc003mda.2	+	4	529	c.391G>A	c.(391-393)GTC>ATC	p.V131I	SFXN1_uc003mdb.1_Missense_Mutation_p.V70I	NM_022754	NP_073591	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	131					iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
DDX41	51428	broad.mit.edu	37	5	176939374	176939374	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176939374C>T	uc003mho.2	-	15	1591	c.1570G>A	c.(1570-1572)GGG>AGG	p.G524R	DOK3_uc003mhi.3_5'Flank|DOK3_uc003mhj.3_5'Flank|DOK3_uc003mhk.2_5'Flank|DOK3_uc003mhl.2_5'Flank|DDX41_uc003mhm.2_Missense_Mutation_p.G304R|DDX41_uc003mhn.2_Missense_Mutation_p.G393R|DDX41_uc003mhp.2_Missense_Mutation_p.G393R	NM_016222	NP_057306	Q9UJV9	DDX41_HUMAN	DEAD-box protein abstrakt	524	Helicase C-terminal.				apoptosis|multicellular organismal development	catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|zinc ion binding				0	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)															---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177682023	177682023	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177682023G>A	uc003mje.2	-	16	1245	c.887C>T	c.(886-888)GCC>GTC	p.A296V	COL23A1_uc010jkt.2_Missense_Mutation_p.A178V	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	296	Extracellular (Potential).|Collagen-like 2.|Gly-rich.					collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177987735	177987735	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177987735T>C	uc003mje.2	-	2	667	c.309A>G	c.(307-309)CTA>CTG	p.L103L		NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	103	Extracellular (Potential).|Gly-rich.					collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
FLT4	2324	broad.mit.edu	37	5	180048190	180048190	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180048190G>A	uc003mma.3	-	14	2162	c.2083C>T	c.(2083-2085)CTG>TTG	p.L695L	FLT4_uc003mlz.3_Silent_p.L695L|FLT4_uc003mmb.1_Silent_p.L228L|FLT4_uc011dgy.1_Silent_p.L695L	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2	695	Ig-like C2-type 7.|Extracellular (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)									Congenital_Hereditary_Lymphedema				---	---	---	---
MGAT1	4245	broad.mit.edu	37	5	180218991	180218991	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180218991C>T	uc003mmg.3	-	2	1476	c.981G>A	c.(979-981)CAG>CAA	p.Q327Q	MGAT1_uc010jlf.2_Silent_p.Q327Q|MGAT1_uc010jlg.2_Silent_p.Q327Q|MGAT1_uc003mmh.3_Silent_p.Q327Q|MGAT1_uc010jlh.2_Silent_p.Q327Q|MGAT1_uc003mmi.3_Silent_p.Q327Q	NM_002406	NP_002397	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein	327	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
BTNL9	153579	broad.mit.edu	37	5	180486594	180486594	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180486594G>A	uc003mmt.2	+	11	1571	c.1340G>A	c.(1339-1341)CGG>CAG	p.R447Q		NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor	447	Cytoplasmic (Potential).|B30.2/SPRY.					integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
HUS1B	135458	broad.mit.edu	37	6	656665	656665	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:656665C>T	uc003mtg.2	-	1	300	c.280G>A	c.(280-282)GCA>ACA	p.A94T	EXOC2_uc003mtd.2_Intron|EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_148959	NP_683762	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint protein B	94											0	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)														---	---	---	---
HUS1B	135458	broad.mit.edu	37	6	656846	656846	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:656846G>A	uc003mtg.2	-	1	119	c.99C>T	c.(97-99)CGC>CGT	p.R33R	EXOC2_uc003mtd.2_Intron|EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_148959	NP_683762	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint protein B	33											0	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)														---	---	---	---
FOXF2	2295	broad.mit.edu	37	6	1390547	1390547	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1390547C>T	uc003mtm.2	+	1	479	c.365C>T	c.(364-366)ACG>ATG	p.T122M	FOXF2_uc003mtn.2_Missense_Mutation_p.T122M	NM_001452	NP_001443	Q12947	FOXF2_HUMAN	forkhead box F2	122	Fork-head.				epithelial to mesenchymal transition|genitalia development|palate development|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)														---	---	---	---
RIPK1	8737	broad.mit.edu	37	6	3085497	3085497	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3085497T>C	uc010jni.2	+	6	925	c.693T>C	c.(691-693)GCT>GCC	p.A231A	RIPK1_uc003muv.3_Silent_p.A68A|RIPK1_uc003muw.3_Silent_p.A166A|RIPK1_uc011dhs.1_Silent_p.A185A|RIPK1_uc003mux.2_Silent_p.A231A	NM_003804	NP_003795	Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine	231	Protein kinase.				activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)																---	---	---	---
PRPF4B	8899	broad.mit.edu	37	6	4044084	4044084	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4044084T>C	uc003mvv.2	+	6	1779	c.1688T>C	c.(1687-1689)GTG>GCG	p.V563A	PRPF4B_uc003mvw.2_RNA|PRPF4B_uc011dhv.1_RNA	NM_003913	NP_003904	Q13523	PRP4B_HUMAN	serine/threonine-protein kinase PRP4K	563						catalytic step 2 spliceosome	ATP binding|protein binding|protein serine/threonine kinase activity			breast(5)	5	Ovarian(93;0.0925)	all_hematologic(90;0.0895)																---	---	---	---
NUP153	9972	broad.mit.edu	37	6	17629625	17629625	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17629625A>G	uc003ncd.1	-	18	3005	c.2805T>C	c.(2803-2805)GGT>GGC	p.G935G	NUP153_uc011dje.1_Silent_p.G966G|NUP153_uc010jpl.1_Silent_p.G893G	NM_005124	NP_005115	P49790	NU153_HUMAN	nucleoporin 153kDa	935					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)															---	---	---	---
GPLD1	2822	broad.mit.edu	37	6	24436838	24436838	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24436838C>T	uc003ned.1	-	22	2435	c.2324G>A	c.(2323-2325)TGC>TAC	p.C775Y		NM_001503	NP_001494	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific	775						extracellular region	glycosylphosphatidylinositol phospholipase D activity			ovary(2)|kidney(1)	3																		---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24569143	24569143	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24569143A>G	uc011djo.1	-	13	2243	c.2006T>C	c.(2005-2007)GTG>GCG	p.V669A	KIAA0319_uc011djp.1_Missense_Mutation_p.V624A|KIAA0319_uc003neh.1_Missense_Mutation_p.V669A|KIAA0319_uc011djq.1_Missense_Mutation_p.V660A|KIAA0319_uc011djr.1_Missense_Mutation_p.V669A|KIAA0319_uc010jpt.1_Missense_Mutation_p.V80A	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor	669	PKD 4.|Extracellular (Potential).				negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
HIST1H1A	3024	broad.mit.edu	37	6	26017954	26017954	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26017954C>T	uc003nfo.2	-	1	87	c.7G>A	c.(7-9)GAA>AAA	p.E3K	HIST1H3A_uc003nfp.1_5'Flank	NM_005325	NP_005316	Q02539	H11_HUMAN	histone cluster 1, H1a	3					nucleosome assembly|spermatogenesis	nucleosome|nucleus	DNA binding			ovary(2)	2																OREG0017237	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HIST1H4G	8369	broad.mit.edu	37	6	26247036	26247036	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26247036C>T	uc003nhf.2	-	1	170	c.170G>A	c.(169-171)CGG>CAG	p.R57Q		NM_003547	NP_003538	Q99525	H4G_HUMAN	histone cluster 1, H4g	57					nucleosome assembly	nucleosome|nucleus	DNA binding				0		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)																---	---	---	---
BTN3A3	10384	broad.mit.edu	37	6	26444334	26444334	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26444334T>C	uc003nhz.2	+	4	415	c.235T>C	c.(235-237)TAT>CAT	p.Y79H	BTN3A3_uc003nia.2_Missense_Mutation_p.Y37H|BTN3A3_uc011dkn.1_Missense_Mutation_p.Y37H	NM_006994	NP_008925	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3 isoform a	79	Extracellular (Potential).|Ig-like V-type 1.					integral to membrane					0																		---	---	---	---
ZNF391	346157	broad.mit.edu	37	6	27368839	27368839	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27368839C>T	uc003njf.1	+	3	1208	c.690C>T	c.(688-690)TTC>TTT	p.F230F		NM_001076781	NP_001070249	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	230	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(2)|skin(1)	3																		---	---	---	---
HIST1H2AM	8336	broad.mit.edu	37	6	27860700	27860700	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27860700C>T	uc003nkb.1	-	1	264	c.228G>A	c.(226-228)AAG>AAA	p.K76K	HIST1H3J_uc003nka.2_5'Flank|HIST1H2BO_uc003nkc.1_5'Flank	NM_003514	NP_003505	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	76					nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding			ovary(2)	2																		---	---	---	---
SCAND3	114821	broad.mit.edu	37	6	28541269	28541269	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28541269A>G	uc003nlo.2	-	4	3015	c.2397T>C	c.(2395-2397)AGT>AGC	p.S799S		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	799					DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
SCAND3	114821	broad.mit.edu	37	6	28554497	28554497	+	5'UTR	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28554497C>T	uc003nlo.2	-	1					uc003nlp.1_5'Flank	NM_052923	NP_443155			SCAN domain containing 3						DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
HLA-A	3105	broad.mit.edu	37	6	29911150	29911150	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29911150T>C	uc003nol.2	+	3	449	c.449T>C	c.(448-450)CTG>CCG	p.L150P	HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_RNA|HLA-A_uc010jrq.2_Missense_Mutation_p.L29P|HLA-A_uc003nok.2_Missense_Mutation_p.L29P|HLA-A_uc003non.2_Missense_Mutation_p.L150P|HLA-A_uc003noo.2_Missense_Mutation_p.L150P|HLA-A_uc010jrr.2_Missense_Mutation_p.L150P|HLA-A_uc003nom.2_Missense_Mutation_p.L29P|HLA-A_uc010klp.2_Missense_Mutation_p.L122P|HLA-A_uc011dmc.1_Missense_Mutation_p.L29P|HLA-A_uc011dmd.1_Missense_Mutation_p.L29P	NM_002116	NP_002107	P30443	1A01_HUMAN	major histocompatibility complex, class I, A	150	Extracellular (Potential).|Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			---	---	---	---
TRIM40	135644	broad.mit.edu	37	6	30114888	30114888	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30114888G>A	uc003npk.2	+	4	954	c.568G>A	c.(568-570)GCC>ACC	p.A190T	TRIM40_uc003npm.2_Missense_Mutation_p.A161T	NM_138700	NP_619645	Q6P9F5	TRI40_HUMAN	tripartite motif-containing 40	190						intracellular	zinc ion binding			ovary(1)	1																		---	---	---	---
KIAA1949	170954	broad.mit.edu	37	6	30653521	30653521	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30653521C>T	uc003nra.2	-	2	506	c.275G>A	c.(274-276)CGG>CAG	p.R92Q	KIAA1949_uc003nrb.3_Missense_Mutation_p.R92Q	NM_001134870	NP_001128342	Q6NYC8	PHTNS_HUMAN	phostensin	92						cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
MDC1	9656	broad.mit.edu	37	6	30680469	30680469	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30680469G>A	uc003nrg.3	-	5	1690	c.1250C>T	c.(1249-1251)GCA>GTA	p.A417V	MDC1_uc003nrf.3_Missense_Mutation_p.A71V|MDC1_uc011dmp.1_Missense_Mutation_p.A289V|MDC1_uc003nrh.1_Missense_Mutation_p.A289V|MDC1_uc003nri.2_Missense_Mutation_p.A417V	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	417	Required for nuclear localization (NLS1).				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4													Other_conserved_DNA_damage_response_genes					---	---	---	---
HLA-C	3107	broad.mit.edu	37	6	31239447	31239447	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31239447T>C	uc003nsy.2	-	2	279	c.272A>G	c.(271-273)TAC>TGC	p.Y91C	HLA-C_uc011dnj.1_Missense_Mutation_p.Y63C|HLA-C_uc003nsx.2_5'UTR|HLA-C_uc003nsz.2_Missense_Mutation_p.Y91C|HLA-C_uc010jsl.2_Missense_Mutation_p.Y91C|HLA-C_uc003nta.2_Missense_Mutation_p.Y91C|HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron|HLA-C_uc011dnl.1_5'UTR|HLA-B_uc003ntf.2_Intron	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C	91	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0																		---	---	---	---
MICB	4277	broad.mit.edu	37	6	31473919	31473919	+	Splice_Site	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31473919G>T	uc003ntn.3	+	3	442	c.326_splice	c.e3-1	p.G109_splice	MICB_uc011dnm.1_Splice_Site_p.G77_splice|MICB_uc003nto.3_Intron	NM_005931	NP_005922			MHC class I polypeptide-related sequence B						antigen processing and presentation|cytolysis|gamma-delta T cell activation|immune response|immune response-activating cell surface receptor signaling pathway|interspecies interaction between organisms|negative regulation of defense response to virus by host|response to heat|response to oxidative stress|response to retinoic acid	integral to plasma membrane|MHC class I protein complex	natural killer cell lectin-like receptor binding				0																		---	---	---	---
BAT1	7919	broad.mit.edu	37	6	31508921	31508921	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31508921A>G	uc003ntt.2	-						BAT1_uc003nts.2_5'Flank|BAT1_uc011dnn.1_Intron|BAT1_uc003ntu.2_Intron|BAT1_uc003ntv.2_Intron|BAT1_uc003ntw.2_5'UTR|BAT1_uc003ntx.2_Intron|BAT1_uc011dno.1_Intron|BAT1_uc011dnp.1_Intron|BAT1_uc011dnq.1_Intron|SNORD84_uc010jsq.1_RNA	NM_004640	NP_004631			HLA-B associated transcript 1						intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0																		---	---	---	---
AIF1	199	broad.mit.edu	37	6	31584673	31584673	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31584673C>T	uc003nuy.2	+	6	514	c.440C>T	c.(439-441)CCC>CTC	p.P147L	AIF1_uc010jsy.2_3'UTR|AIF1_uc003nva.2_Missense_Mutation_p.P93L	NM_001623	NP_001614	P55008	AIF1_HUMAN	allograft inflammatory factor 1 isoform 3	147				KEKPTGPPAKKAISELP -> RKTNTPPSQESPI (in Ref. 2; AAA92457).	actin filament bundle assembly|cell cycle arrest|inflammatory response|negative regulation of cell proliferation	nucleus|ruffle membrane	actin filament binding|calcium ion binding			ovary(1)	1																		---	---	---	---
BAT3	7917	broad.mit.edu	37	6	31608183	31608183	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31608183A>C	uc003nvg.3	-	22	3341	c.3027T>G	c.(3025-3027)CCT>CCG	p.P1009P	BAT3_uc003nvf.3_Silent_p.P1003P|BAT3_uc003nvh.3_Silent_p.P1003P|BAT3_uc003nvi.3_Silent_p.P1003P|BAT3_uc011dnw.1_Silent_p.P1003P|BAT3_uc011dnx.1_Intron	NM_004639	NP_004630	P46379	BAG6_HUMAN	HLA-B associated transcript-3 isoform a	1009					apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process	BAT3 complex|nucleus	polyubiquitin binding|proteasome binding|ribosome binding				0																		---	---	---	---
BAT5	7920	broad.mit.edu	37	6	31668789	31668789	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31668789G>A	uc003nvy.1	-	4	303	c.273C>T	c.(271-273)TCC>TCT	p.S91S	BAT5_uc003nvx.1_5'UTR|BAT5_uc011dny.1_Silent_p.S58S|BAT5_uc003nvz.1_5'UTR|BAT5_uc011dnz.1_5'UTR|BAT5_uc010jtc.1_RNA|BAT5_uc011doa.1_5'UTR	NM_021160	NP_066983	O95870	ABHGA_HUMAN	HLA-B associated transcript 5	91						integral to membrane	hydrolase activity|protein binding				0																		---	---	---	---
RDBP	7936	broad.mit.edu	37	6	31922385	31922385	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31922385C>T	uc003nyk.2	-	7	893	c.689G>A	c.(688-690)CGG>CAG	p.R230Q	RDBP_uc011dot.1_Missense_Mutation_p.R200Q|RDBP_uc003nyl.1_Missense_Mutation_p.R170Q|RDBP_uc003nym.1_Missense_Mutation_p.R225Q	NM_002904	NP_002895	P18615	NELFE_HUMAN	RD RNA-binding protein	230	30 X 2 AA approximate tandem repeats of R-[DSNE].|24.				positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	mitochondrion|nucleoplasm	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
PPT2	9374	broad.mit.edu	37	6	32123767	32123767	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32123767T>C	uc003nzx.2	+						PRRT1_uc003nzu.2_5'Flank|uc003nzv.3_5'Flank|PPT2_uc003nzw.2_Intron|PPT2_uc011dpi.1_Intron|PPT2_uc003nzy.1_Intron|PPT2_uc003nzz.2_Intron|PPT2_uc003oaa.2_Intron|PPT2_uc010jtu.1_Intron	NM_005155	NP_005146			palmitoyl-protein thioesterase 2 isoform a						protein modification process	lysosome	palmitoyl-(protein) hydrolase activity				0																		---	---	---	---
HLA-DRA	3122	broad.mit.edu	37	6	32410986	32410986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32410986C>T	uc003obh.2	+	3	434	c.353C>T	c.(352-354)ACG>ATG	p.T118M	HLA-DRA_uc003obi.2_Intron	NM_019111	NP_061984	P01903	DRA_HUMAN	major histocompatibility complex, class II, DR	118	Ig-like C1-type.|Extracellular (Potential).|Alpha-2.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|Golgi apparatus|integral to plasma membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			ovary(1)|skin(1)	2														T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Kaposi_Sarcoma_Familial_Clustering_of				---	---	---	---
HLA-DQA2	3118	broad.mit.edu	37	6	32713814	32713814	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32713814A>G	uc003obx.2	+	3	636	c.578A>G	c.(577-579)CAC>CGC	p.H193R		NM_020056	NP_064440	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ	193	Alpha-2.|Extracellular (Potential).|Ig-like C1-type.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
TAP2	6891	broad.mit.edu	37	6	32782224	32782224	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32782224G>A	uc011dqf.1	-	14	2459	c.2337C>T	c.(2335-2337)GGC>GGT	p.G779G	HLA-DOB_uc003oca.2_Silent_p.G172G|HLA-DOB_uc011dqg.1_Silent_p.G172G	NM_018833	NP_061313	Q03519	TAP2_HUMAN	transporter 2, ATP-binding cassette, sub-family	Error:Variant_position_missing_in_Q03519_after_alignment					antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent|cytosol to ER transport|intracellular transport of viral proteins in host cell|peptide antigen transport|positive regulation of antigen processing and presentation of peptide antigen via MHC class I|positive regulation of T cell mediated cytotoxicity	nucleus|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|tapasin binding				0																		---	---	---	---
BRD2	6046	broad.mit.edu	37	6	32946137	32946137	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32946137T>C	uc003ocn.3	+	10	3514	c.1813T>C	c.(1813-1815)TTT>CTT	p.F605L	BRD2_uc003oco.2_RNA|BRD2_uc003ocq.3_Missense_Mutation_p.F605L|BRD2_uc003ocp.3_Missense_Mutation_p.F485L|BRD2_uc010juh.2_Missense_Mutation_p.F605L	NM_005104	NP_005095	P25440	BRD2_HUMAN	bromodomain containing 2	605					spermatogenesis	nucleus	protein serine/threonine kinase activity			central_nervous_system(3)|stomach(2)	5																		---	---	---	---
BRD2	6046	broad.mit.edu	37	6	32948188	32948188	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32948188G>A	uc003ocn.3	+	12	3917	c.2216G>A	c.(2215-2217)CGG>CAG	p.R739Q	BRD2_uc003ocq.3_Missense_Mutation_p.R739Q|BRD2_uc003ocp.3_Missense_Mutation_p.R619Q|BRD2_uc010juh.2_Missense_Mutation_p.R774Q	NM_005104	NP_005095	P25440	BRD2_HUMAN	bromodomain containing 2	739	ET.				spermatogenesis	nucleus	protein serine/threonine kinase activity			central_nervous_system(3)|stomach(2)	5																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33133489	33133489	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33133489C>T	uc003ocx.1	-	63	4815	c.4587G>A	c.(4585-4587)CCG>CCA	p.P1529P	COL11A2_uc010jul.1_Silent_p.P99P|COL11A2_uc003ocy.1_Silent_p.P1443P|COL11A2_uc003ocz.1_Silent_p.P1422P	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1529					cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33135571	33135571	+	Intron	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33135571C>A	uc003ocx.1	-						COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Intron|COL11A2_uc003ocz.1_Intron	NM_080680	NP_542411			collagen, type XI, alpha 2 isoform 1						cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5																		---	---	---	---
VPS52	6293	broad.mit.edu	37	6	33236883	33236883	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33236883T>C	uc003odm.1	-	6	666	c.456A>G	c.(454-456)GGA>GGG	p.G152G	VPS52_uc003odn.1_Silent_p.G27G|VPS52_uc003odo.1_Silent_p.G77G|VPS52_uc011dqy.1_Silent_p.G27G|VPS52_uc011dqz.1_Silent_p.G27G|RPS18_uc003odp.1_5'Flank|RPS18_uc010jum.1_5'Flank	NM_022553	NP_072047	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52	152					protein transport	endosome membrane|Golgi apparatus				ovary(4)|skin(1)	5																		---	---	---	---
RGL2	5863	broad.mit.edu	37	6	33259893	33259893	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33259893G>A	uc003odv.2	-	18	2453	c.2320C>T	c.(2320-2322)CGG>TGG	p.R774W	WDR46_uc003ods.2_5'Flank|WDR46_uc011dra.1_5'Flank|RGL2_uc003odu.2_Missense_Mutation_p.R334W|RGL2_uc010jur.2_Missense_Mutation_p.R334W|RGL2_uc003odw.2_Missense_Mutation_p.R692W	NM_004761	NP_004752	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation	774					Ras protein signal transduction|regulation of small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity			skin(3)|lung(1)|breast(1)|pancreas(1)	6																		---	---	---	---
DAXX	1616	broad.mit.edu	37	6	33287897	33287897	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33287897T>C	uc003oec.2	-	5	1560	c.1356A>G	c.(1354-1356)GAA>GAG	p.E452E	ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Silent_p.E377E|DAXX_uc011dre.1_Silent_p.E464E|DAXX_uc003oed.2_Silent_p.E452E	NM_001350	NP_001341	Q9UER7	DAXX_HUMAN	death-domain associated protein isoform a	452	Asp/Glu-rich (acidic).|Potential.|Necessary for interaction with USP7.				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23								Mis|F|N		Pancreatic neuroendocrine tumors								---	---	---	---
DAXX	1616	broad.mit.edu	37	6	33288217	33288217	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33288217C>T	uc003oec.2	-	4	1395	c.1191G>A	c.(1189-1191)CGG>CGA	p.R397R	ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Silent_p.R322R|DAXX_uc011dre.1_Silent_p.R409R|DAXX_uc003oed.2_Silent_p.R397R|DAXX_uc010juw.2_Silent_p.R322R	NM_001350	NP_001341	Q9UER7	DAXX_HUMAN	death-domain associated protein isoform a	397	Potential.|Necessary for interaction with USP7.				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23								Mis|F|N		Pancreatic neuroendocrine tumors								---	---	---	---
SYNGAP1	8831	broad.mit.edu	37	6	33400582	33400582	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33400582C>T	uc011dri.1	+	5	703	c.508C>T	c.(508-510)CGG>TGG	p.R170W	SYNGAP1_uc003oeo.1_Missense_Mutation_p.R155W|SYNGAP1_uc010juy.2_Missense_Mutation_p.R155W	NM_006772	NP_006763	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	170	PH.				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4																		---	---	---	---
SYNGAP1	8831	broad.mit.edu	37	6	33411637	33411637	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33411637G>A	uc011dri.1	+	15	3503	c.3308G>A	c.(3307-3309)CGT>CAT	p.R1103H	SYNGAP1_uc010juy.2_Missense_Mutation_p.R1074H|SYNGAP1_uc010juz.2_Missense_Mutation_p.R815H	NM_006772	NP_006763	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1103					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4																		---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33638551	33638551	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33638551G>A	uc011drk.1	+	20	2764	c.2545G>A	c.(2545-2547)GTG>ATG	p.V849M		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	849	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19																		---	---	---	---
TEAD3	7005	broad.mit.edu	37	6	35443481	35443481	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35443481G>A	uc003oku.3	-	11	1139	c.903C>T	c.(901-903)GCC>GCT	p.A301A	TEAD3_uc003okt.2_Silent_p.A190A|TEAD3_uc010jvx.2_Silent_p.A241A	NM_003214	NP_003205	Q99594	TEAD3_HUMAN	TEA domain family member 3	301	Transcriptional activation (Potential).				female pregnancy|hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
PNPLA1	285848	broad.mit.edu	37	6	36274154	36274154	+	Splice_Site	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36274154G>A	uc010jwf.2	+	7	1469	c.1469_splice	c.e7+1	p.T490_splice	PNPLA1_uc003olw.1_Splice_Site_p.T395_splice|PNPLA1_uc010jwe.1_Splice_Site_p.T404_splice	NM_001145717	NP_001139189			patatin-like phospholipase domain containing 1						lipid catabolic process		hydrolase activity			large_intestine(1)|pancreas(1)|breast(1)|skin(1)	4																		---	---	---	---
MDGA1	266727	broad.mit.edu	37	6	37626035	37626035	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37626035C>T	uc003onu.1	-	3	1547	c.368G>A	c.(367-369)CGC>CAC	p.R123H		NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	123	Ig-like 1.				brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38690822	38690822	+	5'UTR	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38690822G>A	uc003ooe.1	+	1					DNAH8_uc003ood.1_Silent_p.A79A	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
FRS3	10817	broad.mit.edu	37	6	41739124	41739124	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41739124C>A	uc003orc.1	-	7	956	c.712G>T	c.(712-714)GGC>TGC	p.G238C		NM_006653	NP_006644	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	238					fibroblast growth factor receptor signaling pathway	plasma membrane	fibroblast growth factor receptor binding|insulin receptor binding			ovary(2)	2	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
CCND3	896	broad.mit.edu	37	6	41903835	41903835	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41903835C>T	uc003orn.2	-	5	887	c.722G>A	c.(721-723)CGG>CAG	p.R241Q	CCND3_uc003orp.2_Missense_Mutation_p.R160Q|CCND3_uc011duk.1_Missense_Mutation_p.R45Q|CCND3_uc003orm.2_Missense_Mutation_p.R191Q|CCND3_uc003oro.2_Missense_Mutation_p.R169Q	NM_001760	NP_001751	P30281	CCND3_HUMAN	cyclin D3 isoform 2	241					cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding				0	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)					T	IGH@	MM						OREG0017437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GUCA1A	2978	broad.mit.edu	37	6	42146991	42146991	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42146991C>A	uc003orx.2	+	6	1101	c.456C>A	c.(454-456)TCC>TCA	p.S152S	GUCA1A_uc011duo.1_RNA|GUCA1A_uc010jxt.2_Silent_p.S152S	NM_000409	NP_000400	P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	152	EF-hand 4.|3 (Potential).				signal transduction|visual perception	membrane	calcium ion binding|calcium sensitive guanylate cyclase activator activity				0	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
KIAA0240	23506	broad.mit.edu	37	6	42797828	42797828	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42797828G>A	uc003osn.1	+	6	1908	c.1757G>A	c.(1756-1758)CGT>CAT	p.R586H	KIAA0240_uc003osm.1_Missense_Mutation_p.R586H|KIAA0240_uc011duw.1_Missense_Mutation_p.R586H|KIAA0240_uc003oso.1_Missense_Mutation_p.R586H|KIAA0240_uc003osp.1_Missense_Mutation_p.R586H	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	586										ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)															---	---	---	---
PEX6	5190	broad.mit.edu	37	6	42933450	42933450	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42933450G>A	uc003otf.2	-	13	2533	c.2440C>T	c.(2440-2442)CGA>TGA	p.R814*	PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	814					protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)															---	---	---	---
PEX6	5190	broad.mit.edu	37	6	42946217	42946217	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42946217C>A	uc003otf.2	-	1	765	c.672G>T	c.(670-672)TGG>TGT	p.W224C	PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	224					protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)															---	---	---	---
PTK7	5754	broad.mit.edu	37	6	43113108	43113108	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43113108C>T	uc003oub.1	+	16	2776	c.2578C>T	c.(2578-2580)CGG>TGG	p.R860W	PTK7_uc003ouc.1_Missense_Mutation_p.R804W|PTK7_uc003oud.1_Missense_Mutation_p.R820W|PTK7_uc003oue.1_Missense_Mutation_p.R730W|PTK7_uc003ouf.1_Intron|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Missense_Mutation_p.R868W|PTK7_uc010jyj.1_Missense_Mutation_p.R186W	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a	860	Cytoplasmic (Potential).|Protein kinase; inactive.|Interaction with CTNNB1.				actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|large_intestine(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)															---	---	---	---
ZNF318	24149	broad.mit.edu	37	6	43323194	43323194	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43323194T>C	uc003oux.2	-	4	1956	c.1878A>G	c.(1876-1878)TTA>TTG	p.L626L	ZNF318_uc003ouw.2_RNA	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	626					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)															---	---	---	---
DLK2	65989	broad.mit.edu	37	6	43418614	43418614	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43418614A>G	uc003ova.2	-	6	1024	c.815T>C	c.(814-816)GTA>GCA	p.V272A	DLK2_uc003ovb.2_Missense_Mutation_p.V272A	NM_023932	NP_076421	Q6UY11	DLK2_HUMAN	EGF-like-domain, multiple 9 precursor	272	Extracellular (Potential).					integral to membrane	calcium ion binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
XPO5	57510	broad.mit.edu	37	6	43494448	43494448	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43494448A>G	uc003ovp.2	-	27	3169	c.2958T>C	c.(2956-2958)AGT>AGC	p.S986S	POLR1C_uc003ovo.1_Intron	NM_020750	NP_065801	Q9HAV4	XPO5_HUMAN	exportin 5	986					gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)															---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44360532	44360532	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44360532C>T	uc003oxl.2	+	3	537	c.278C>T	c.(277-279)GCG>GTG	p.A93V		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	93	H-T-H motif (By similarity).|HTH myb-type 2.				cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
CYP39A1	51302	broad.mit.edu	37	6	46620180	46620180	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46620180T>C	uc003oyf.1	-	1	344	c.140A>G	c.(139-141)AAA>AGA	p.K47R	CYP39A1_uc011dwa.1_Missense_Mutation_p.K47R|CYP39A1_uc010jzd.1_5'UTR|SLC25A27_uc011dwb.1_5'Flank|SLC25A27_uc003oyg.2_5'Flank|SLC25A27_uc003oyh.2_5'Flank|SLC25A27_uc011dwc.1_5'Flank	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,	47					bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1																		---	---	---	---
PLA2G7	7941	broad.mit.edu	37	6	46679343	46679343	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46679343A>G	uc010jzf.2	-	7	822	c.553T>C	c.(553-555)TCT>CCT	p.S185P	PLA2G7_uc010jzg.1_Missense_Mutation_p.S185P|PLA2G7_uc011dwd.1_Missense_Mutation_p.S140P|PLA2G7_uc011dwe.1_Missense_Mutation_p.S58P	NM_005084	NP_005075	Q13093	PAFA_HUMAN	phospholipase A2, group VII	185					inflammatory response|lipid catabolic process	extracellular space	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding				0			Lung(136;0.192)															---	---	---	---
DEFB110	245913	broad.mit.edu	37	6	49986805	49986805	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49986805T>C	uc003pac.2	-	2	135	c.89A>G	c.(88-90)GAC>GGC	p.D30G	DEFB110_uc011dwr.1_Intron	NM_001037497	NP_001032586	Q30KQ9	DB110_HUMAN	beta-defensin 110 isoform a	30					defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)																	---	---	---	---
GCLC	2729	broad.mit.edu	37	6	53370226	53370226	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53370226A>G	uc003pbw.1	-	12	1747	c.1359T>C	c.(1357-1359)CTT>CTC	p.L453L	GCLC_uc003pbv.1_Silent_p.L177L	NM_001498	NP_001489	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	453					anti-apoptosis|cell redox homeostasis|cysteine metabolic process|glutamate metabolic process|glutathione biosynthetic process|negative regulation of transcription, DNA-dependent|regulation of blood vessel size|response to heat|response to hormone stimulus|response to oxidative stress|xenobiotic metabolic process	cytosol	ADP binding|ATP binding|coenzyme binding|glutamate binding|glutamate-cysteine ligase activity|magnesium ion binding			ovary(1)|central_nervous_system(1)	2	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)													---	---	---	---
DST	667	broad.mit.edu	37	6	56483162	56483162	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56483162C>T	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Silent_p.Q1890Q	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
DST	667	broad.mit.edu	37	6	56484558	56484558	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56484558T>C	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Missense_Mutation_p.E1425G	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
DST	667	broad.mit.edu	37	6	56485459	56485459	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56485459G>A	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Missense_Mutation_p.R1125C	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
BAI3	577	broad.mit.edu	37	6	70070871	70070871	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70070871A>T	uc003pev.3	+	29	4154	c.3706A>T	c.(3706-3708)AGC>TGC	p.S1236C	BAI3_uc010kak.2_Missense_Mutation_p.S1236C|BAI3_uc011dxx.1_Missense_Mutation_p.S442C	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1236	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
COL9A1	1297	broad.mit.edu	37	6	71004132	71004132	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71004132T>G	uc003pfg.3	-	5	593	c.434A>C	c.(433-435)AAG>ACG	p.K145T		NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	145	Nonhelical region (NC4).|TSP N-terminal.				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4																		---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	73100438	73100438	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73100438A>C	uc003pga.2	+	30	4582	c.4505A>C	c.(4504-4506)AAT>ACT	p.N1502T	RIMS1_uc011dyb.1_Missense_Mutation_p.N899T|RIMS1_uc003pgc.2_Missense_Mutation_p.N951T|RIMS1_uc010kaq.2_Missense_Mutation_p.N822T|RIMS1_uc011dyc.1_Missense_Mutation_p.N627T|RIMS1_uc010kar.2_Missense_Mutation_p.N570T|RIMS1_uc011dyd.1_Missense_Mutation_p.N636T|RIMS1_uc003pgf.2_Missense_Mutation_p.N502T|RIMS1_uc003pgg.2_Missense_Mutation_p.N398T|RIMS1_uc003pgi.2_Missense_Mutation_p.N318T|RIMS1_uc003pgh.2_Missense_Mutation_p.N369T|RIMS1_uc003pgd.2_Missense_Mutation_p.N568T|RIMS1_uc003pge.2_Missense_Mutation_p.N542T|RIMS1_uc011dye.1_Missense_Mutation_p.N308T|RIMS1_uc011dyf.1_Missense_Mutation_p.N126T|RIMS1_uc011dyg.1_Missense_Mutation_p.N29T	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1502					calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
DPPA5	340168	broad.mit.edu	37	6	74063580	74063580	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74063580C>T	uc003pgs.1	-	2	293	c.288G>A	c.(286-288)GAG>GAA	p.E96E		NM_001025290	NP_001020461	A6NC42	DPPA5_HUMAN	developmental pluripotency associated 5	96					multicellular organismal development	cytoplasm	RNA binding				0																		---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79655139	79655139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79655139C>T	uc003pir.2	-	39	4932	c.4706G>A	c.(4705-4707)GGC>GAC	p.G1569D	PHIP_uc003piq.2_Missense_Mutation_p.G593D|PHIP_uc011dyp.1_Missense_Mutation_p.G1568D|IRAK1BP1_uc010kbg.1_RNA|PHIP_uc003pio.3_Missense_Mutation_p.G455D	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1569					insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)														---	---	---	---
PGM3	5238	broad.mit.edu	37	6	83891504	83891504	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83891504A>G	uc003pjv.2	-	6	778	c.738T>C	c.(736-738)AAT>AAC	p.N246N	PGM3_uc003pjw.2_Silent_p.N165N|PGM3_uc011dyz.1_Silent_p.N274N	NM_015599	NP_056414	O95394	AGM1_HUMAN	phosphoglucomutase 3	246					dolichol-linked oligosaccharide biosynthetic process|embryo development ending in birth or egg hatching|glucose 1-phosphate metabolic process|hemopoiesis|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	magnesium ion binding|phosphoacetylglucosamine mutase activity|phosphoglucomutase activity				0		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)														---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85470085	85470085	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85470085A>G	uc003pkl.1	-						TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977			T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
GABRR1	2569	broad.mit.edu	37	6	89888745	89888745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89888745G>A	uc003pna.2	-	10	1639	c.1184C>T	c.(1183-1185)GCG>GTG	p.A395V	GABRR1_uc011dzv.1_Missense_Mutation_p.A372V	NM_002042	NP_002033	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 1	395	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway|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			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)													---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90499923	90499923	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90499923A>G	uc003pnn.1	-	6	1169	c.1053T>C	c.(1051-1053)CCT>CCC	p.P351P	MDN1_uc003pnp.1_Silent_p.P351P	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	351					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90572134	90572134	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90572134G>A	uc003pnr.2	+	7	902	c.706G>A	c.(706-708)GAG>AAG	p.E236K	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.E236K|CASP8AP2_uc011dzz.1_Missense_Mutation_p.E236K	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	236					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
EPHA7	2045	broad.mit.edu	37	6	94120499	94120499	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94120499A>C	uc003poe.2	-	3	793	c.552T>G	c.(550-552)CTT>CTG	p.L184L	EPHA7_uc003pof.2_Silent_p.L184L|EPHA7_uc011eac.1_Silent_p.L184L|EPHA7_uc003pog.3_Silent_p.L184L	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	184	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)														---	---	---	---
MANEA	79694	broad.mit.edu	37	6	96053641	96053641	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96053641C>T	uc003poo.1	+	5	889	c.749C>T	c.(748-750)GCC>GTC	p.A250V		NM_024641	NP_078917	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	250	Catalytic (Probable).|Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)														---	---	---	---
KIAA0776	23376	broad.mit.edu	37	6	96974275	96974275	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96974275T>C	uc003por.2	+	5	477	c.429T>C	c.(427-429)TGT>TGC	p.C143C	KIAA0776_uc010kck.2_RNA	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376	143	Required for E3 UFM1-protein ligase activity.|Involved in CDK5RAP3-binding.				negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)														---	---	---	---
SIM1	6492	broad.mit.edu	37	6	100896103	100896103	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100896103G>T	uc003pqj.3	-	7	976	c.769C>A	c.(769-771)CCT>ACT	p.P257T	SIM1_uc010kcu.2_Missense_Mutation_p.P257T	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	257	PAS 2.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101049723	101049723	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101049723A>G	uc003pqk.2	-	34	5595	c.5266T>C	c.(5266-5268)TGG>CGG	p.W1756R		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	1756					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
BVES	11149	broad.mit.edu	37	6	105563668	105563668	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105563668C>T	uc003pqw.2	-	7	1008	c.851G>A	c.(850-852)TGC>TAC	p.C284Y	BVES_uc003pqx.2_Missense_Mutation_p.C284Y|BVES_uc003pqy.2_Missense_Mutation_p.C284Y	NM_147147	NP_671488	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance isoform 5	284	Cytoplasmic (Potential).				epithelial cell-cell adhesion|muscle organ development|positive regulation of locomotion|positive regulation of receptor recycling|regulation of Cdc42 GTPase activity|regulation of cell shape|regulation of Rac GTPase activity|substrate adhesion-dependent cell spreading|vesicle-mediated transport	integral to membrane|lateral plasma membrane|tight junction	structural molecule activity				0		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)																---	---	---	---
PRDM1	639	broad.mit.edu	37	6	106552778	106552778	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106552778A>G	uc003prd.2	+	5	977	c.743A>G	c.(742-744)TAC>TGC	p.Y248C	PRDM1_uc003pre.2_Missense_Mutation_p.Y114C	NM_001198	NP_001189	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain isoform	248					negative regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(54)|ovary(1)|skin(1)	56	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)				D|N|Mis|F|S		DLBCL								---	---	---	---
FIG4	9896	broad.mit.edu	37	6	110056341	110056341	+	Intron	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110056341T>A	uc003ptt.2	+						FIG4_uc011eau.1_Intron	NM_014845	NP_055660			Sac domain-containing inositol phosphatase 3						cell death	endosome membrane	protein binding			ovary(1)	1		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)														---	---	---	---
WASF1	8936	broad.mit.edu	37	6	110423338	110423338	+	Silent	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110423338T>G	uc003ptv.1	-	10	1812	c.975A>C	c.(973-975)CCA>CCC	p.P325P	WASF1_uc003ptw.1_Silent_p.P325P|WASF1_uc003ptx.1_Silent_p.P325P|WASF1_uc003pty.1_Silent_p.P325P	NM_003931	NP_003922	Q92558	WASF1_HUMAN	Wiskott-Aldrich syndrome protein family member	325	Poly-Pro.				actin filament polymerization|cellular component movement	actin cytoskeleton	actin binding				0		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)														---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110530384	110530384	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110530384G>T	uc003pua.2	+	5	612	c.588G>T	c.(586-588)TGG>TGT	p.W196C		NM_015891	NP_056975	O60508	PRP17_HUMAN	cell division cycle 40 homolog	196					mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm					0		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)														---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111697457	111697457	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111697457T>C	uc003puy.3	-	13	2424	c.2101A>G	c.(2101-2103)ACA>GCA	p.T701A	REV3L_uc003pux.3_Missense_Mutation_p.T623A|REV3L_uc003puz.3_Missense_Mutation_p.T623A	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	701					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
FYN	2534	broad.mit.edu	37	6	112025235	112025235	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112025235T>C	uc003pvj.2	-	6	854	c.514A>G	c.(514-516)ACC>GCC	p.T172A	FYN_uc003pvi.2_Missense_Mutation_p.T172A|FYN_uc003pvk.2_Missense_Mutation_p.T172A|FYN_uc003pvh.2_Missense_Mutation_p.T172A|FYN_uc010kdy.1_5'Flank	NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a	172	SH2.				axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
LAMA4	3910	broad.mit.edu	37	6	112460455	112460455	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112460455T>C	uc003pvu.2	-	24	3458	c.3149A>G	c.(3148-3150)TAC>TGC	p.Y1050C	LAMA4_uc003pvv.2_Missense_Mutation_p.Y1043C|LAMA4_uc003pvt.2_Missense_Mutation_p.Y1043C	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1050	Laminin G-like 2.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)														---	---	---	---
LAMA4	3910	broad.mit.edu	37	6	112510396	112510396	+	Missense_Mutation	SNP	C	T	T	rs147078770	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112510396C>T	uc003pvu.2	-	7	1039	c.730G>A	c.(730-732)GGG>AGG	p.G244R	LAMA4_uc003pvv.2_Missense_Mutation_p.G244R|LAMA4_uc003pvt.2_Missense_Mutation_p.G244R	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	244	Laminin EGF-like 4; truncated.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)														---	---	---	---
COL10A1	1300	broad.mit.edu	37	6	116442889	116442889	+	Silent	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116442889T>A	uc003pwm.2	-	3	486	c.390A>T	c.(388-390)GGA>GGT	p.G130G	NT5DC1_uc003pwj.2_Intron|NT5DC1_uc003pwk.2_Intron|NT5DC1_uc003pwl.2_Intron	NM_000493	NP_000484	Q03692	COAA1_HUMAN	type X collagen alpha 1 precursor	130	Triple-helical region.				skeletal system development	collagen	metal ion binding			central_nervous_system(1)	1		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)														---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119285926	119285926	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119285926T>G	uc003pyj.2	-	16	3392	c.3044A>C	c.(3043-3045)AAG>ACG	p.K1015T	FAM184A_uc003pyk.3_Missense_Mutation_p.K846T|FAM184A_uc003pyl.3_Intron|FAM184A_uc003pyi.2_RNA	NM_024581	NP_078857	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 1	1015										ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7																		---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128505813	128505813	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128505813A>G	uc003qbk.2	-	7	1293	c.926T>C	c.(925-927)CTG>CCG	p.L309P	PTPRK_uc003qbj.2_Missense_Mutation_p.L309P|PTPRK_uc010kfc.2_Missense_Mutation_p.L309P|PTPRK_uc011ebu.1_Missense_Mutation_p.L309P|PTPRK_uc003qbl.1_Missense_Mutation_p.L179P|PTPRK_uc011ebv.1_Missense_Mutation_p.L309P	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	309	Fibronectin type-III 1.|Extracellular (Potential).				cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129781432	129781432	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129781432C>T	uc003qbn.2	+	48	7060	c.6955C>T	c.(6955-6957)CGA>TGA	p.R2319*	LAMA2_uc003qbo.2_Nonsense_Mutation_p.R2319*	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2319	Laminin G-like 1.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
ARG1	383	broad.mit.edu	37	6	131904532	131904532	+	Missense_Mutation	SNP	G	A	A	rs104893948		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131904532G>A	uc003qcp.1	+	7	761	c.703G>A	c.(703-705)GGA>AGA	p.G235R	ARG1_uc003qco.1_Intron|ARG1_uc010kfm.1_Missense_Mutation_p.G243R|MED23_uc003qcq.2_Intron	NM_000045	NP_000036	P05089	ARGI1_HUMAN	arginase 1	235			G -> R (in ARGIN).		arginine catabolic process|urea cycle	cytosol	arginase activity			ovary(1)	1	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0106)|OV - Ovarian serous cystadenocarcinoma(155;0.0713)	L-Ornithine(DB00129)													---	---	---	---
TAAR6	319100	broad.mit.edu	37	6	132892319	132892319	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132892319A>G	uc011eck.1	+	1	859	c.859A>G	c.(859-861)ATA>GTA	p.I287V		NM_175067	NP_778237	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	287	Helical; Name=7; (Potential).					plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(1)	3	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)														---	---	---	---
BCLAF1	9774	broad.mit.edu	37	6	136599456	136599456	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136599456T>C	uc003qgx.1	-	4	816	c.563A>G	c.(562-564)AAA>AGA	p.K188R	BCLAF1_uc003qgw.1_Missense_Mutation_p.K188R|BCLAF1_uc003qgy.1_Missense_Mutation_p.K186R|BCLAF1_uc011edc.1_RNA|BCLAF1_uc011edd.1_RNA|BCLAF1_uc011ede.1_Missense_Mutation_p.K186R	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	188					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)														---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138584224	138584224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138584224G>A	uc003qhu.2	+	12	1604	c.1604G>A	c.(1603-1605)AGT>AAT	p.S535N		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	535					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
TXLNB	167838	broad.mit.edu	37	6	139563773	139563773	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139563773C>T	uc011eds.1	-	10	2110	c.1945G>A	c.(1945-1947)GAG>AAG	p.E649K		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	649						cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144898277	144898277	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144898277G>A	uc003qkt.2	+	50	7424	c.7332G>A	c.(7330-7332)ACG>ACA	p.T2444T		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	2444	Spectrin 17.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
EPM2A	7957	broad.mit.edu	37	6	145948713	145948713	+	Missense_Mutation	SNP	C	T	T	rs137852917		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145948713C>T	uc003qkw.2	-	4	1192	c.835G>A	c.(835-837)GGC>AGC	p.G279S	EPM2A_uc003qkv.2_Missense_Mutation_p.G279S|EPM2A_uc010khr.2_Missense_Mutation_p.R198Q|EPM2A_uc003qkx.2_Missense_Mutation_p.G141S|EPM2A_uc003qku.2_Missense_Mutation_p.G125S	NM_005670	NP_005661	O95278	EPM2A_HUMAN	laforin isoform a	279	Tyrosine-protein phosphatase.		G -> S (in EPM2; results in ubiquitin- positive perinuclear aggregates; loss of phosphatase activity; affects glycogen binding; disrupts the interaction with PPP1R5).		glycogen metabolic process	cytosol|endoplasmic reticulum|nucleus|plasma membrane|polysome	carbohydrate binding|identical protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)														---	---	---	---
FBXO30	84085	broad.mit.edu	37	6	146127271	146127271	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146127271T>C	uc003qla.2	-	2	470	c.271A>G	c.(271-273)ACT>GCT	p.T91A	uc003qky.1_Intron	NM_032145	NP_115521	Q8TB52	FBX30_HUMAN	F-box only protein 30	91	TRAF-type.						ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146247355	146247355	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146247355G>A	uc003qlf.2	-	16	3678	c.3279C>T	c.(3277-3279)GGC>GGT	p.G1093G	SHPRH_uc003qld.2_Silent_p.G1102G|SHPRH_uc003qle.2_Silent_p.G1102G|SHPRH_uc003qlg.1_Silent_p.G649G|SHPRH_uc003qlh.2_Silent_p.G18G|SHPRH_uc003qli.1_Silent_p.G18G	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1093					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146755082	146755082	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146755082G>A	uc010khw.1	+	9	3205	c.2735G>A	c.(2734-2736)CGC>CAC	p.R912H	GRM1_uc010khv.1_3'UTR|GRM1_uc003qll.2_3'UTR|GRM1_uc011edz.1_3'UTR|GRM1_uc011eea.1_Silent_p.P900P	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	912	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
SUMO4	387082	broad.mit.edu	37	6	149721537	149721537	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149721537G>A	uc003qml.2	+	1	43	c.10G>A	c.(10-12)GAA>AAA	p.E4K	TAB2_uc011eec.1_Intron|TAB2_uc003qmj.2_Intron|TAB2_uc003qmk.3_Intron	NM_001002255	NP_001002255	Q6EEV6	SUMO4_HUMAN	SMT3 suppressor of mif two 3 homolog 4	4											0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;7.91e-12)|GBM - Glioblastoma multiforme(68;0.0282)														---	---	---	---
ULBP3	79465	broad.mit.edu	37	6	150385828	150385828	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150385828C>T	uc003qns.3	-	4	650	c.650G>A	c.(649-651)GGC>GAC	p.G217D	ULBP3_uc011eej.1_Missense_Mutation_p.G92D	NM_024518	NP_078794	Q9BZM4	N2DL3_HUMAN	UL16 binding protein 3 precursor	217					antigen processing and presentation|immune response|natural killer cell activation	anchored to membrane|MHC class I protein complex	MHC class I receptor activity				0		Ovarian(120;0.12)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.45e-12)														---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151281413	151281413	+	Silent	SNP	G	A	A	rs146093887	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151281413G>A	uc003qob.2	+	18	2074	c.1806G>A	c.(1804-1806)GCG>GCA	p.A602A	MTHFD1L_uc011een.1_RNA|MTHFD1L_uc011eeo.1_Silent_p.A603A|MTHFD1L_uc003qoc.2_Silent_p.A550A	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+	602	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)														---	---	---	---
AKAP12	9590	broad.mit.edu	37	6	151670579	151670579	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151670579C>T	uc011eep.1	+	4	1293	c.1053C>T	c.(1051-1053)ACC>ACT	p.T351T	AKAP12_uc003qoe.2_Silent_p.T351T|AKAP12_uc003qof.2_Silent_p.T253T|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Silent_p.T246T	NM_005100	NP_005091	Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12 isoform 1	351	Involved in PKC-binding (Probable).				G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	8		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)														---	---	---	---
C6orf211	79624	broad.mit.edu	37	6	151775736	151775736	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151775736T>C	uc003qok.1	+	2	354	c.95T>C	c.(94-96)GTT>GCT	p.V32A	C6orf211_uc011ees.1_Intron|RMND1_uc003qoi.2_5'Flank	NM_024573	NP_078849	Q9H993	CF211_HUMAN	hypothetical protein LOC79624	32							protein binding				0			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152782789	152782789	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152782789T>C	uc010kiw.2	-	21	2939	c.2337A>G	c.(2335-2337)CAA>CAG	p.Q779Q	SYNE1_uc003qot.3_Silent_p.Q786Q|SYNE1_uc003qou.3_Silent_p.Q779Q|SYNE1_uc010kjb.1_Silent_p.Q762Q|SYNE1_uc003qow.2_Silent_p.Q74Q|SYNE1_uc003qox.1_Silent_p.Q295Q|SYNE1_uc003qoz.2_Silent_p.Q211Q|SYNE1_uc003qoy.2_Silent_p.Q346Q	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	779	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)			---	---	---	---
MYCT1	80177	broad.mit.edu	37	6	153043068	153043068	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153043068G>A	uc003qpd.3	+	2	396	c.388G>A	c.(388-390)GGC>AGC	p.G130S	MYCT1_uc010kjc.1_Intron|MYCT1_uc003qpc.3_Missense_Mutation_p.G130S	NM_025107	NP_079383	Q8N699	MYCT1_HUMAN	myc target 1	130						nucleus				ovary(1)	1		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)														---	---	---	---
TFB1M	51106	broad.mit.edu	37	6	155635562	155635562	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155635562T>C	uc003qqj.3	-	1	65	c.1A>G	c.(1-3)ATG>GTG	p.M1V	TFB1M_uc003qqk.2_RNA	NM_016020	NP_057104	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	1					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial nucleoid	DNA binding|protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			skin(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)														---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157525016	157525016	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157525016G>A	uc003qqn.2	+	19	5009	c.4857G>A	c.(4855-4857)TGG>TGA	p.W1619*	ARID1B_uc003qqo.2_Nonsense_Mutation_p.W1579*|ARID1B_uc003qqp.2_Nonsense_Mutation_p.W1566*	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1624					chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
C6orf35	729515	broad.mit.edu	37	6	157744464	157744464	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157744464T>A	uc003sih.3	-	1	331	c.68A>T	c.(67-69)GAC>GTC	p.D23V		NM_018452	NP_060922	Q9NWH2	CF035_HUMAN	hypothetical protein LOC729515	23						integral to membrane					0																		---	---	---	---
SNX9	51429	broad.mit.edu	37	6	158358567	158358567	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158358567G>A	uc003qqv.1	+							NM_016224	NP_057308			sorting nexin 9						cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158923938	158923938	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158923938C>T	uc003qrf.2	+	13	4600	c.3243C>T	c.(3241-3243)ACC>ACT	p.T1081T	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	1081					intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
RSPH3	83861	broad.mit.edu	37	6	159399367	159399367	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159399367C>A	uc003qrx.2	-	7	1487	c.1297G>T	c.(1297-1299)GGA>TGA	p.G433*	RSPH3_uc010kju.2_Nonsense_Mutation_p.G337*	NM_031924	NP_114130	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog	433										ovary(1)|skin(1)	2		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160483631	160483631	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160483631G>T	uc003qta.2	+	26	3798	c.3650G>T	c.(3649-3651)TGT>TTT	p.C1217F		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	1217	8.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	166833418	166833418	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166833418G>A	uc003qvb.1	-	18	1991	c.1772C>T	c.(1771-1773)GCG>GTG	p.A591V	RPS6KA2_uc011ego.1_Missense_Mutation_p.A502V|RPS6KA2_uc010kkl.1_Missense_Mutation_p.A502V|RPS6KA2_uc003qvc.1_Missense_Mutation_p.A599V|RPS6KA2_uc003qvd.1_Missense_Mutation_p.A616V|RPS6KA2_uc010kkk.1_Missense_Mutation_p.A23V	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	591	Protein kinase 2.				axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168226614	168226614	+	5'Flank	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168226614A>G	uc003qwd.2	+						MLLT4_uc003qwb.1_5'Flank|MLLT4_uc003qwc.1_5'Flank|C6orf124_uc003qwa.2_RNA	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
KIF25	3834	broad.mit.edu	37	6	168439368	168439368	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168439368A>G	uc003qwk.1	+	5	715	c.453A>G	c.(451-453)ACA>ACG	p.T151T	KIF25_uc003qwl.1_Silent_p.T151T	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN	kinesin family member 25 isoform 1	151	Kinesin-motor.				microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)														---	---	---	---
TBP	6908	broad.mit.edu	37	6	170871119	170871119	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170871119G>T	uc003qxt.2	+	3	527	c.295G>T	c.(295-297)GCT>TCT	p.A99S	TBP_uc003qxu.2_Missense_Mutation_p.A99S|TBP_uc011ehf.1_Missense_Mutation_p.A79S|TBP_uc011ehg.1_Missense_Mutation_p.A99S	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein	99					cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)														---	---	---	---
SUN1	23353	broad.mit.edu	37	7	892561	892561	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:892561C>T	uc011jvp.1	+	10	1104	c.1025C>T	c.(1024-1026)ACG>ATG	p.T342M	GET4_uc003sjj.1_RNA|SUN1_uc003sjf.2_Missense_Mutation_p.T259M|SUN1_uc011jvq.1_Missense_Mutation_p.T239M|SUN1_uc003sjg.2_Missense_Mutation_p.T247M|SUN1_uc011jvr.1_Missense_Mutation_p.T151M|SUN1_uc003sji.2_Missense_Mutation_p.T180M|SUN1_uc003sjk.2_Translation_Start_Site	NM_001130965	NP_001124437	O94901	SUN1_HUMAN	unc-84 homolog A isoform a	369	Perinuclear space.				cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0																		---	---	---	---
ADAP1	11033	broad.mit.edu	37	7	938896	938896	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:938896G>A	uc003sjo.3	-	10	1046	c.870C>T	c.(868-870)GAC>GAT	p.D290D	ADAP1_uc003sjm.3_Silent_p.D116D|ADAP1_uc011jvs.1_Silent_p.D195D|ADAP1_uc003sjn.3_Silent_p.D218D|ADAP1_uc010ksc.2_Silent_p.D218D	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1	290	PH 2.				cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1535897	1535897	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1535897G>A	uc003skn.2	-	12	1707	c.1606C>T	c.(1606-1608)CGC>TGC	p.R536C	INTS1_uc003skp.1_5'Flank	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	536					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)														---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1538426	1538426	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1538426G>A	uc003skn.2	-	9	1301	c.1200C>T	c.(1198-1200)TCC>TCT	p.S400S	INTS1_uc003skq.2_Silent_p.S400S	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	400					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)														---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1539893	1539893	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1539893G>A	uc003skn.2	-	4	560	c.459C>T	c.(457-459)CGC>CGT	p.R153R	INTS1_uc003skq.2_Silent_p.R153R	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	153					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)														---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2979408	2979408	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2979408T>G	uc003smv.2	-	6	1243	c.839A>C	c.(838-840)AAC>ACC	p.N280T		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	280	Potential.				positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4213858	4213858	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4213858C>A	uc003smx.2	+	33	4944	c.4805C>A	c.(4804-4806)CCG>CAG	p.P1602Q	SDK1_uc010kso.2_Missense_Mutation_p.P878Q|SDK1_uc003smy.2_Missense_Mutation_p.P89Q	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1602	Fibronectin type-III 10.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
WIPI2	26100	broad.mit.edu	37	7	5267842	5267842	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5267842G>A	uc003snv.2	+	11	1337	c.1121G>A	c.(1120-1122)CGG>CAG	p.R374Q	WIPI2_uc003snw.2_Missense_Mutation_p.R374Q|WIPI2_uc003snx.2_Missense_Mutation_p.R356Q|WIPI2_uc003sny.2_Missense_Mutation_p.R356Q|WIPI2_uc010ksv.2_Missense_Mutation_p.R230Q|WIPI2_uc003soa.2_Missense_Mutation_p.R315Q|WIPI2_uc003sob.2_Missense_Mutation_p.R117Q	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	374					autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)														---	---	---	---
FSCN1	6624	broad.mit.edu	37	7	5632671	5632671	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5632671C>T	uc003sou.2	+	1	218	c.104C>T	c.(103-105)GCG>GTG	p.A35V		NM_003088	NP_003079	Q16658	FSCN1_HUMAN	fascin 1	35					actin filament bundle assembly|cell migration|cell proliferation	cell junction|cytoplasm|filopodium|invadopodium|stress fiber	actin filament binding|drug binding|protein binding, bridging			ovary(1)	1		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)														---	---	---	---
USP42	84132	broad.mit.edu	37	7	6189801	6189801	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6189801C>T	uc011jwo.1	+	13	2097	c.1974C>T	c.(1972-1974)AAC>AAT	p.N658N	USP42_uc010kth.1_Silent_p.N591N|USP42_uc011jwp.1_Silent_p.N658N|USP42_uc011jwq.1_Silent_p.N465N|USP42_uc011jwr.1_Silent_p.N503N	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	658					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11514158	11514158	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11514158T>G	uc003ssf.3	-	8	2307	c.2055A>C	c.(2053-2055)GAA>GAC	p.E685D		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	685	TSP type-1 6.|Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
AGR3	155465	broad.mit.edu	37	7	16900996	16900996	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16900996T>G	uc003sts.2	-							NM_176813	NP_789783			breast cancer membrane protein 11 precursor							extracellular region					0	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)														---	---	---	---
AHR	196	broad.mit.edu	37	7	17374530	17374530	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17374530T>C	uc011jxz.1	+	8	1541	c.928T>C	c.(928-930)TAT>CAT	p.Y310H	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	310	PAS 2.				apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)																	---	---	---	---
TWISTNB	221830	broad.mit.edu	37	7	19739896	19739896	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19739896A>G	uc003sup.1	-	3	425	c.404T>C	c.(403-405)GTT>GCT	p.V135A		NM_001002926	NP_001002926	Q3B726	RPA43_HUMAN	TWIST neighbor	135						microtubule cytoskeleton|nucleolus	DNA-directed RNA polymerase activity			ovary(1)	1																		---	---	---	---
MACC1	346389	broad.mit.edu	37	7	20198704	20198704	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20198704A>G	uc003sus.3	-	5	1589	c.1280T>C	c.(1279-1281)CTT>CCT	p.L427P	MACC1_uc010kug.2_Missense_Mutation_p.L427P	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5	427					positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21818688	21818688	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21818688G>A	uc003svc.2	+	58	9501	c.9470G>A	c.(9469-9471)CGG>CAG	p.R3157Q		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3157	Stalk (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
SNX10	29887	broad.mit.edu	37	7	26411438	26411438	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26411438T>C	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron|SNX10_uc010kuv.2_Intron|SNX10_uc010kuw.2_Intron	NM_013322	NP_037454			sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0																		---	---	---	---
HIBADH	11112	broad.mit.edu	37	7	27672063	27672063	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27672063A>G	uc003szf.2	-	3	449	c.254T>C	c.(253-255)GTA>GCA	p.V85A	HIBADH_uc003szg.2_Missense_Mutation_p.V36A|HIBADH_uc003szh.2_5'UTR|HIBADH_uc003szi.2_Missense_Mutation_p.V36A	NM_152740	NP_689953	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase precursor	85					branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)													---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29552299	29552299	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29552299A>G	uc003szz.2	+	13	1792	c.1355A>G	c.(1354-1356)TAC>TGC	p.Y452C	CHN2_uc011jzs.1_Missense_Mutation_p.Y527C|CHN2_uc010kva.2_3'UTR|CHN2_uc010kvb.2_RNA|CHN2_uc010kvc.2_Missense_Mutation_p.Y417C|CHN2_uc011jzt.1_Missense_Mutation_p.Y465C|CHN2_uc010kvd.2_Missense_Mutation_p.Y308C|CHN2_uc011jzu.1_Missense_Mutation_p.Y437C|CHN2_uc010kvg.2_Missense_Mutation_p.Y270C|CHN2_uc010kvh.2_Missense_Mutation_p.Y212C|CHN2_uc010kvi.2_Missense_Mutation_p.Y244C|CHN2_uc010kve.2_3'UTR|CHN2_uc003taa.2_Missense_Mutation_p.Y316C|CHN2_uc010kvf.2_Missense_Mutation_p.Y258C|CHN2_uc010kvj.2_Missense_Mutation_p.Y225C|CHN2_uc010kvk.2_Missense_Mutation_p.Y127C|CHN2_uc010kvl.2_RNA|CHN2_uc010kvm.2_Missense_Mutation_p.Y271C|CHN2_uc011jzv.1_Missense_Mutation_p.Y245C	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2	452	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
GARS	2617	broad.mit.edu	37	7	30671954	30671954	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30671954C>T	uc003tbm.2	+	16	2352	c.1995C>T	c.(1993-1995)GGC>GGT	p.G665G		NM_002047	NP_002038	P41250	SYG_HUMAN	glycyl-tRNA synthetase	665					cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33545142	33545142	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33545142A>C	uc003tdn.1	+	20	2696	c.2183A>C	c.(2182-2184)AAG>ACG	p.K728T	BBS9_uc003tdo.1_Missense_Mutation_p.K693T|BBS9_uc003tdp.1_Missense_Mutation_p.K723T|BBS9_uc003tdq.1_Missense_Mutation_p.K688T|BBS9_uc010kwn.1_RNA|BBS9_uc003tdr.1_Missense_Mutation_p.K252T|BBS9_uc003tds.1_Missense_Mutation_p.K151T|BBS9_uc003tdt.2_RNA	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	728					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
TBX20	57057	broad.mit.edu	37	7	35289643	35289643	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35289643A>G	uc011kas.1	-	2	311	c.300T>C	c.(298-300)ATT>ATC	p.I100I		NM_001077653	NP_001071121	Q9UMR3	TBX20_HUMAN	T-box transcription factor TBX20	100						nucleus	DNA binding			central_nervous_system(1)	1																		---	---	---	---
EEPD1	80820	broad.mit.edu	37	7	36194770	36194770	+	Silent	SNP	C	T	T	rs143445715		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36194770C>T	uc003tfa.2	+	2	1477	c.837C>T	c.(835-837)CCC>CCT	p.P279P		NM_030636	NP_085139	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family	279					DNA repair		DNA binding				0																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37264616	37264616	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37264616T>G	uc003tfk.1	-	9	876	c.569A>C	c.(568-570)AAG>ACG	p.K190T	ELMO1_uc011kbc.1_Missense_Mutation_p.K94T|ELMO1_uc010kxg.1_Missense_Mutation_p.K190T	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	190					actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
TARP	445347	broad.mit.edu	37	7	38305159	38305159	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38305159A>T	uc003tge.1	-	5	925	c.548T>A	c.(547-549)GTT>GAT	p.V183D	uc003tfz.1_Intron|TARP_uc003tgb.2_5'UTR|TARP_uc003tgc.1_5'UTR|TARP_uc003tgd.1_5'UTR|TARP_uc010kxi.1_RNA|TARP_uc003tgf.1_RNA|TARP_uc003tgj.1_RNA|TARP_uc003tgh.1_RNA|TARP_uc003tgi.1_RNA|TARP_uc003tgg.1_RNA			A2JGV3	A2JGV3_HUMAN	Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.	Error:Variant_position_missing_in_A2JGV3_after_alignment											0																		---	---	---	---
AMPH	273	broad.mit.edu	37	7	38505777	38505777	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38505777G>A	uc003tgu.2	-	8	731	c.662C>T	c.(661-663)GCG>GTG	p.A221V	AMPH_uc003tgv.2_Missense_Mutation_p.A221V|AMPH_uc003tgt.2_5'Flank	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	221	BAR.				endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40900046	40900046	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40900046G>A	uc003thn.1	+	14	1330	c.1285G>A	c.(1285-1287)GCT>ACT	p.A429T	C7orf10_uc003thm.1_Missense_Mutation_p.A425T|C7orf10_uc003tho.1_Missense_Mutation_p.A381T|C7orf10_uc003thp.1_RNA	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13	436							transferase activity			ovary(2)	2																		---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42005569	42005569	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42005569C>T	uc011kbh.1	-	15	3193	c.3102G>A	c.(3100-3102)GCG>GCA	p.A1034A	GLI3_uc011kbg.1_Silent_p.A975A	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1034					negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42007444	42007444	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42007444C>T	uc011kbh.1	-	14	2272	c.2181G>A	c.(2179-2181)GGG>GGA	p.G727G	GLI3_uc011kbg.1_Silent_p.G668G	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	727			G -> R (in PAPA1 and PAPB).		negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
PGAM2	5224	broad.mit.edu	37	7	44105024	44105024	+	Silent	SNP	G	A	A	rs147733064		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44105024G>A	uc003tjs.2	-	1	140	c.105C>T	c.(103-105)ACC>ACT	p.T35T		NM_000290	NP_000281	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2	35					gluconeogenesis|glycolysis|striated muscle contraction	cytosol	2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity				0																		---	---	---	---
NPC1L1	29881	broad.mit.edu	37	7	44553055	44553055	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44553055C>T	uc003tlb.2	-	20	4127	c.4071G>A	c.(4069-4071)CGG>CGA	p.R1357R	NPC1L1_uc003tlc.2_Silent_p.R1330R|NPC1L1_uc011kbw.1_Silent_p.R1284R|NPC1L1_uc003tla.2_3'UTR	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	1357	Cytoplasmic (Potential).				cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)													---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44664027	44664027	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44664027G>A	uc003tln.2	+	2	194	c.85G>A	c.(85-87)GCA>ACA	p.A29T	OGDH_uc003tlm.2_Missense_Mutation_p.A29T|OGDH_uc011kbx.1_Missense_Mutation_p.A29T|OGDH_uc011kby.1_Missense_Mutation_p.A29T|OGDH_uc003tlp.2_Missense_Mutation_p.A29T|OGDH_uc011kbz.1_5'UTR	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	29					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)													---	---	---	---
RAMP3	10268	broad.mit.edu	37	7	45216981	45216981	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45216981C>T	uc003tnb.2	+	2	193	c.132C>T	c.(130-132)TTC>TTT	p.F44F	RAMP3_uc003tnc.2_Silent_p.F12F	NM_005856	NP_005847	O60896	RAMP3_HUMAN	receptor activity modifying protein 3 precursor	44	Extracellular (Potential).				intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane|lysosome	protein transporter activity				0					Pramlintide(DB01278)													---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45701761	45701761	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45701761T>C	uc003tne.3	+	8	1571	c.1553T>C	c.(1552-1554)TTC>TCC	p.F518S	ADCY1_uc003tnd.2_Missense_Mutation_p.F293S	NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	518	Interaction with calmodulin (By similarity).|Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47385797	47385797	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47385797C>T	uc003tnv.2	-	18	2806	c.2439G>A	c.(2437-2439)GCG>GCA	p.A813A	TNS3_uc003tnw.2_Silent_p.A813A	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	813						focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48682920	48682920	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48682920T>C	uc003toq.2	+	60	14899	c.14874T>C	c.(14872-14874)TGT>TGC	p.C4958C	ABCA13_uc010kys.1_Silent_p.C2033C|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Silent_p.C688C	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4958					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
COBL	23242	broad.mit.edu	37	7	51096403	51096403	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51096403G>A	uc003tpr.3	-	10	2575	c.2390C>T	c.(2389-2391)CCC>CTC	p.P797L	COBL_uc003tps.2_Missense_Mutation_p.P854L|COBL_uc011kcl.1_Missense_Mutation_p.P797L|COBL_uc003tpp.3_Missense_Mutation_p.P583L|COBL_uc003tpq.3_Missense_Mutation_p.P738L|COBL_uc003tpo.3_Missense_Mutation_p.P339L	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	797										skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69064858	69064858	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69064858G>A	uc003tvw.3	+	1	962	c.219G>A	c.(217-219)CCG>CCA	p.P73P	AUTS2_uc003tvv.3_Silent_p.P73P|AUTS2_uc003tvx.3_Silent_p.P73P	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	73										ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70242168	70242168	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70242168C>T	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron|AUTS2_uc011keg.1_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70254984	70254984	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70254984G>A	uc003tvw.3	+	19	3525	c.2782G>A	c.(2782-2784)GCC>ACC	p.A928T	AUTS2_uc003tvx.3_Missense_Mutation_p.A904T|AUTS2_uc011keg.1_Missense_Mutation_p.A380T	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	928										ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
NSUN5	55695	broad.mit.edu	37	7	72722714	72722714	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72722714A>G	uc003txw.2	-	1	110	c.74T>C	c.(73-75)GTG>GCG	p.V25A	FKBP6_uc003twz.2_Intron|NSUN5_uc003txv.2_Missense_Mutation_p.V25A|NSUN5_uc003txx.2_Missense_Mutation_p.V25A|NSUN5_uc011kev.1_Missense_Mutation_p.V25A	NM_018044	NP_060514	Q96P11	NSUN5_HUMAN	NOL1/NOP2/Sun domain family, member 5 isoform 2	25							methyltransferase activity				0		Lung NSC(55;0.163)																---	---	---	---
FKBP6	8468	broad.mit.edu	37	7	72743360	72743360	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72743360T>C	uc003tya.2	+						FKBP6_uc003twz.2_Intron|FKBP6_uc011kew.1_Intron|FKBP6_uc010lbe.1_Intron|TRIM50_uc003txy.1_5'Flank|TRIM50_uc003txz.1_5'Flank	NM_003602	NP_003593			FK506 binding protein 6 isoform a						protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
WBSCR22	114049	broad.mit.edu	37	7	73107983	73107983	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73107983C>T	uc003tyt.2	+	9	684	c.626C>T	c.(625-627)TCG>TTG	p.S209L	WBSCR22_uc010lbi.1_RNA|WBSCR22_uc003tyu.2_Missense_Mutation_p.S209L|WBSCR22_uc003tyv.2_Missense_Mutation_p.S171L|WBSCR22_uc003tyw.1_Missense_Mutation_p.S72L	NM_017528	NP_059998	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22	209						nucleus	methyltransferase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
LIMK1	3984	broad.mit.edu	37	7	73535232	73535232	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73535232G>A	uc003uaa.1	+	15	1799	c.1634G>A	c.(1633-1635)CGG>CAG	p.R545Q	RFC2_uc011kfa.1_Intron|LIMK1_uc010lbl.1_RNA|LIMK1_uc003uab.2_Missense_Mutation_p.R511Q	NM_002314	NP_002305	P53667	LIMK1_HUMAN	LIM domain kinase 1	545	Protein kinase.				actin cytoskeleton organization|axon guidance|negative regulation of ubiquitin-protein ligase activity|positive regulation of actin filament bundle assembly|positive regulation of axon extension|Rho protein signal transduction	cytosol|growth cone|nucleus	ATP binding|heat shock protein binding|protein serine/threonine kinase activity|zinc ion binding			stomach(2)|ovary(1)	3		Lung NSC(55;0.137)																---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73954296	73954296	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73954296C>T	uc003uaq.2	+	14	2009	c.1616C>T	c.(1615-1617)ACA>ATA	p.T539I	GTF2IRD1_uc010lbq.2_Missense_Mutation_p.T571I|GTF2IRD1_uc003uap.2_Missense_Mutation_p.T539I|GTF2IRD1_uc003uar.1_Missense_Mutation_p.T539I	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	539						nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74148279	74148279	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74148279A>G	uc003uau.2	+	16	1689	c.1319A>G	c.(1318-1320)AAT>AGT	p.N440S	GTF2I_uc003uav.2_Missense_Mutation_p.N419S|GTF2I_uc003uaw.2_Missense_Mutation_p.N420S|GTF2I_uc003uay.2_Missense_Mutation_p.N418S|GTF2I_uc003uax.2_Missense_Mutation_p.N399S	NM_032999	NP_127492	P78347	GTF2I_HUMAN	general transcription factor IIi isoform 1	440	GTF2I-like 2.				negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75186991	75186991	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75186991C>T	uc003uds.1	-	16	1589	c.1548G>A	c.(1546-1548)TCG>TCA	p.S516S	HIP1_uc011kfz.1_Silent_p.S393S	NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1	516	Potential.				activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
POR	5447	broad.mit.edu	37	7	75608819	75608819	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75608819G>A	uc003udy.2	+	4	370	c.288G>A	c.(286-288)GAG>GAA	p.E96E	POR_uc011kgb.1_RNA|POR_uc011kgc.1_5'Flank|POR_uc011kgd.1_5'Flank|POR_uc011kge.1_5'Flank	NM_000941	NP_000932	P16435	NCPR_HUMAN	cytochrome P450 reductase	93	Flavodoxin-like.				cellular organofluorine metabolic process|positive regulation of monooxygenase activity	endoplasmic reticulum membrane	iron ion binding|NADPH-hemoprotein reductase activity			central_nervous_system(1)	1					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Lipoic Acid(DB00166)|Menadione(DB00170)|Methoxyflurane(DB01028)|Mitomycin(DB00305)|Nilutamide(DB00665)													---	---	---	---
SRCRB4D	136853	broad.mit.edu	37	7	76019658	76019658	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76019658G>A	uc003ufb.2	-	11	1794	c.1446C>T	c.(1444-1446)TGC>TGT	p.C482C	SRCRB4D_uc003ufa.2_5'UTR	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	482	SRCR 4.					extracellular region|membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77649302	77649302	+	Intron	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77649302G>C	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77885613	77885613	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77885613G>A	uc003ugx.2	-	10	1948	c.1694C>T	c.(1693-1695)CCG>CTG	p.P565L	MAGI2_uc003ugy.2_Missense_Mutation_p.P565L|MAGI2_uc010ldx.1_Missense_Mutation_p.P174L|MAGI2_uc010ldy.1_Missense_Mutation_p.P174L|MAGI2_uc011kgr.1_Missense_Mutation_p.P397L|MAGI2_uc011kgs.1_Missense_Mutation_p.P402L	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	565						cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
CD36	948	broad.mit.edu	37	7	80276128	80276128	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80276128T>C	uc003uhc.2	+	6	756	c.72T>C	c.(70-72)GGT>GGC	p.G24G	CD36_uc003uhd.3_Silent_p.G24G|CD36_uc011kgv.1_Intron|CD36_uc003uhe.3_Silent_p.G24G|CD36_uc003uhf.3_Silent_p.G24G|CD36_uc003uhg.3_Silent_p.G24G|CD36_uc003uhh.3_Silent_p.G24G	NM_001127444	NP_001120916	P16671	CD36_HUMAN	CD36 antigen	24	Helical; (Potential).				cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
HGF	3082	broad.mit.edu	37	7	81340814	81340814	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81340814G>A	uc003uhl.2	-	12	1592	c.1427C>T	c.(1426-1428)ACA>ATA	p.T476I	HGF_uc003uhm.2_Missense_Mutation_p.T471I	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	476					epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
HGF	3082	broad.mit.edu	37	7	81372669	81372669	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81372669C>T	uc003uhl.2	-	7	1030	c.865G>A	c.(865-867)GCT>ACT	p.A289T	HGF_uc003uhm.2_Missense_Mutation_p.A284T|HGF_uc003uhn.1_Missense_Mutation_p.E289K|HGF_uc003uho.1_Missense_Mutation_p.E284K	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	289					epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82581873	82581873	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82581873G>A	uc003uhx.2	-	5	8685	c.8396C>T	c.(8395-8397)ACA>ATA	p.T2799I	PCLO_uc003uhv.2_Missense_Mutation_p.T2799I|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2730					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82763950	82763950	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82763950C>T	uc003uhx.2	-	3	3205	c.2916G>A	c.(2914-2916)CAG>CAA	p.Q972Q	PCLO_uc003uhv.2_Silent_p.Q972Q	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	918	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82764620	82764620	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82764620A>C	uc003uhx.2	-	3	2535	c.2246T>G	c.(2245-2247)GTT>GGT	p.V749G	PCLO_uc003uhv.2_Missense_Mutation_p.V749G	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	695	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
GRM3	2913	broad.mit.edu	37	7	86468223	86468223	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86468223C>T	uc003uid.2	+	4	2492	c.1393C>T	c.(1393-1395)CGA>TGA	p.R465*	GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Nonsense_Mutation_p.R337*|GRM3_uc010leh.2_Nonsense_Mutation_p.R57*	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	465	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87815942	87815942	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87815942A>G	uc003ujn.2	+						ADAM22_uc003ujm.2_Silent_p.P827P|ADAM22_uc003ujo.2_Intron	NM_021723	NP_068369			ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88847534	88847534	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88847534A>C	uc011khi.1	+	2	712	c.174A>C	c.(172-174)GAA>GAC	p.E58D		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	58	C2H2-type.					intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88956722	88956722	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88956722A>C	uc011khi.1	+	3	852	c.314A>C	c.(313-315)GAG>GCG	p.E105A		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	105						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91724394	91724394	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91724394T>C	uc003ulg.2	+	40	9861	c.9636T>C	c.(9634-9636)AGT>AGC	p.S3212S	AKAP9_uc003ulf.2_Silent_p.S3204S|AKAP9_uc003uli.2_Silent_p.S2835S|AKAP9_uc003ulj.2_Silent_p.S982S|AKAP9_uc003ull.2_Silent_p.S108S	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	3216	Potential.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
SAMD9L	219285	broad.mit.edu	37	7	92763746	92763746	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92763746T>G	uc003umh.1	-	5	2755	c.1539A>C	c.(1537-1539)GAA>GAC	p.E513D	SAMD9L_uc003umj.1_Missense_Mutation_p.E513D|SAMD9L_uc003umi.1_Missense_Mutation_p.E513D|SAMD9L_uc010lfb.1_Missense_Mutation_p.E513D|SAMD9L_uc003umk.1_Missense_Mutation_p.E513D|SAMD9L_uc010lfc.1_Missense_Mutation_p.E513D|SAMD9L_uc010lfd.1_Missense_Mutation_p.E513D|SAMD9L_uc011khx.1_Intron	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	513										ovary(4)	4	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)															---	---	---	---
CALCR	799	broad.mit.edu	37	7	93055810	93055810	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93055810G>A	uc003umv.1	-	15	1646	c.1385C>T	c.(1384-1386)GCT>GTT	p.A462V	CALCR_uc011kia.1_Missense_Mutation_p.A242V|CALCR_uc003ums.1_RNA|CALCR_uc003umt.1_RNA|CALCR_uc003umu.1_Missense_Mutation_p.A428V|CALCR_uc003umw.2_Missense_Mutation_p.A428V	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor isoform 2 precursor	444	Poly-Ala.|Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding	p.I462I(1)		ovary(3)|lung(3)|skin(2)|pancreas(1)	9	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)													---	---	---	---
PON3	5446	broad.mit.edu	37	7	94991695	94991695	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94991695A>G	uc003unt.2	-	8	910	c.885T>C	c.(883-885)CCT>CCC	p.P295P	PON1_uc011kih.1_Intron	NM_000940	NP_000931	Q15166	PON3_HUMAN	paraoxonase 3	295					aromatic compound catabolic process|carboxylic acid catabolic process|response to external stimulus	extracellular space	aryldialkylphosphatase activity|arylesterase activity|metal ion binding|protein homodimerization activity			ovary(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)															---	---	---	---
TAC1	6863	broad.mit.edu	37	7	97364165	97364165	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97364165A>C	uc003uop.3	+						TAC1_uc003uoq.3_Intron|TAC1_uc003uor.3_Intron|TAC1_uc003uos.3_Intron	NM_003182	NP_003173			tachykinin 1 isoform beta precursor						detection of abiotic stimulus|elevation of cytosolic calcium ion concentration|insemination|neuropeptide signaling pathway|synaptic transmission|tachykinin receptor signaling pathway	extracellular space					0	all_cancers(62;3.95e-09)|all_epithelial(64;1.1e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0358)|all_lung(186;0.0384)				Bacitracin(DB00626)													---	---	---	---
NPTX2	4885	broad.mit.edu	37	7	98254224	98254224	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98254224C>T	uc003upl.2	+							NM_002523	NP_002514			neuronal pentraxin II precursor						synaptic transmission	extracellular region	metal ion binding|sugar binding			central_nervous_system(2)|skin(1)	3	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
SMURF1	57154	broad.mit.edu	37	7	98649829	98649829	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98649829G>A	uc003upu.1	-	7	1040	c.720C>T	c.(718-720)TAC>TAT	p.Y240Y	SMURF1_uc003upv.1_Silent_p.Y240Y|SMURF1_uc003upt.2_Silent_p.Y240Y	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform	240	WW 1.				BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)															---	---	---	---
ZNF789	285989	broad.mit.edu	37	7	99079810	99079810	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99079810T>C	uc003uqq.1	+						ZNF789_uc003uqp.2_Missense_Mutation_p.I59T|ZNF789_uc010lfw.1_Intron|ZNF789_uc003uqr.1_5'Flank	NM_213603	NP_998768			zinc finger protein 789 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)																	---	---	---	---
CYP3A4	1576	broad.mit.edu	37	7	99361615	99361615	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99361615C>T	uc003urv.1	-	10	993	c.889G>A	c.(889-891)GCC>ACC	p.A297T	CYP3A4_uc003urw.1_Missense_Mutation_p.A296T|CYP3A4_uc011kiz.1_Missense_Mutation_p.A256T|CYP3A4_uc011kja.1_Missense_Mutation_p.A248T|CYP3A4_uc011kjb.1_Missense_Mutation_p.A147T	NM_017460	NP_059488	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A,	297					alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process	cell surface|endoplasmic reticulum membrane|integral to membrane|microsome	albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity			central_nervous_system(3)|ovary(1)	4	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)													---	---	---	---
ZKSCAN1	7586	broad.mit.edu	37	7	99621904	99621904	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99621904G>A	uc003usk.1	+	3	773	c.554G>A	c.(553-555)CGG>CAG	p.R185Q	ZKSCAN1_uc003usj.2_Missense_Mutation_p.R184Q|ZKSCAN1_uc003usl.1_Missense_Mutation_p.R149Q|ZKSCAN1_uc003usm.1_Intron	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36	185					viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99710462	99710462	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99710462A>G	uc003uti.2	-	6	614	c.533T>C	c.(532-534)CTG>CCG	p.L178P	TAF6_uc003utg.2_Missense_Mutation_p.L100P|TAF6_uc003uth.2_Missense_Mutation_p.L235P|TAF6_uc003utk.2_Missense_Mutation_p.L178P|TAF6_uc011kji.1_Missense_Mutation_p.L215P|TAF6_uc003utj.2_Missense_Mutation_p.L168P|TAF6_uc003utl.2_Missense_Mutation_p.L178P|TAF6_uc003utm.2_Missense_Mutation_p.L178P|TAF6_uc003utn.1_RNA	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	178					negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
SPDYE3	441272	broad.mit.edu	37	7	99913460	99913460	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99913460A>G	uc003uug.1	+	2	363	c.123A>G	c.(121-123)TCA>TCG	p.S41S		NM_001004351	NP_001004351	A6NKU9	SPDE3_HUMAN	speedy homolog E3	418											0																		---	---	---	---
GIGYF1	64599	broad.mit.edu	37	7	100279802	100279802	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100279802A>G	uc003uwg.1	-	22	3827	c.2818T>C	c.(2818-2820)TAT>CAT	p.Y940H		NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1	940										large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)																	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100350272	100350272	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100350272A>G	uc003uwj.2	+	14	2709	c.2544A>G	c.(2542-2544)GAA>GAG	p.E848E	ZAN_uc003uwk.2_Silent_p.E848E|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	848	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100366269	100366269	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100366269G>A	uc003uwj.2	+	27	5243	c.5078G>A	c.(5077-5079)CGC>CAC	p.R1693H	ZAN_uc003uwk.2_Missense_Mutation_p.R1693H|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA|ZAN_uc011kkd.1_Missense_Mutation_p.R270H	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	1693	Extracellular (Potential).|VWFD 2.				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
ACHE	43	broad.mit.edu	37	7	100491627	100491627	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100491627C>T	uc003uxd.2	-	1	383	c.227G>A	c.(226-228)CGT>CAT	p.R76H	ACHE_uc003uxe.2_Missense_Mutation_p.R76H|ACHE_uc003uxf.2_Missense_Mutation_p.R76H|ACHE_uc003uxg.2_Missense_Mutation_p.R76H|ACHE_uc003uxh.2_Missense_Mutation_p.R76H|ACHE_uc003uxi.2_Missense_Mutation_p.R76H|ACHE_uc003uxj.1_Missense_Mutation_p.R195H	NM_000665	NP_000656	P22303	ACES_HUMAN	acetylcholinesterase isoform E4-E6 precursor	76					acetylcholine catabolic process in synaptic cleft|amyloid precursor protein metabolic process|cell adhesion|cell proliferation|choline metabolic process|DNA replication|muscle organ development|neurotransmitter biosynthetic process|osteoblast development|positive regulation of protein secretion|regulation of axonogenesis|regulation of dendrite morphogenesis|response to wounding|synapse assembly	anchored to membrane|axon|basal lamina|cell junction|cell surface|dendrite|endoplasmic reticulum lumen|extracellular space|Golgi apparatus|neuromuscular junction|nucleus|perinuclear region of cytoplasm|postsynaptic membrane|presynaptic membrane|synaptic cleft	acetylcholine binding|acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|collagen binding|laminin-1 binding|protein homodimerization activity|serine hydrolase activity			skin(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Atropine(DB00572)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium bromide(DB00944)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tacrine(DB00382)|Tubocurarine(DB01199)													---	---	---	---
MOGAT3	346606	broad.mit.edu	37	7	100841524	100841524	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100841524A>T	uc003uyc.2	-	5	783	c.616T>A	c.(616-618)TGC>AGC	p.C206S	MOGAT3_uc010lhr.2_Missense_Mutation_p.C206S	NM_178176	NP_835470	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3	206					glycerol metabolic process|lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity|diacylglycerol O-acyltransferase activity			ovary(2)	2	Lung NSC(181;0.168)|all_lung(186;0.215)																	---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101844765	101844765	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101844765C>T	uc003uyx.3	+	18	2226	c.2188C>T	c.(2188-2190)CAG>TAG	p.Q730*	CUX1_uc003uys.3_Nonsense_Mutation_p.Q741*|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a	730					negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
PIK3CG	5294	broad.mit.edu	37	7	106508571	106508571	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106508571G>A	uc003vdv.3	+	2	650	c.565G>A	c.(565-567)GCC>ACC	p.A189T	PIK3CG_uc003vdu.2_Missense_Mutation_p.A189T|PIK3CG_uc003vdw.2_Missense_Mutation_p.A189T	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	189					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38																		---	---	---	---
DUS4L	11062	broad.mit.edu	37	7	107216881	107216881	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107216881A>G	uc003veh.2	+	7	883	c.550A>G	c.(550-552)ACA>GCA	p.T184A	DUS4L_uc003veg.2_Missense_Mutation_p.T63A|DUS4L_uc011klw.1_RNA|DUS4L_uc011klx.1_Missense_Mutation_p.T63A|DUS4L_uc010ljl.2_Missense_Mutation_p.T94A	NM_181581	NP_853559	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like	184					tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity				0																		---	---	---	---
BCAP29	55973	broad.mit.edu	37	7	107234461	107234461	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107234461C>T	uc003vej.2	+	4	594	c.255C>T	c.(253-255)AGC>AGT	p.S85S	BCAP29_uc011kly.1_5'UTR|BCAP29_uc011klz.1_Silent_p.S85S|BCAP29_uc011kma.1_Silent_p.S85S	NM_018844	NP_061332	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein BAP29 isoform	85	Lumenal (Potential).				apoptosis|intracellular protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane				large_intestine(1)|ovary(1)	2																		---	---	---	---
DNAJB9	4189	broad.mit.edu	37	7	108212352	108212352	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108212352C>A	uc003vfn.2	+	2	384	c.182C>A	c.(181-183)CCG>CAG	p.P61Q	THAP5_uc003vfl.2_5'Flank|THAP5_uc003vfm.2_5'Flank	NM_012328	NP_036460	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	61	J.				ER-associated protein catabolic process|protein folding	endoplasmic reticulum|nucleolus	heat shock protein binding|misfolded protein binding|unfolded protein binding				0																		---	---	---	---
DNAJB9	4189	broad.mit.edu	37	7	108213767	108213767	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108213767T>C	uc003vfn.2	+	3	844	c.642T>C	c.(640-642)GTT>GTC	p.V214V		NM_012328	NP_036460	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	214					ER-associated protein catabolic process|protein folding	endoplasmic reticulum|nucleolus	heat shock protein binding|misfolded protein binding|unfolded protein binding				0																		---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110763303	110763303	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110763303G>A	uc003vft.3	+	4	1521	c.475G>A	c.(475-477)GCC>ACC	p.A159T	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.A159T|LRRN3_uc003vfs.3_Missense_Mutation_p.A159T	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	159	LRR 4.|Extracellular (Potential).					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
TMEM168	64418	broad.mit.edu	37	7	112423777	112423777	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112423777C>T	uc003vgn.2	-	2	1496	c.1104G>A	c.(1102-1104)GCG>GCA	p.A368A	TMEM168_uc010lju.2_Silent_p.A368A|TMEM168_uc011kmr.1_Intron	NM_022484	NP_071929	Q9H0V1	TM168_HUMAN	transmembrane protein 168	368	Helical; (Potential).					integral to membrane|transport vesicle				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PPP1R3A	5506	broad.mit.edu	37	7	113519686	113519686	+	Missense_Mutation	SNP	T	G	G	rs139605314		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113519686T>G	uc010ljy.1	-	4	1492	c.1461A>C	c.(1459-1461)AGA>AGC	p.R487S		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	487					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34																		---	---	---	---
KCND2	3751	broad.mit.edu	37	7	119915142	119915142	+	Silent	SNP	G	A	A	rs116322872	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119915142G>A	uc003vjj.1	+	1	1421	c.456G>A	c.(454-456)GCG>GCA	p.A152A		NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related	152	Cytoplasmic (Potential).				regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
WNT16	51384	broad.mit.edu	37	7	120979236	120979236	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120979236G>A	uc003vjw.2	+	4	1192	c.935G>A	c.(934-936)CGT>CAT	p.R312H	WNT16_uc003vjv.2_Missense_Mutation_p.R302H|WNT16_uc010lkl.2_Missense_Mutation_p.R96H	NM_057168	NP_476509	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family,	312					anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|keratinocyte differentiation|keratinocyte proliferation|negative regulation of cell death|optic cup formation involved in camera-type eye development|oxidative stress-induced premature senescence|positive regulation of gene expression|positive regulation of JNK cascade|positive regulation of phosphatidylinositol 3-kinase cascade|replicative senescence|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled binding|signal transducer activity			lung(2)|ovary(2)|large_intestine(1)	5	all_neural(327;0.117)																	---	---	---	---
FEZF1	389549	broad.mit.edu	37	7	121942278	121942278	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121942278T>C	uc003vkd.2	-	4	1275	c.1201A>G	c.(1201-1203)ACC>GCC	p.T401A	FEZF1_uc003vkc.2_Missense_Mutation_p.T351A|uc010lko.1_5'Flank	NM_001024613	NP_001019784	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1 isoform 1	401	C2H2-type 6.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3																		---	---	---	---
GPR37	2861	broad.mit.edu	37	7	124404743	124404743	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124404743C>T	uc003vli.2	-	1	939	c.288G>A	c.(286-288)CCG>CCA	p.P96P		NM_005302	NP_005293	O15354	GPR37_HUMAN	G protein-coupled receptor 37 precursor	96	Extracellular (Potential).					endoplasmic reticulum membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126544185	126544185	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126544185A>C	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						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)			---	---	---	---
LRRC4	64101	broad.mit.edu	37	7	127669622	127669622	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127669622C>T	uc003vmk.2	-	2	1209	c.1072G>A	c.(1072-1074)GCA>ACA	p.A358T	SND1_uc003vmi.2_Intron|SND1_uc010lle.2_Intron	NM_022143	NP_071426	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4 precursor	358	Extracellular (Potential).|Ig-like.					cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4				Lung(243;0.124)														---	---	---	---
SND1	27044	broad.mit.edu	37	7	127729706	127729706	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127729706A>G	uc003vmi.2	+	22	2810	c.2584A>G	c.(2584-2586)ATG>GTG	p.M862V	SND1_uc010lle.2_Missense_Mutation_p.M515V	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1	862					gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
IMPDH1	3614	broad.mit.edu	37	7	128036978	128036978	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128036978G>A	uc011kol.1	-						IMPDH1_uc011kom.1_Intron|IMPDH1_uc003vmt.2_Intron|IMPDH1_uc003vmu.2_Intron|IMPDH1_uc003vmw.2_Intron|IMPDH1_uc011kon.1_Intron|IMPDH1_uc003vmv.2_Intron|IMPDH1_uc003vmx.2_Intron|IMPDH1_uc003vmy.2_Intron	NM_001142573	NP_001136045			inosine monophosphate dehydrogenase 1 isoform e						GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)													---	---	---	---
TNPO3	23534	broad.mit.edu	37	7	128597313	128597313	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128597313C>T	uc003vol.1	-	22	3142	c.2768G>A	c.(2767-2769)CGA>CAA	p.R923Q	TNPO3_uc010llx.1_Intron|TNPO3_uc003vom.1_Missense_Mutation_p.R857Q|TNPO3_uc010lly.1_Missense_Mutation_p.R957Q|TNPO3_uc010llz.1_Missense_Mutation_p.R859Q	NM_012470	NP_036602	Q9Y5L0	TNPO3_HUMAN	transportin 3	923					splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity	p.R923*(1)		ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
KLHDC10	23008	broad.mit.edu	37	7	129764387	129764387	+	Intron	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129764387T>A	uc003vpj.1	+						KLHDC10_uc003vpk.1_Intron|KLHDC10_uc010lmb.1_Intron	NM_014997	NP_055812			kelch domain containing 10												0																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131859616	131859616	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131859616G>A	uc003vra.3	-	21	4167	c.3938C>T	c.(3937-3939)CCG>CTG	p.P1313L		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1313	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131895837	131895837	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131895837C>T	uc003vra.3	-	10	2392	c.2163G>A	c.(2161-2163)ACG>ACA	p.T721T		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	721	Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133580444	133580444	+	Silent	SNP	C	T	T	rs34995232		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133580444C>T	uc003vrk.2	+	12	1862	c.1827C>T	c.(1825-1827)TGC>TGT	p.C609C	EXOC4_uc011kpo.1_Silent_p.C508C|EXOC4_uc003vrl.2_Silent_p.C219C|EXOC4_uc011kpp.1_Silent_p.C141C	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a	609					vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
AKR1B1	231	broad.mit.edu	37	7	134132069	134132069	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134132069C>T	uc003vrp.1	-	8	880	c.806G>A	c.(805-807)CGC>CAC	p.R269H	AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1	269	NADP.				C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)													---	---	---	---
AKR1B1	231	broad.mit.edu	37	7	134132123	134132123	+	Missense_Mutation	SNP	C	T	T	rs145261078		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134132123C>T	uc003vrp.1	-	8	826	c.752G>A	c.(751-753)CGG>CAG	p.R251Q	AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1	251	NADP.				C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)													---	---	---	---
AKR1B1	231	broad.mit.edu	37	7	134136454	134136454	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134136454A>G	uc003vrp.1	-	2	192	c.118T>C	c.(118-120)TAC>CAC	p.Y40H	AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1	40					C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)													---	---	---	---
CALD1	800	broad.mit.edu	37	7	134644737	134644737	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134644737G>A	uc003vrz.2	+	12	2533	c.2074G>A	c.(2074-2076)GCA>ACA	p.A692T	CALD1_uc003vry.2_Missense_Mutation_p.A437T|CALD1_uc003vsa.2_Missense_Mutation_p.A463T|CALD1_uc003vsb.2_Missense_Mutation_p.A437T|CALD1_uc010lmm.2_Missense_Mutation_p.A462T|CALD1_uc011kpt.1_Missense_Mutation_p.A211T|CALD1_uc003vsc.2_Missense_Mutation_p.A457T|CALD1_uc003vsd.2_Missense_Mutation_p.A431T|CALD1_uc011kpu.1_Missense_Mutation_p.A442T|CALD1_uc011kpv.1_Missense_Mutation_p.A301T|CALD1_uc003vse.2_Missense_Mutation_p.A555T|CALD1_uc010lmn.2_RNA	NM_033138	NP_149129	Q05682	CALD1_HUMAN	caldesmon 1 isoform 1	692					cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0																		---	---	---	---
STRA8	346673	broad.mit.edu	37	7	134927575	134927575	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134927575G>T	uc011kpx.1	+	3	301	c.301G>T	c.(301-303)GAG>TAG	p.E101*		NM_182489	NP_872295	Q7Z7C7	STRA8_HUMAN	STRA8	101	Potential.				DNA replication|regulation of transcription, DNA-dependent	cytoplasm|nucleus					0																		---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138546182	138546182	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138546182G>A	uc011kql.1	-	16	4999	c.4950C>T	c.(4948-4950)GCC>GCT	p.A1650A	KIAA1549_uc011kqi.1_Silent_p.A434A|KIAA1549_uc003vuk.3_Silent_p.A1600A|KIAA1549_uc011kqj.1_Silent_p.A1650A|KIAA1549_uc011kqk.1_Silent_p.A434A	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1650						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138936727	138936727	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138936727A>G	uc011kqr.1	+	3	587	c.587A>G	c.(586-588)AAG>AGG	p.K196R		NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	196										ovary(1)|skin(1)	2																		---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138944059	138944059	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138944059G>A	uc011kqr.1	+	5	848	c.848G>A	c.(847-849)CGG>CAG	p.R283Q	UBN2_uc003vuv.2_Missense_Mutation_p.R6Q	NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	283	Lys-rich.									ovary(1)|skin(1)	2																		---	---	---	---
KLRG2	346689	broad.mit.edu	37	7	139167663	139167663	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139167663G>A	uc003vvb.2	-	1	795	c.726C>T	c.(724-726)GAC>GAT	p.D242D	KLRG2_uc010lnc.2_Silent_p.D242D	NM_198508	NP_940910	A4D1S0	KLRG2_HUMAN	killer cell lectin-like receptor subfamily G,	242						integral to membrane	sugar binding			central_nervous_system(1)	1	Melanoma(164;0.233)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140227168	140227168	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140227168C>T	uc010lnj.2	-	13	2600	c.2455G>A	c.(2455-2457)GGG>AGG	p.G819R	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Missense_Mutation_p.G819R|DENND2A_uc003vvw.2_Missense_Mutation_p.G819R	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	819	DENN.									ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140380868	140380868	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140380868G>A	uc003vvy.1	+	4	1414	c.1236G>A	c.(1234-1236)CAG>CAA	p.Q412Q	ADCK2_uc003vvz.2_Silent_p.Q412Q	NM_052853	NP_443085	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	412	Protein kinase.					integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	142119822	142119822	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142119822T>C	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142499092	142499092	+	RNA	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142499092C>T	uc011ksh.1	+	3		c.471C>T			uc011ksi.1_RNA|uc003vzw.1_RNA|uc010loj.1_RNA|uc003wad.2_RNA|uc003wag.1_3'UTR|uc003wbe.3_RNA|uc003wbf.3_RNA|uc003wbg.3_RNA|uc003wbh.3_Silent_p.A169A|uc003wbi.3_RNA|uc003wbj.3_RNA|uc003wbm.3_RNA|uc003wbn.3_RNA|uc010los.2_RNA					Homo sapiens mRNA for T-cell receptor beta chain, partial cds, clone:TCRVB.3.																														---	---	---	---
TAS2R39	259285	broad.mit.edu	37	7	142880774	142880774	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142880774G>T	uc011ksw.1	+	1	263	c.263G>T	c.(262-264)AGC>ATC	p.S88I		NM_176881	NP_795362	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	88	Helical; Name=2; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			skin(1)	1	Melanoma(164;0.059)																	---	---	---	---
FAM131B	9715	broad.mit.edu	37	7	143053849	143053849	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143053849C>T	uc003wct.2	-	6	2499	c.793G>A	c.(793-795)GCA>ACA	p.A265T	FAM131B_uc010loz.2_Missense_Mutation_p.A233T|FAM131B_uc003wcu.3_Missense_Mutation_p.A265T|FAM131B_uc010lpa.2_Missense_Mutation_p.A293T	NM_014690	NP_055505	Q86XD5	F131B_HUMAN	hypothetical protein LOC9715 isoform b	265											0	Melanoma(164;0.205)																	---	---	---	---
OR2A2	442361	broad.mit.edu	37	7	143807240	143807240	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143807240G>A	uc011ktz.1	+	1	565	c.565G>A	c.(565-567)GCT>ACT	p.A189T		NM_001005480	NP_001005480	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A,	189	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Melanoma(164;0.0783)																	---	---	---	---
ZNF786	136051	broad.mit.edu	37	7	148767606	148767606	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148767606A>G	uc003wfh.2	-	4	2395	c.2258T>C	c.(2257-2259)GTA>GCA	p.V753A	ZNF786_uc011kuk.1_Missense_Mutation_p.V716A|ZNF786_uc003wfi.2_Missense_Mutation_p.V667A	NM_152411	NP_689624	Q8N393	ZN786_HUMAN	zinc finger protein 786	753	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)															---	---	---	---
ZNF282	8427	broad.mit.edu	37	7	148909543	148909543	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148909543T>A	uc003wfm.2	+	6	1151	c.1046T>A	c.(1045-1047)ATT>AAT	p.I349N	ZNF282_uc011kun.1_Missense_Mutation_p.I349N|ZNF282_uc003wfn.2_Missense_Mutation_p.I289N|ZNF282_uc003wfo.2_Intron	NM_003575	NP_003566	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	349					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)														---	---	---	---
KRBA1	84626	broad.mit.edu	37	7	149423093	149423093	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149423093C>T	uc003wfz.2	+	11	1815	c.1416C>T	c.(1414-1416)ACC>ACT	p.T472T	KRBA1_uc010lpj.2_RNA|KRBA1_uc003wga.2_RNA|KRBA1_uc003wgb.2_Silent_p.T140T	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	472										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149474079	149474079	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149474079G>T	uc010lpk.2	+	3	289	c.289G>T	c.(289-291)GGC>TGC	p.G97C	SSPO_uc010lpl.1_Intron	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	97	EMI.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
TMEM176B	28959	broad.mit.edu	37	7	150490222	150490222	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150490222T>C	uc003wht.3	-	5	720	c.554A>G	c.(553-555)AAC>AGC	p.N185S	TMEM176B_uc003whu.3_Missense_Mutation_p.N185S|TMEM176B_uc003whv.3_Missense_Mutation_p.N148S|TMEM176B_uc003whw.3_Missense_Mutation_p.N185S	NM_001101313	NP_001094783	Q3YBM2	T176B_HUMAN	transmembrane protein 176B isoform a	185					cell differentiation|organ morphogenesis	integral to membrane|nuclear membrane				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
ACCN3	9311	broad.mit.edu	37	7	150747186	150747186	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150747186G>A	uc003win.2	+						ACCN3_uc003wio.2_Intron|ACCN3_uc003wip.2_Intron|ACCN3_uc003wiq.2_Intron	NM_004769	NP_004760			amiloride-sensitive cation channel 3 isoform a						sensory perception|signal transduction	cytoplasm|integral to plasma membrane	ligand-gated sodium channel activity			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
SLC4A2	6522	broad.mit.edu	37	7	150771788	150771788	+	Silent	SNP	G	A	A	rs17852574		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150771788G>A	uc003wit.3	+	19	3163	c.2907G>A	c.(2905-2907)TCG>TCA	p.S969S	SLC4A2_uc011kve.1_Silent_p.S960S|SLC4A2_uc003wiu.3_Silent_p.S955S|SLC4A2_uc003wiv.3_Silent_p.S163S	NM_003040	NP_003031	P04920	B3A2_HUMAN	solute carrier family 4, anion exchanger, member	969	Membrane (anion exchange).				bicarbonate transport	integral to membrane|membrane fraction	inorganic anion exchanger activity				0			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
FASTK	10922	broad.mit.edu	37	7	150774091	150774091	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150774091C>T	uc003wix.1	-	9	1549	c.1451G>A	c.(1450-1452)CGC>CAC	p.R484H	uc011kvf.1_5'Flank|FASTK_uc003wiw.1_Missense_Mutation_p.R245H|FASTK_uc003wiy.1_Missense_Mutation_p.R343H|FASTK_uc003wiz.1_Missense_Mutation_p.R457H|FASTK_uc003wja.1_3'UTR	NM_006712	NP_006703	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase isoform 1	484	RAP.				apoptosis|induction of apoptosis by extracellular signals|regulation of RNA splicing		ATP binding|Fas-activated serine/threonine kinase activity|protein binding			lung(2)|stomach(2)	4			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)														---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151810452	151810452	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151810452G>A	uc010lqg.1	+	8	1432	c.1202G>A	c.(1201-1203)CGG>CAG	p.R401Q	GALNT11_uc011kvm.1_Missense_Mutation_p.R320Q|GALNT11_uc003wku.2_Missense_Mutation_p.R401Q|GALNT11_uc003wkw.1_Missense_Mutation_p.R149Q	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	401	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151836261	151836261	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151836261G>A	uc003wla.2	-						MLL3_uc003wkz.2_Intron|MLL3_uc003wkx.2_Intron|MLL3_uc003wky.2_Intron	NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151970781	151970781	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151970781T>C	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						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								---	---	---	---
LMBR1	64327	broad.mit.edu	37	7	156520652	156520652	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156520652T>G	uc003wmw.3	-	12	1180	c.965A>C	c.(964-966)GAT>GCT	p.D322A	LMBR1_uc003wmv.3_Missense_Mutation_p.D170A|LMBR1_uc003wmx.3_Missense_Mutation_p.D170A|LMBR1_uc010lqn.2_Missense_Mutation_p.D363A|LMBR1_uc011kvx.1_Missense_Mutation_p.D301A	NM_022458	NP_071903	Q8WVP7	LMBR1_HUMAN	limb region 1 protein	322	Extracellular (Potential).					integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)														---	---	---	---
MIR153-2	406945	broad.mit.edu	37	7	157367111	157367111	+	RNA	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157367111C>A	hsa-mir-153-2|MI0000464	-			c.4C>A			PTPRN2_uc003wno.2_Intron|PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron|uc011kwb.1_RNA																	0																		---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157985114	157985114	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157985114G>A	uc003wno.2	-	5	575	c.454C>T	c.(454-456)CGA>TGA	p.R152*	PTPRN2_uc003wnp.2_Nonsense_Mutation_p.R135*|PTPRN2_uc003wnq.2_Nonsense_Mutation_p.R152*|PTPRN2_uc003wnr.2_Nonsense_Mutation_p.R114*|PTPRN2_uc011kwa.1_Nonsense_Mutation_p.R175*	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	152	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
NCAPG2	54892	broad.mit.edu	37	7	158486107	158486107	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158486107A>G	uc003wnv.1	-	3	306	c.161T>C	c.(160-162)CTG>CCG	p.L54P	NCAPG2_uc003wnw.1_RNA|NCAPG2_uc003wnx.1_Missense_Mutation_p.L54P|NCAPG2_uc011kwe.1_Missense_Mutation_p.L54P	NM_017760	NP_060230	Q86XI2	CNDG2_HUMAN	leucine zipper protein 5	54					cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
ESYT2	57488	broad.mit.edu	37	7	158531742	158531742	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158531742T>C	uc003wob.1	-	18	2386	c.2320A>G	c.(2320-2322)AAG>GAG	p.K774E	ESYT2_uc003wny.1_RNA|ESYT2_uc003wnz.1_Missense_Mutation_p.K213E|ESYT2_uc003woa.1_Missense_Mutation_p.K351E	NM_020728	NP_065779	A0FGR8	ESYT2_HUMAN	family with sequence similarity 62 (C2 domain	802	C2 3.					integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3																		---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2808696	2808696	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2808696T>C	uc011kwk.1	-	66	10534	c.10144A>G	c.(10144-10146)ACA>GCA	p.T3382A	CSMD1_uc011kwj.1_Missense_Mutation_p.T2696A|CSMD1_uc010lrg.2_Missense_Mutation_p.T1273A	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	3382	Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3200878	3200878	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3200878A>G	uc011kwk.1	-	23	3962	c.3572T>C	c.(3571-3573)CTG>CCG	p.L1191P	CSMD1_uc011kwj.1_Missense_Mutation_p.L583P|CSMD1_uc003wqe.2_Missense_Mutation_p.L347P	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1191	Extracellular (Potential).|CUB 7.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3216843	3216843	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3216843A>G	uc011kwk.1	-	21	3528	c.3138T>C	c.(3136-3138)TGT>TGC	p.C1046C	CSMD1_uc011kwj.1_Silent_p.C438C|CSMD1_uc003wqe.2_Silent_p.C202C	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1046	Sushi 6.|Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6302587	6302587	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6302587T>C	uc003wqi.2	+	8	1412	c.1344T>C	c.(1342-1344)TCT>TCC	p.S448S	MCPH1_uc003wqh.2_Silent_p.S448S|MCPH1_uc011kwl.1_Silent_p.S400S	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin	448						microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
PRSS55	203074	broad.mit.edu	37	8	10383222	10383222	+	Missense_Mutation	SNP	C	T	T	rs148104469		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10383222C>T	uc003wta.2	+	1	142	c.127C>T	c.(127-129)CCC>TCC	p.P43S	uc010lru.2_Intron	NM_198464	NP_940866	Q6UWB4	PRS55_HUMAN	hypothetical protein LOC203074 precursor	43	Extracellular (Potential).				proteolysis	integral to membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12948849	12948849	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12948849G>C	uc003wwm.2	-	14	4277	c.3833C>G	c.(3832-3834)GCC>GGC	p.A1278G	DLC1_uc003wwk.1_Missense_Mutation_p.A841G|DLC1_uc003wwl.1_Missense_Mutation_p.A875G|DLC1_uc011kxx.1_Missense_Mutation_p.A767G	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	1278	Rho-GAP.				actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7																		---	---	---	---
FGF20	26281	broad.mit.edu	37	8	16850819	16850819	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16850819A>C	uc003wxc.1	-	3	531	c.398T>G	c.(397-399)CTT>CGT	p.L133R	FGF20_uc010lsv.1_RNA|FGF20_uc010lsw.1_Silent_p.T98T	NM_019851	NP_062825	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	133					cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	extracellular region|soluble fraction	growth factor activity			lung(1)	1				Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)														---	---	---	---
MTMR7	9108	broad.mit.edu	37	8	17157580	17157580	+	Missense_Mutation	SNP	G	A	A	rs140365611		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17157580G>A	uc003wxm.2	-	14	2013	c.1774C>T	c.(1774-1776)CGG>TGG	p.R592W	MTMR7_uc011kya.1_Missense_Mutation_p.R226W|MTMR7_uc011kyb.1_Missense_Mutation_p.R183W	NM_004686	NP_004677	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	592							protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)														---	---	---	---
ASAH1	427	broad.mit.edu	37	8	17916887	17916887	+	Missense_Mutation	SNP	G	A	A	rs147233112	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17916887G>A	uc003wyl.2	-	12	1316	c.1004C>T	c.(1003-1005)ACG>ATG	p.T335M	ASAH1_uc010ltb.1_RNA|ASAH1_uc003wym.2_Missense_Mutation_p.T310M|ASAH1_uc003wyn.2_Missense_Mutation_p.T351M|ASAH1_uc003wyo.2_Missense_Mutation_p.T329M	NM_177924	NP_808592	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase 1 isoform a	335					ceramide metabolic process	lysosome	ceramidase activity				0				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)														---	---	---	---
LZTS1	11178	broad.mit.edu	37	8	20112401	20112401	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20112401A>T	uc003wzr.2	-	1	403	c.292T>A	c.(292-294)TTT>ATT	p.F98I	LZTS1_uc010ltg.1_Missense_Mutation_p.F98I	NM_021020	NP_066300	Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	98					cell cycle|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	cell junction|dendritic spine|Golgi apparatus|nucleolus|nucleoplasm|postsynaptic density|postsynaptic membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)														---	---	---	---
CHMP7	91782	broad.mit.edu	37	8	23115862	23115862	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23115862C>A	uc003xdc.2	+	7	1508	c.860C>A	c.(859-861)GCC>GAC	p.A287D	CHMP7_uc011kzs.1_RNA|CHMP7_uc003xdd.2_Missense_Mutation_p.A177D|CHMP7_uc003xde.2_Missense_Mutation_p.A145D	NM_152272	NP_689485	Q8WUX9	CHMP7_HUMAN	CHMP family, member 7	287	Potential.				cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)														---	---	---	---
NEFM	4741	broad.mit.edu	37	8	24773231	24773231	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24773231C>T	uc003xed.3	+	2	1227	c.1194C>T	c.(1192-1194)ATC>ATT	p.I398I	NEFM_uc011lac.1_Silent_p.I398I|NEFM_uc010lue.2_Silent_p.I22I	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	398	Rod.|Coil 2B.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25158099	25158099	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25158099T>C	uc003xeg.2	+	9	909	c.772T>C	c.(772-774)TAT>CAT	p.Y258H	DOCK5_uc010luf.1_RNA|DOCK5_uc003xeh.1_Intron|DOCK5_uc003xef.2_Missense_Mutation_p.Y258H	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	258						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25902252	25902252	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25902252C>T	uc003xes.1	-	1	141	c.124G>A	c.(124-126)GCG>ACG	p.A42T	PPP2R2A_uc003xek.2_Intron|EBF2_uc003xet.1_Missense_Mutation_p.A42T	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	42					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)														---	---	---	---
ELP3	55140	broad.mit.edu	37	8	28013468	28013468	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28013468A>G	uc003xgo.3	+	11	1258	c.1110A>G	c.(1108-1110)CCA>CCG	p.P370P	ELP3_uc003xgn.3_Silent_p.P355P|ELP3_uc011laq.1_Silent_p.P298P|ELP3_uc011lar.1_Silent_p.P278P|ELP3_uc011las.1_Silent_p.P251P|ELP3_uc011lat.1_Silent_p.P251P	NM_018091	NP_060561	Q9H9T3	ELP3_HUMAN	elongation protein 3 homolog	370					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	histone acetyltransferase activity|iron-sulfur cluster binding|metal ion binding|phosphorylase kinase regulator activity|protein binding				0		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)														---	---	---	---
EXTL3	2137	broad.mit.edu	37	8	28575417	28575417	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28575417T>C	uc003xgz.1	+	3	2434	c.1841T>C	c.(1840-1842)TTC>TCC	p.F614S		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	614	Lumenal (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding			skin(2)	2		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)														---	---	---	---
BRF2	55290	broad.mit.edu	37	8	37702451	37702451	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37702451G>A	uc003xkk.2	-	4	927	c.817C>T	c.(817-819)CTG>TTG	p.L273L		NM_018310	NP_060780	Q9HAW0	BRF2_HUMAN	RNA polymerase III transcription initiation	273					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter|transcription initiation, DNA-dependent	nucleoplasm	protein binding|zinc ion binding				0		Lung NSC(58;0.118)|all_lung(54;0.195)	BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;1.81e-10)															---	---	---	---
FGFR1	2260	broad.mit.edu	37	8	38275753	38275753	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38275753G>A	uc003xlp.2	-	11	2365	c.1423C>T	c.(1423-1425)CGG>TGG	p.R475W	FGFR1_uc010lwf.2_RNA|FGFR1_uc011lbo.1_Missense_Mutation_p.R473W|FGFR1_uc011lbp.1_Missense_Mutation_p.R386W|FGFR1_uc011lbq.1_Missense_Mutation_p.R384W|FGFR1_uc010lwk.2_Missense_Mutation_p.R465W	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1	475	Cytoplasmic (Potential).				axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						---	---	---	---
GINS4	84296	broad.mit.edu	37	8	41399516	41399516	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41399516C>T	uc003xnx.2	+	8	792	c.582C>T	c.(580-582)TAC>TAT	p.Y194Y	GINS4_uc003xny.2_Silent_p.Y194Y	NM_032336	NP_115712	Q9BRT9	SLD5_HUMAN	GINS complex subunit 4	194	Important for GINS complex assembly.				DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				skin(1)	1	Ovarian(28;0.014)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.00732)|Lung NSC(58;0.0207)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00329)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
CHRNA6	8973	broad.mit.edu	37	8	42611479	42611479	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42611479A>G	uc003xpj.2	-	5	909	c.863T>C	c.(862-864)GTC>GCC	p.V288A	CHRNA6_uc011lcw.1_Missense_Mutation_p.V273A	NM_004198	NP_004189	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6	288	Helical; (Potential).					cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48846583	48846583	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48846583G>T	uc003xqi.2	-	15	1622	c.1565C>A	c.(1564-1566)CCC>CAC	p.P522H	PRKDC_uc003xqj.2_Missense_Mutation_p.P522H|PRKDC_uc011ldh.1_Missense_Mutation_p.P522H	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	522					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
EFCAB1	79645	broad.mit.edu	37	8	49647703	49647703	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49647703C>T	uc003xqo.2	-	1	168	c.8G>A	c.(7-9)CGC>CAC	p.R3H	EFCAB1_uc003xqn.3_RNA|EFCAB1_uc011ldj.1_Missense_Mutation_p.R3H|EFCAB1_uc010lxx.2_RNA|EFCAB1_uc011ldk.1_RNA	NM_024593	NP_078869	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1 isoform a	3							calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51449331	51449331	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51449331C>T	uc010lxy.1	+	12	1014	c.643C>T	c.(643-645)CGC>TGC	p.R215C	SNTG1_uc003xqs.1_Missense_Mutation_p.R215C|SNTG1_uc010lxz.1_Missense_Mutation_p.R215C|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	215					cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52366130	52366130	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52366130C>A	uc003xqu.3	-	10	1299	c.1198G>T	c.(1198-1200)GCC>TCC	p.A400S		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	400	Ig-like C2-type 2.				hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
NPBWR1	2831	broad.mit.edu	37	8	53852727	53852727	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53852727C>T	uc011ldu.1	+	1	260	c.260C>T	c.(259-261)ACG>ATG	p.T87M		NM_005285	NP_005276	P48145	NPBW1_HUMAN	G protein-coupled receptor 7	87	Helical; Name=2; (Potential).				synaptic transmission	plasma membrane	opioid receptor activity|protein binding			ovary(2)|breast(1)	3		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)																---	---	---	---
MRPL15	29088	broad.mit.edu	37	8	55055348	55055348	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55055348T>C	uc003xsa.2	+	4	616	c.553_splice	c.e4+2	p.D185_splice		NM_014175	NP_054894			mitochondrial ribosomal protein L15 precursor						translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome				0		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)															---	---	---	---
MRPL15	29088	broad.mit.edu	37	8	55059939	55059939	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55059939T>C	uc003xsa.2	+							NM_014175	NP_054894			mitochondrial ribosomal protein L15 precursor						translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome				0		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)															---	---	---	---
MOS	4342	broad.mit.edu	37	8	57026447	57026447	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57026447G>A	uc011leb.1	-	1	95	c.95C>T	c.(94-96)GCG>GTG	p.A32V		NM_005372	NP_005363	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene	32							ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|ovary(1)|central_nervous_system(1)	4			Epithelial(17;0.00117)|all cancers(17;0.00879)															---	---	---	---
UBXN2B	137886	broad.mit.edu	37	8	59352181	59352181	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59352181C>T	uc003xtl.2	+							NM_001077619	NP_001071087			UBX domain protein 2B							cytosol|endoplasmic reticulum|Golgi apparatus|nucleus				ovary(2)	2																		---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59502106	59502106	+	Missense_Mutation	SNP	G	A	A	rs146901191	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59502106G>A	uc003xtt.2	-	26	2330	c.2116C>T	c.(2116-2118)CGC>TGC	p.R706C	NSMAF_uc011lee.1_Missense_Mutation_p.R737C	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation	706					ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)																---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61736543	61736543	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61736543A>G	uc003xue.2	+	13	3823	c.3346A>G	c.(3346-3348)AAG>GAG	p.K1116E	CHD7_uc003xuf.2_Missense_Mutation_p.K229E	NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1116	Helicase ATP-binding.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61764728	61764728	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61764728G>A	uc003xue.2	+	29	6293	c.5816G>A	c.(5815-5817)CGG>CAG	p.R1939Q		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1939	Poly-Arg.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
TTPA	7274	broad.mit.edu	37	8	63973933	63973933	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63973933C>A	uc003xux.1	-	5	747	c.715G>T	c.(715-717)GAC>TAC	p.D239Y		NM_000370	NP_000361	P49638	TTPA_HUMAN	tocopherol (alpha) transfer protein	239	CRAL-TRIO.				lipid metabolic process		transporter activity|vitamin E binding				0	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)													---	---	---	---
BHLHE22	27319	broad.mit.edu	37	8	65493774	65493774	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65493774G>A	uc003xvi.2	+	1	961	c.427G>A	c.(427-429)GGC>AGC	p.G143S	LOC401463_uc003xvh.2_Intron	NM_152414	NP_689627	Q8NFJ8	BHE22_HUMAN	basic helix-loop-helix domain containing, class	143	Gly-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
C8orf44	56260	broad.mit.edu	37	8	67592020	67592020	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67592020A>G	uc003xwo.1	+	3	464	c.311A>G	c.(310-312)AAG>AGG	p.K104R	SGK3_uc003xwp.2_5'UTR|C8orf44_uc003xwq.1_Missense_Mutation_p.K104R	NM_019607	NP_062553	Q96CB5	CH044_HUMAN	hypothetical protein LOC56260	104											0	Breast(64;0.186)		Epithelial(68;0.000959)|OV - Ovarian serous cystadenocarcinoma(28;0.00318)|all cancers(69;0.00363)|BRCA - Breast invasive adenocarcinoma(89;0.149)															---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67771720	67771720	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67771720T>C	uc003xwr.2	+	17	1694	c.1395T>C	c.(1393-1395)TCT>TCC	p.S465S	SGK3_uc003xwp.2_Silent_p.S459S|SGK3_uc003xwt.2_Silent_p.S465S|SGK3_uc003xwu.2_Silent_p.S433S	NM_001033578	NP_001028750	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase 3 isoform	465	AGC-kinase C-terminal.				cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68204282	68204282	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68204282T>C	uc003xxo.1	-	6	1106	c.716A>G	c.(715-717)CAC>CGC	p.H239R		NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	239					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69005938	69005938	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69005938T>C	uc003xxv.1	+	21	2376	c.2349T>C	c.(2347-2349)GCT>GCC	p.A783A	PREX2_uc003xxu.1_Silent_p.A783A|PREX2_uc011lez.1_Silent_p.A718A	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	783					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69028025	69028025	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69028025C>T	uc003xxv.1	+	26	3211	c.3184C>T	c.(3184-3186)CGT>TGT	p.R1062C		NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1062					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69031710	69031710	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69031710G>T	uc003xxv.1	+	28	3492	c.3465G>T	c.(3463-3465)CAG>CAT	p.Q1155H		NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1155					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
TRPA1	8989	broad.mit.edu	37	8	72975152	72975152	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72975152A>G	uc003xza.2	-	6	864	c.689T>C	c.(688-690)TTG>TCG	p.L230S		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	230	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)													---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74525998	74525998	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74525998C>T	uc003xzm.2	-	9	1108	c.872G>A	c.(871-873)CGC>CAC	p.R291H	STAU2_uc011lfg.1_Missense_Mutation_p.R119H|STAU2_uc003xzn.2_Missense_Mutation_p.R259H|STAU2_uc011lfh.1_Missense_Mutation_p.R187H|STAU2_uc003xzo.2_Missense_Mutation_p.R291H|STAU2_uc003xzp.2_Missense_Mutation_p.R259H|STAU2_uc011lfi.1_Missense_Mutation_p.R253H|STAU2_uc003xzq.2_Missense_Mutation_p.R71H|STAU2_uc010lzk.2_Missense_Mutation_p.R259H|STAU2_uc010lzl.1_Missense_Mutation_p.R119H	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e	291	Nuclear localization signal 1 (By similarity).				transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81412237	81412237	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81412237G>A	uc003ybx.3	+	2	2079	c.1481G>A	c.(1480-1482)CGG>CAG	p.R494Q	ZBTB10_uc003ybv.3_Missense_Mutation_p.R202Q|ZBTB10_uc003ybw.3_Missense_Mutation_p.R494Q|ZBTB10_uc010lzt.2_Missense_Mutation_p.R494Q	NM_001105539	NP_001099009	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10 isoform	494					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)															---	---	---	---
PAG1	55824	broad.mit.edu	37	8	81897572	81897572	+	Silent	SNP	G	A	A	rs113484085		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81897572G>A	uc003ybz.2	-	7	1026	c.315C>T	c.(313-315)TAC>TAT	p.Y105Y		NM_018440	NP_060910	Q9NWQ8	PAG1_HUMAN	phosphoprotein associated with glycosphingolipid	105	Cytoplasmic (Potential).			Y->F: No effect on interaction with FYN or CSK.	epidermal growth factor receptor signaling pathway|intracellular signal transduction|T cell receptor signaling pathway	integral to membrane|intracellular|membrane raft|plasma membrane	SH2 domain binding|SH3/SH2 adaptor activity				0	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)															---	---	---	---
SNX16	64089	broad.mit.edu	37	8	82736084	82736084	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82736084T>C	uc011lft.1	-	5	1061	c.554A>G	c.(553-555)CAA>CGA	p.Q185R	SNX16_uc003ycn.2_Missense_Mutation_p.Q185R|SNX16_uc003yco.2_Missense_Mutation_p.Q156R	NM_022133	NP_071416	P57768	SNX16_HUMAN	sorting nexin 16 isoform a	185	PX.				cell communication|early endosome to late endosome transport|endosome to lysosome transport|protein targeting to lysosome	early endosome membrane|extrinsic to endosome membrane|late endosome membrane|lysosome	identical protein binding|phosphatidylinositol binding			ovary(1)|pancreas(1)	2																		---	---	---	---
ATP6V0D2	245972	broad.mit.edu	37	8	87151682	87151682	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87151682C>T	uc003ydp.1	+							NM_152565	NP_689778			ATPase, H+ transporting, lysosomal 38kDa, V0						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0																		---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89086858	89086858	+	Silent	SNP	G	A	A	rs143304974	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89086858G>A	uc003yeb.3	-	7	1479	c.1197C>T	c.(1195-1197)AGC>AGT	p.S399S	MMP16_uc003yec.2_Silent_p.S399S	NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	399	Hemopexin-like 2.|Extracellular (Potential).				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8																		---	---	---	---
OSGIN2	734	broad.mit.edu	37	8	90937290	90937290	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90937290T>C	uc003yeg.2	+	6	1394	c.1048T>C	c.(1048-1050)TAT>CAT	p.Y350H	OSGIN2_uc003yeh.2_Missense_Mutation_p.Y394H	NM_004337	NP_004328	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family	350					germ cell development|meiosis						0			BRCA - Breast invasive adenocarcinoma(11;0.0344)															---	---	---	---
DECR1	1666	broad.mit.edu	37	8	91029419	91029419	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91029419C>A	uc003yek.1	+	2	278	c.137C>A	c.(136-138)CCT>CAT	p.P46H	DECR1_uc011lgc.1_Missense_Mutation_p.P37H|DECR1_uc011lgd.1_Intron	NM_001359	NP_001350	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1 precursor	46					fatty acid beta-oxidation|protein homotetramerization	mitochondrial matrix|nucleus|plasma membrane	2,4-dienoyl-CoA reductase (NADPH) activity|NADPH binding|oxidoreductase activity, acting on NADH or NADPH				0			BRCA - Breast invasive adenocarcinoma(11;0.00953)															---	---	---	---
DECR1	1666	broad.mit.edu	37	8	91055016	91055016	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91055016T>C	uc003yek.1	+	7	867	c.726T>C	c.(724-726)CCT>CCC	p.P242P	DECR1_uc011lgc.1_Silent_p.P233P|DECR1_uc011lgd.1_RNA	NM_001359	NP_001350	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1 precursor	242					fatty acid beta-oxidation|protein homotetramerization	mitochondrial matrix|nucleus|plasma membrane	2,4-dienoyl-CoA reductase (NADPH) activity|NADPH binding|oxidoreductase activity, acting on NADH or NADPH				0			BRCA - Breast invasive adenocarcinoma(11;0.00953)															---	---	---	---
TMEM55A	55529	broad.mit.edu	37	8	92008941	92008941	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92008941G>A	uc003yes.2	-	6	797	c.571C>T	c.(571-573)CGC>TGC	p.R191C		NM_018710	NP_061180	Q8N4L2	TM55A_HUMAN	transmembrane protein 55A	191						integral to membrane|late endosome membrane|lysosomal membrane	hydrolase activity				0			BRCA - Breast invasive adenocarcinoma(11;0.033)															---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94747757	94747757	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94747757A>G	uc003yfz.2	-	3	1075	c.882T>C	c.(880-882)AGT>AGC	p.S294S		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	294	RRM 2.						nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
STK3	6788	broad.mit.edu	37	8	99591885	99591885	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99591885T>C	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100147927	100147927	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100147927G>A	uc003yiv.2	+	11	1640	c.1529G>A	c.(1528-1530)CGC>CAC	p.R510H	VPS13B_uc003yiw.2_Missense_Mutation_p.R510H|VPS13B_uc003yit.2_Missense_Mutation_p.R510H|VPS13B_uc003yiu.1_Missense_Mutation_p.R510H|VPS13B_uc003yix.1_5'Flank	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	510					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100779005	100779005	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100779005C>T	uc003yiv.2	+	40	7240	c.7129C>T	c.(7129-7131)CCT>TCT	p.P2377S	VPS13B_uc003yiw.2_Missense_Mutation_p.P2352S	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	2377					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
PABPC1	26986	broad.mit.edu	37	8	101721808	101721808	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101721808T>C	uc003yjs.1	-	8	1628	c.1124A>G	c.(1123-1125)CAG>CGG	p.Q375R	PABPC1_uc011lhc.1_Missense_Mutation_p.Q343R|PABPC1_uc011lhd.1_Missense_Mutation_p.Q330R|PABPC1_uc003yjt.1_Missense_Mutation_p.Q372R|PABPC1_uc003yju.2_RNA	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	375					mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103305825	103305825	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103305825C>T	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986			ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
CTHRC1	115908	broad.mit.edu	37	8	104394834	104394834	+	3'UTR	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104394834T>C	uc003ylk.2	+	4						NM_138455	NP_612464			collagen triple helix repeat containing 1							collagen				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)															---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104922742	104922742	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104922742T>G	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Missense_Mutation_p.H414Q|RIMS2_uc003ylt.2_5'Flank	NM_014677	NP_055492			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
TRHR	7201	broad.mit.edu	37	8	110099786	110099786	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110099786G>A	uc003ymz.3	+	1	61	c.45G>A	c.(43-45)CAG>CAA	p.Q15Q		NM_003301	NP_003292	P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	15	Extracellular (Potential).					integral to plasma membrane	thyrotropin-releasing hormone receptor activity			skin(2)|lung(1)	3			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)															---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110587852	110587852	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110587852A>G	uc003ynj.3	-	7	1438	c.1275T>C	c.(1273-1275)GCT>GCC	p.A425A	SYBU_uc003yni.3_Silent_p.A422A|SYBU_uc003ynk.3_Silent_p.A306A|SYBU_uc010mco.2_Silent_p.A424A|SYBU_uc003ynl.3_Silent_p.A424A|SYBU_uc010mcp.2_Silent_p.A425A|SYBU_uc010mcq.2_Silent_p.A425A|SYBU_uc003yno.3_Silent_p.A306A|SYBU_uc010mcr.2_Silent_p.A425A|SYBU_uc003ynm.3_Silent_p.A424A|SYBU_uc003ynn.3_Silent_p.A424A|SYBU_uc010mcs.2_Silent_p.A306A|SYBU_uc010mct.2_Silent_p.A425A|SYBU_uc010mcu.2_Silent_p.A424A|SYBU_uc003ynp.3_Silent_p.A357A|SYBU_uc010mcv.2_Silent_p.A425A|SYBU_uc003ynh.3_Silent_p.A219A|SYBU_uc011lhw.1_Silent_p.A295A	NM_001099754	NP_001093224	Q9NX95	SYBU_HUMAN	Golgi-localized syntaphilin-related protein	425						cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113293501	113293501	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113293501A>C	uc003ynu.2	-	59	9569	c.9410T>G	c.(9409-9411)GTC>GGC	p.V3137G	CSMD3_uc003yns.2_Missense_Mutation_p.V2339G|CSMD3_uc003ynt.2_Missense_Mutation_p.V3097G|CSMD3_uc011lhx.1_Missense_Mutation_p.V2968G	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3137	Extracellular (Potential).|Sushi 23.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113694851	113694851	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113694851C>T	uc003ynu.2	-	16	2656	c.2497G>A	c.(2497-2499)GAA>AAA	p.E833K	CSMD3_uc003yns.2_Missense_Mutation_p.E105K|CSMD3_uc003ynt.2_Missense_Mutation_p.E793K|CSMD3_uc011lhx.1_Missense_Mutation_p.E729K	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	833	Sushi 4.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116616692	116616692	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116616692T>G	uc003ynz.2	-	3	1924	c.1465A>C	c.(1465-1467)AGT>CGT	p.S489R	TRPS1_uc011lhy.1_Missense_Mutation_p.S493R|TRPS1_uc003yny.2_Missense_Mutation_p.S502R|TRPS1_uc010mcy.2_Missense_Mutation_p.S489R	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	489					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116616856	116616856	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116616856T>C	uc003ynz.2	-	3	1760	c.1301A>G	c.(1300-1302)TAC>TGC	p.Y434C	TRPS1_uc011lhy.1_Missense_Mutation_p.Y438C|TRPS1_uc003yny.2_Missense_Mutation_p.Y447C|TRPS1_uc010mcy.2_Missense_Mutation_p.Y434C	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	434					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
RAD21	5885	broad.mit.edu	37	8	117859879	117859879	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117859879G>A	uc003yod.2	-	14	2044	c.1756C>T	c.(1756-1758)CGA>TGA	p.R586*		NM_006265	NP_006256	O60216	RAD21_HUMAN	RAD21 homolog	586					apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)																	---	---	---	---
NOV	4856	broad.mit.edu	37	8	120430323	120430323	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120430323C>T	uc003yoq.2	+	3	557	c.336C>T	c.(334-336)TTC>TTT	p.F112F		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	112	VWFC.				regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120844807	120844807	+	5'UTR	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120844807A>G	uc003you.2	-	1						NM_003184	NP_003175			TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121259946	121259946	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121259946C>A	uc003yox.2	+	21	2839	c.2574C>A	c.(2572-2574)GGC>GGA	p.G858G	COL14A1_uc003yoy.2_Silent_p.G536G	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	858	Fibronectin type-III 7.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
FAM83A	84985	broad.mit.edu	37	8	124195581	124195581	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124195581C>T	uc003ypv.2	+						FAM83A_uc003ypw.2_Intron|FAM83A_uc003ypy.2_Intron|FAM83A_uc003ypx.2_Intron|FAM83A_uc003ypz.2_Intron	NM_032899	NP_116288			hypothetical protein LOC84985 isoform a											ovary(3)|skin(1)	4	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
SQLE	6713	broad.mit.edu	37	8	126015640	126015640	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126015640T>C	uc011liq.1	+	2	1440	c.514T>C	c.(514-516)TAT>CAT	p.Y172H		NM_003129	NP_003120	Q14534	ERG1_HUMAN	squalene epoxidase	172					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome	flavin adenine dinucleotide binding|squalene monooxygenase activity			ovary(1)|breast(1)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)													---	---	---	---
GSDMC	56169	broad.mit.edu	37	8	130788386	130788386	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130788386A>G	uc003ysr.2	-	3	1248	c.366T>C	c.(364-366)GTT>GTC	p.V122V		NM_031415	NP_113603	Q9BYG8	GSDMC_HUMAN	melanoma-derived leucine zipper, extra-nuclear	122						mitochondrion				ovary(2)|skin(1)	3																		---	---	---	---
TG	7038	broad.mit.edu	37	8	133881992	133881992	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133881992C>T	uc003ytw.2	+	3	236	c.195C>T	c.(193-195)AAC>AAT	p.N65N		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	65	Thyroglobulin type-1 1.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
WISP1	8840	broad.mit.edu	37	8	134225358	134225358	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134225358C>T	uc003yub.2	+	2	397	c.321C>T	c.(319-321)CGC>CGT	p.R107R	WISP1_uc003yuc.2_Silent_p.R107R|WISP1_uc010meb.2_Intron|WISP1_uc010mec.2_Silent_p.R107R|WISP1_uc010med.2_Intron|WISP1_uc003yud.2_RNA	NM_003882	NP_003873	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	107	IGFBP N-terminal.				cell adhesion|cell-cell signaling|regulation of cell growth|Wnt receptor signaling pathway	extracellular region|soluble fraction	insulin-like growth factor binding			central_nervous_system(1)|kidney(1)	2	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)															---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135612635	135612635	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135612635A>G	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron|ZFAT_uc003yur.2_Missense_Mutation_p.L828P|ZFATAS_uc003yus.1_RNA	NM_020863	NP_065914			zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139833608	139833608	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139833608G>A	uc003yvd.2	-	7	1463	c.1016C>T	c.(1015-1017)GCT>GTT	p.A339V		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	339	TSP N-terminal.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139845316	139845316	+	Missense_Mutation	SNP	G	A	A	rs141938188		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139845316G>A	uc003yvd.2	-	5	1258	c.811C>T	c.(811-813)CGG>TGG	p.R271W		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	271	TSP N-terminal.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
LYPD2	137797	broad.mit.edu	37	8	143833859	143833859	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143833859G>A	uc003ywz.2	-	1	94	c.11C>T	c.(10-12)ACG>ATG	p.T4M		NM_205545	NP_991108	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2 precursor	4				T -> A (in Ref. 2; BAF83020).		anchored to membrane|plasma membrane					0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
TOP1MT	116447	broad.mit.edu	37	8	144403476	144403476	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144403476G>A	uc003yxz.2	-	8	1060	c.1041C>T	c.(1039-1041)CAC>CAT	p.H347H	TOP1MT_uc011lkd.1_Silent_p.H249H|TOP1MT_uc011lke.1_Silent_p.H249H|TOP1MT_uc010mfb.2_Silent_p.H249H|TOP1MT_uc011lkf.1_Silent_p.H142H|TOP1MT_uc010mfd.1_Silent_p.H142H	NM_052963	NP_443195	Q969P6	TOP1M_HUMAN	mitochondrial topoisomerase I precursor	347					DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)													---	---	---	---
RHPN1	114822	broad.mit.edu	37	8	144463474	144463474	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144463474G>A	uc003yyb.2	+	12	1581	c.1448G>A	c.(1447-1449)CGC>CAC	p.R483H		NM_052924	NP_443156	Q8TCX5	RHPN1_HUMAN	rhophilin 1	508					signal transduction	intracellular				large_intestine(1)	1	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)															---	---	---	---
ZNF623	9831	broad.mit.edu	37	8	144732671	144732671	+	Missense_Mutation	SNP	C	T	T	rs144210785	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144732671C>T	uc003yzd.2	+	1	718	c.629C>T	c.(628-630)GCG>GTG	p.A210V	ZNF623_uc011lkp.1_Missense_Mutation_p.A170V|ZNF623_uc003yzc.2_Missense_Mutation_p.A170V	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1	210	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
MAPK15	225689	broad.mit.edu	37	8	144803497	144803497	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144803497G>A	uc003yzj.2	+	11	1161	c.1120G>A	c.(1120-1122)GAC>AAC	p.D374N		NM_139021	NP_620590	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	374					protein autophosphorylation	extracellular region	ATP binding|MAP kinase activity|SH3 domain binding			lung(2)	2	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
FAM83H	286077	broad.mit.edu	37	8	144811129	144811129	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144811129G>A	uc003yzk.2	-						FAM83H_uc010mfk.1_5'Flank	NM_198488	NP_940890			FAM83H						biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
FAM83H	286077	broad.mit.edu	37	8	144812314	144812314	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144812314C>T	uc003yzk.2	-	2	508	c.439G>A	c.(439-441)GCC>ACC	p.A147T	FAM83H_uc010mfk.1_5'Flank	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	FAM83H	147					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144940592	144940592	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144940592C>T	uc003zaa.1	-	2	14853	c.14840G>A	c.(14839-14841)CGC>CAC	p.R4947H		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	4947	Plectin 62.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145003396	145003396	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145003396G>T	uc003zaf.1	-	25	3716	c.3546C>A	c.(3544-3546)GCC>GCA	p.A1182A	PLEC_uc003zab.1_Silent_p.A1045A|PLEC_uc003zac.1_Silent_p.A1049A|PLEC_uc003zad.2_Silent_p.A1045A|PLEC_uc003zae.1_Silent_p.A1013A|PLEC_uc003zag.1_Silent_p.A1023A|PLEC_uc003zah.2_Silent_p.A1031A|PLEC_uc003zaj.2_Silent_p.A1072A	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	1182	Globular 1.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
PARP10	84875	broad.mit.edu	37	8	145057410	145057410	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145057410G>A	uc003zal.3	-	8	2455	c.2347C>T	c.(2347-2349)CGC>TGC	p.R783C	PARP10_uc003zak.3_Missense_Mutation_p.R480C|PARP10_uc011lku.1_Missense_Mutation_p.R795C|PARP10_uc011lkv.1_Intron|PARP10_uc003zam.2_Missense_Mutation_p.R774C	NM_032789	NP_116178	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	783	Myc binding.					Golgi apparatus|nucleolus	NAD+ ADP-ribosyltransferase activity|nucleotide binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)|pancreas(1)	6	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
OPLAH	26873	broad.mit.edu	37	8	145111995	145111995	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145111995C>A	uc003zar.3	-	12	1644	c.1562G>T	c.(1561-1563)GGG>GTG	p.G521V	OPLAH_uc003zas.1_5'Flank	NM_017570	NP_060040	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	521							5-oxoprolinase (ATP-hydrolyzing) activity|ATP binding				0	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		L-Glutamic Acid(DB00142)													---	---	---	---
HSF1	3297	broad.mit.edu	37	8	145535505	145535505	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145535505C>T	uc003zbt.3	+	8	1013	c.843C>T	c.(841-843)GGC>GGT	p.G281G	HSF1_uc003zbu.3_RNA	NM_005526	NP_005517	Q00613	HSF1_HUMAN	heat shock transcription factor 1	281	Regulatory domain.					cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)															---	---	---	---
FBXL6	26233	broad.mit.edu	37	8	145579704	145579704	+	Missense_Mutation	SNP	T	C	C	rs61747069		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145579704T>C	uc003zcb.2	-	8	1421	c.1396A>G	c.(1396-1398)AGC>GGC	p.S466G	C8ORFK29_uc011llb.1_5'Flank|C8ORFK29_uc010mfw.2_5'Flank|C8ORFK29_uc003zby.3_5'Flank|FBXL6_uc003zbz.2_Missense_Mutation_p.S193G|FBXL6_uc003zca.2_Missense_Mutation_p.S460G|FBXL6_uc010mfx.2_Missense_Mutation_p.S227G|GPR172A_uc003zcc.1_5'Flank|GPR172A_uc003zcd.1_5'Flank|GPR172A_uc003zce.1_5'Flank|GPR172A_uc010mfy.1_5'Flank|GPR172A_uc003zcf.1_5'Flank|GPR172A_uc011llc.1_5'Flank	NM_012162	NP_036294	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6 isoform	466	LRR 10.				proteolysis		ubiquitin-protein ligase activity			ovary(1)|lung(1)	2	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)															---	---	---	---
FBXL6	26233	broad.mit.edu	37	8	145580161	145580161	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145580161G>A	uc003zcb.2	-	7	1049	c.1024C>T	c.(1024-1026)CCC>TCC	p.P342S	C8ORFK29_uc011llb.1_5'Flank|C8ORFK29_uc010mfw.2_5'Flank|C8ORFK29_uc003zby.3_5'Flank|FBXL6_uc003zbz.2_Missense_Mutation_p.P69S|FBXL6_uc003zca.2_Missense_Mutation_p.P336S|FBXL6_uc010mfx.2_Missense_Mutation_p.P103S|GPR172A_uc003zcc.1_5'Flank|GPR172A_uc003zcd.1_5'Flank|GPR172A_uc003zce.1_5'Flank|GPR172A_uc010mfy.1_5'Flank|GPR172A_uc003zcf.1_5'Flank|GPR172A_uc011llc.1_5'Flank	NM_012162	NP_036294	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6 isoform	342	LRR 6.				proteolysis		ubiquitin-protein ligase activity			ovary(1)|lung(1)	2	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)															---	---	---	---
ADCK5	203054	broad.mit.edu	37	8	145608327	145608327	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145608327G>A	uc003zch.2	+	3	216	c.162G>A	c.(160-162)GCG>GCA	p.A54A	ADCK5_uc003zcg.2_RNA	NM_174922	NP_777582	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	54	Helical; (Potential).					integral to membrane	protein serine/threonine kinase activity			stomach(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)															---	---	---	---
CPSF1	29894	broad.mit.edu	37	8	145623932	145623932	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145623932G>A	uc003zcj.2	-	18	1810	c.1735C>T	c.(1735-1737)CGG>TGG	p.R579W		NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	579					mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding			skin(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)															---	---	---	---
NFKBIL2	4796	broad.mit.edu	37	8	145662159	145662159	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145662159A>G	uc011llg.1	-	15	1886	c.1871T>C	c.(1870-1872)GTC>GCC	p.V624A	uc011llh.1_RNA	NM_013432	NP_038460	Q96HA7	TONSL_HUMAN	NF-kappa-B inhibitor-like protein 2	624	ANK 3.				cytoplasmic sequestering of transcription factor|double-strand break repair via homologous recombination|replication fork processing	cytoplasm|nuclear replication fork	histone binding|transcription corepressor activity				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)															---	---	---	---
C8orf33	65265	broad.mit.edu	37	8	146278679	146278679	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146278679G>A	uc003zfc.3	+						C8orf33_uc003zfd.2_Intron	NM_023080	NP_075568			hypothetical protein LOC65265												0	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;9.1e-38)|all cancers(56;7.37e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.243)														---	---	---	---
CBWD1	55871	broad.mit.edu	37	9	164038	164038	+	Splice_Site	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:164038C>G	uc003zga.3	-	5	537	c.431_splice	c.e5-1	p.G144_splice	CBWD1_uc010mgs.2_Splice_Site|CBWD1_uc003zgb.3_Splice_Site_p.G108_splice|CBWD1_uc003zgc.3_Splice_Site_p.G144_splice|CBWD1_uc011llr.1_Splice_Site_p.G108_splice	NM_018491	NP_060961			COBW domain containing 1 isoform 1								ATP binding|protein binding			ovary(1)	1	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	376262	376262	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:376262T>C	uc003zgf.2	+	19	2274	c.2162T>C	c.(2161-2163)GTA>GCA	p.V721A	DOCK8_uc010mgu.2_Missense_Mutation_p.V23A|DOCK8_uc010mgv.2_Missense_Mutation_p.V653A|DOCK8_uc010mgw.1_Missense_Mutation_p.V23A|DOCK8_uc003zgk.2_Missense_Mutation_p.V179A|DOCK8_uc003zgh.2_RNA	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	721					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)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	711731	711731	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:711731G>T	uc003zgl.1	+	7	1614	c.965G>T	c.(964-966)CGG>CTG	p.R322L	KANK1_uc003zgm.2_Missense_Mutation_p.R322L|KANK1_uc003zgn.1_Missense_Mutation_p.R322L|KANK1_uc003zgo.1_Missense_Mutation_p.R322L|KANK1_uc003zgp.1_Missense_Mutation_p.R322L|KANK1_uc003zgq.2_Missense_Mutation_p.R164L|KANK1_uc003zgr.1_Missense_Mutation_p.R164L|KANK1_uc003zgs.1_Missense_Mutation_p.R164L	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	322					negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	3829471	3829471	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3829471T>G	uc003zhw.1	-	9	2224	c.2030A>C	c.(2029-2031)AAG>ACG	p.K677T	GLIS3_uc003zhx.1_Missense_Mutation_p.K832T|GLIS3_uc010mhf.1_Missense_Mutation_p.K226T|GLIS3_uc003zhv.1_RNA	NM_152629	NP_689842	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform b	677					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
INSL6	11172	broad.mit.edu	37	9	5185339	5185339	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5185339C>T	uc003zix.2	-	1	280	c.264G>A	c.(262-264)CCG>CCA	p.P88P		NM_007179	NP_009110	Q9Y581	INSL6_HUMAN	insulin-like 6 precursor	88						extracellular region	hormone activity				0	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)														---	---	---	---
CD274	29126	broad.mit.edu	37	9	5467858	5467858	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5467858C>T	uc003zje.2	+	7	921	c.869C>T	c.(868-870)ACG>ATG	p.T290M	C9orf46_uc003zjd.2_Intron|CD274_uc010mhn.2_RNA|CD274_uc003zjf.2_Missense_Mutation_p.T176M	NM_014143	NP_054862	Q9NZQ7	PD1L1_HUMAN	CD274 molecule precursor	290	Cytoplasmic (Potential).				cell proliferation|cell surface receptor linked signaling pathway|immune response|T cell costimulation	endomembrane system|integral to membrane	receptor activity			lung(1)|central_nervous_system(1)	2	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)				T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
UHRF2	115426	broad.mit.edu	37	9	6498070	6498070	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6498070G>A	uc003zjy.2	+	12	2160	c.1820G>A	c.(1819-1821)CGC>CAC	p.R607H	UHRF2_uc003zjz.2_RNA|UHRF2_uc003zkb.2_RNA	NM_152896	NP_690856	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains	607	YDG.|Methyl-CpG binding and interaction with HDAC1.				cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)														---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6605272	6605272	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6605272A>G	uc003zkc.2	-	6	913	c.720T>C	c.(718-720)ACT>ACC	p.T240T		NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	240					glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7013988	7013988	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7013988A>G	uc003zkh.2	+	14	2749	c.2169A>G	c.(2167-2169)GTA>GTG	p.V723V	KDM4C_uc010mhu.2_Silent_p.V745V|KDM4C_uc011lmi.1_Silent_p.V723V|KDM4C_uc011lmj.1_RNA|KDM4C_uc003zkg.2_Silent_p.V723V|KDM4C_uc011lmk.1_Silent_p.V468V|KDM4C_uc011lml.1_Silent_p.V410V	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1	723	PHD-type 1.				positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13110068	13110068	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13110068G>A	uc010mhy.2	-						MPDZ_uc003zkx.3_Intron|MPDZ_uc003zky.3_Intron|MPDZ_uc010mib.2_Intron|MPDZ_uc010mhx.2_Intron|MPDZ_uc011lmm.1_Intron|MPDZ_uc003zkz.3_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820			multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13110649	13110649	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13110649A>G	uc010mhy.2	-	42	5779	c.5728T>C	c.(5728-5730)TCC>CCC	p.S1910P	MPDZ_uc003zkx.3_Missense_Mutation_p.S134P|MPDZ_uc003zky.3_Missense_Mutation_p.S473P|MPDZ_uc010mib.2_Missense_Mutation_p.S644P|MPDZ_uc010mhx.2_Missense_Mutation_p.S761P|MPDZ_uc011lmm.1_Missense_Mutation_p.S798P|MPDZ_uc003zkz.3_Missense_Mutation_p.S632P|MPDZ_uc010mhz.2_Missense_Mutation_p.S1906P|MPDZ_uc011lmn.1_Missense_Mutation_p.S1877P|MPDZ_uc003zlb.3_Missense_Mutation_p.S1910P	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1939	PDZ 12.				interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13221391	13221391	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13221391G>T	uc010mia.1	-	6	913	c.856C>A	c.(856-858)CCT>ACT	p.P286T	MPDZ_uc010mhy.2_Missense_Mutation_p.P286T|MPDZ_uc010mhz.2_Missense_Mutation_p.P286T|MPDZ_uc011lmn.1_Missense_Mutation_p.P286T|MPDZ_uc003zlb.3_Missense_Mutation_p.P286T	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	286	PDZ 2.				interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
SH3GL2	6456	broad.mit.edu	37	9	17795624	17795624	+	Silent	SNP	C	T	T	rs146755876		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17795624C>T	uc003zna.2	+	9	1230	c.942C>T	c.(940-942)GGC>GGT	p.G314G	SH3GL2_uc011lmy.1_Silent_p.G267G	NM_003026	NP_003017	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	314	SH3.				axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)														---	---	---	---
FAM154A	158297	broad.mit.edu	37	9	18928326	18928326	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18928326A>G	uc003zni.1	-	4	1427	c.1149T>C	c.(1147-1149)CCT>CCC	p.P383P	FAM154A_uc010mip.1_Silent_p.P191P	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297	383										pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)														---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19305374	19305374	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19305374T>C	uc003znq.2	+	6	661	c.628T>C	c.(628-630)TGC>CGC	p.C210R	DENND4C_uc011lnc.1_5'UTR	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	210	DENN.|Helical; (Potential).					integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
IFNA17	3451	broad.mit.edu	37	9	21227953	21227953	+	Missense_Mutation	SNP	T	C	C	rs150705157	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21227953T>C	uc003zos.1	-	1	269	c.220A>G	c.(220-222)ACT>GCT	p.T74A	IFNA14_uc003zoo.1_Intron	NM_021268	NP_067091	P01571	IFN17_HUMAN	interferon, alpha 17 precursor	74					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|interferon-alpha/beta receptor binding				0				Lung(24;2.13e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)														---	---	---	---
CDKN2A	1029	broad.mit.edu	37	9	21970967	21970967	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21970967G>A	uc003zpk.2	-	2	603	c.391C>T	c.(391-393)CGC>TGC	p.R131C	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_3'UTR	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	131	ANK 4.				cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.?(13)|p.R131H(4)|p.R128fs*12(3)|p.R128fs*9(2)|p.R131R(2)|p.R131L(1)|p.A118fs*10(1)|p.R131C(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)			17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			---	---	---	---
TEK	7010	broad.mit.edu	37	9	27206671	27206671	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27206671T>C	uc003zqi.3	+	15	2898	c.2456T>C	c.(2455-2457)CTT>CCT	p.L819P	TEK_uc011lno.1_Missense_Mutation_p.L776P|TEK_uc011lnp.1_Missense_Mutation_p.L671P|TEK_uc003zqj.1_Missense_Mutation_p.L753P	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	819	Cytoplasmic (Potential).				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)														---	---	---	---
TEK	7010	broad.mit.edu	37	9	27229174	27229174	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27229174C>T	uc003zqi.3	+	23	3761	c.3319C>T	c.(3319-3321)CTT>TTT	p.L1107F	TEK_uc011lno.1_Missense_Mutation_p.L1064F|TEK_uc011lnp.1_Missense_Mutation_p.L959F	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	1107	Cytoplasmic (Potential).				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	27949193	27949193	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27949193T>C	uc003zqu.1	-	2	1671	c.1477A>G	c.(1477-1479)ACC>GCC	p.T493A	LINGO2_uc010mjf.1_Missense_Mutation_p.T493A|LINGO2_uc003zqv.1_Missense_Mutation_p.T493A	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	493	Ig-like C2-type.|Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
DDX58	23586	broad.mit.edu	37	9	32466435	32466435	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32466435T>C	uc003zra.2	-	16	2348	c.2190A>G	c.(2188-2190)AGA>AGG	p.R730R	DDX58_uc010mjj.2_RNA|DDX58_uc010mjk.1_Silent_p.R685R|DDX58_uc011lnr.1_Missense_Mutation_p.E526G|DDX58_uc010mji.2_Silent_p.R659R	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	730	Helicase C-terminal.				detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)														---	---	---	---
TOPORS	10210	broad.mit.edu	37	9	32543953	32543953	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32543953A>G	uc003zrb.2	-	3	737	c.570T>C	c.(568-570)GCT>GCC	p.A190A	TOPORS_uc003zrc.2_Silent_p.A123A	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	190	E3 ubiquitin-protein ligase activity.|Required for DNA-binding.				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)														---	---	---	---
TAF1L	138474	broad.mit.edu	37	9	32630337	32630337	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32630337T>A	uc003zrg.1	-	1	5331	c.5241A>T	c.(5239-5241)GAA>GAT	p.E1747D		NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1747					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)														---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33295421	33295421	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33295421C>T	uc003zsq.2	+	2	1090	c.1029C>T	c.(1027-1029)CAC>CAT	p.H343H	SUGT1P1_uc010mjq.1_Intron|NFX1_uc011lnw.1_Silent_p.H343H|NFX1_uc003zso.2_Silent_p.H343H|NFX1_uc003zsp.1_Silent_p.H343H|NFX1_uc010mjr.1_Silent_p.H343H|NFX1_uc003zsr.2_Silent_p.H343H	NM_002504	NP_002495	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	343					inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)														---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33318813	33318813	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33318813T>C	uc003zsq.2	+	8	1734	c.1673T>C	c.(1672-1674)TTA>TCA	p.L558S	SUGT1P1_uc010mjq.1_Intron|NFX1_uc011lnw.1_Missense_Mutation_p.L558S|NFX1_uc003zso.2_Missense_Mutation_p.L558S|NFX1_uc003zsp.1_Missense_Mutation_p.L558S|NFX1_uc010mjr.1_Missense_Mutation_p.L558S|NFX1_uc003zsr.2_Missense_Mutation_p.L558S	NM_002504	NP_002495	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	558					inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)														---	---	---	---
NOL6	65083	broad.mit.edu	37	9	33466161	33466161	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33466161G>A	uc003zsz.2	-	18	2373	c.2272C>T	c.(2272-2274)CGA>TGA	p.R758*	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zsy.2_5'Flank|NOL6_uc003zta.2_Intron|NOL6_uc010mjv.2_Nonsense_Mutation_p.R755*|NOL6_uc011lob.1_Nonsense_Mutation_p.R706*|NOL6_uc003ztb.1_Nonsense_Mutation_p.R758*	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	758					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)														---	---	---	---
UBAP2	55833	broad.mit.edu	37	9	33948364	33948364	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33948364A>G	uc003ztq.1	-						UBAP2_uc011loc.1_Intron|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_Intron|UBAP2_uc011lof.1_Intron|UBAP2_uc011log.1_Intron|UBAP2_uc003ztr.2_Intron|UBAP2_uc003zts.2_Intron	NM_018449	NP_060919			ubiquitin associated protein 2											ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)														---	---	---	---
VCP	7415	broad.mit.edu	37	9	35065361	35065361	+	Missense_Mutation	SNP	G	A	A	rs121909330		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35065361G>A	uc003zvy.2	-	5	852	c.463C>T	c.(463-465)CGT>TGT	p.R155C	VCP_uc003zvz.2_RNA|VCP_uc010mkh.1_5'UTR|VCP_uc010mki.1_Missense_Mutation_p.R110C	NM_007126	NP_009057	P55072	TERA_HUMAN	valosin-containing protein	155			R -> C (in IBMPFD; also in one patient without evidence of Paget disease of the bone).|R -> H (in IBMPFD; strongly reduced affinity for ADP and increased affinity for ATP).|R -> P (in IBMPFD).		activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding			upper_aerodigestive_tract(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)															---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35719097	35719097	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35719097G>A	uc003zxt.2	-	16	2224	c.1870C>T	c.(1870-1872)CGC>TGC	p.R624C		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	624					axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
OR13J1	392309	broad.mit.edu	37	9	35869832	35869832	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35869832G>A	uc011lph.1	-	1	567	c.567C>T	c.(565-567)TGC>TGT	p.C189C		NM_001004487	NP_001004487	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J,	189	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
RNF38	152006	broad.mit.edu	37	9	36369774	36369774	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36369774A>G	uc003zzh.2	-	4	703	c.512T>C	c.(511-513)CTA>CCA	p.L171P	RNF38_uc003zzi.2_Missense_Mutation_p.L121P|RNF38_uc003zzj.2_Missense_Mutation_p.L88P|RNF38_uc003zzk.2_Missense_Mutation_p.L88P|RNF38_uc003zzl.2_Missense_Mutation_p.L95P|RNF38_uc003zzm.2_Missense_Mutation_p.L88P	NM_022781	NP_073618	Q9H0F5	RNF38_HUMAN	ring finger protein 38 isoform 1	171							zinc ion binding			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
GRHPR	9380	broad.mit.edu	37	9	37430513	37430513	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37430513A>G	uc003zzu.1	+	7	645	c.604A>G	c.(604-606)ACC>GCC	p.T202A	GRHPR_uc010mlv.1_Missense_Mutation_p.T122A|GRHPR_uc003zzt.1_Missense_Mutation_p.T122A|GRHPR_uc003zzv.1_Missense_Mutation_p.T59A|GRHPR_uc003zzw.1_Missense_Mutation_p.T59A	NM_012203	NP_036335	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	202					cellular nitrogen compound metabolic process|excretion|glyoxylate metabolic process	peroxisomal matrix	glycerate dehydrogenase activity|glyoxylate reductase (NADP) activity|hydroxypyruvate reductase activity|NAD binding|protein binding				0				GBM - Glioblastoma multiforme(29;0.00687)														---	---	---	---
POLR1E	64425	broad.mit.edu	37	9	37493650	37493650	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37493650G>A	uc003zzz.1	+	5	971	c.683G>A	c.(682-684)CGT>CAT	p.R228H	POLR1E_uc011lqj.1_Intron|POLR1E_uc003zzy.1_Missense_Mutation_p.R166H|POLR1E_uc011lqk.1_Missense_Mutation_p.R95H	NM_022490	NP_071935	Q9GZS1	RPA49_HUMAN	RNA polymerase I associated factor 53	228					rRNA transcription	cell junction|cytoplasm|nucleolus	DNA binding|DNA-directed RNA polymerase activity|protein binding				0				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)														---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37744582	37744582	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37744582A>G	uc004aag.1	+	16	2597	c.2553A>G	c.(2551-2553)TCA>TCG	p.S851S	FRMPD1_uc004aah.1_Silent_p.S851S	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	851						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993145	70993145	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70993145A>G	uc004agr.2	+	2	521	c.292A>G	c.(292-294)ATC>GTC	p.I98V		NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5	98					cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71836092	71836092	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71836092G>A	uc004ahe.2	+	5	832	c.632G>A	c.(631-633)CGC>CAC	p.R211H	TJP2_uc011lrs.1_Missense_Mutation_p.R188H|TJP2_uc004ahb.1_Missense_Mutation_p.R188H|TJP2_uc011lrt.1_Missense_Mutation_p.R188H|TJP2_uc004ahd.2_Missense_Mutation_p.R211H|TJP2_uc004ahf.2_Missense_Mutation_p.R211H|TJP2_uc011lru.1_Missense_Mutation_p.R215H|TJP2_uc011lrv.1_Missense_Mutation_p.R233H	NM_004817	NP_004808	Q9UDY2	ZO2_HUMAN	tight junction protein 2 (zona occludens 2)	211					cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73152166	73152166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73152166G>A	uc004aid.2	-	25	4071	c.3827C>T	c.(3826-3828)GCC>GTC	p.A1276V	TRPM3_uc004ahu.2_Missense_Mutation_p.A1118V|TRPM3_uc004ahv.2_Missense_Mutation_p.A1078V|TRPM3_uc004ahw.2_Missense_Mutation_p.A1148V|TRPM3_uc004ahx.2_Missense_Mutation_p.A1135V|TRPM3_uc004ahy.2_Missense_Mutation_p.A1138V|TRPM3_uc004ahz.2_Missense_Mutation_p.A1125V|TRPM3_uc004aia.2_Missense_Mutation_p.A1123V|TRPM3_uc004aib.2_Missense_Mutation_p.A1113V|TRPM3_uc004aic.2_Missense_Mutation_p.A1276V	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	1301	Cytoplasmic (Potential).|Potential.					integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74332975	74332975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74332975G>A	uc011lsa.1	-	13	2828	c.2288C>T	c.(2287-2289)GCA>GTA	p.A763V	TMEM2_uc010mos.2_Missense_Mutation_p.A700V|TMEM2_uc011lsb.1_RNA	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	763						integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)														---	---	---	---
RORB	6096	broad.mit.edu	37	9	77300472	77300472	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77300472A>G	uc004aji.2	+	10	1400	c.1351A>G	c.(1351-1353)ACA>GCA	p.T451A	RORB_uc004ajh.2_Missense_Mutation_p.T440A	NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B	451	Ligand-binding (Potential).				eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
RFK	55312	broad.mit.edu	37	9	79002309	79002309	+	3'UTR	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79002309T>C	uc004akd.2	-	4					RFK_uc004ake.2_3'UTR	NM_018339	NP_060809			riboflavin kinase						riboflavin biosynthetic process	cytosol	ATP binding|metal ion binding|riboflavin kinase activity				0					Riboflavin(DB00140)													---	---	---	---
FOXB2	442425	broad.mit.edu	37	9	79635851	79635851	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79635851G>A	uc004ako.1	+	1	1281	c.1281G>A	c.(1279-1281)TCG>TCA	p.S427S		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	427					brain development|embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	82006325	82006325	+	IGR	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82006325C>T								None (None upstream) : TLE4 (180553 downstream)																																			---	---	---	---
TLE4	7091	broad.mit.edu	37	9	82321726	82321726	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82321726G>A	uc004ald.2	+	11	1676	c.827G>A	c.(826-828)CGC>CAC	p.R276H	TLE4_uc004alc.2_Missense_Mutation_p.R283H|TLE4_uc010mpr.2_Missense_Mutation_p.R162H|TLE4_uc004ale.2_5'UTR|TLE4_uc011lsq.1_Missense_Mutation_p.R251H|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Missense_Mutation_p.R222H	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4	Error:Variant_position_missing_in_O60756_after_alignment										lung(2)|ovary(1)|breast(1)|skin(1)	5																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84225140	84225140	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84225140C>T	uc004aly.2	-	14	1767	c.1326G>A	c.(1324-1326)GGG>GGA	p.G442G	TLE1_uc004alz.2_Silent_p.G452G|TLE1_uc011lsr.1_Silent_p.G427G|TLE1_uc004ama.1_Silent_p.G441G	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1	442	Pro/Ser-rich.				negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
FLJ46321	389763	broad.mit.edu	37	9	84607025	84607025	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84607025T>G	uc004amn.2	+	4	1687	c.1640T>G	c.(1639-1641)CTT>CGT	p.L547R		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	547						integral to membrane					0																		---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90264945	90264945	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90264945C>T	uc004apc.2	+	16	1676	c.1538C>T	c.(1537-1539)ACG>ATG	p.T513M	DAPK1_uc004ape.2_Missense_Mutation_p.T513M|DAPK1_uc004apd.2_Missense_Mutation_p.T513M|DAPK1_uc011ltg.1_Missense_Mutation_p.T513M|DAPK1_uc011lth.1_Missense_Mutation_p.T250M|DAPK1_uc004apf.1_Missense_Mutation_p.T67M	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1	513	ANK 5.				apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
CDK20	23552	broad.mit.edu	37	9	90585553	90585553	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90585553G>T	uc004apr.2	-						CDK20_uc004aps.2_Intron|CDK20_uc004apt.2_Intron|CDK20_uc004apu.2_Intron	NM_001039803	NP_001034892			cell cycle related kinase isoform 3						cell division|multicellular organismal development	cilium|mitochondrion|nucleus	ATP binding|cyclin-dependent protein kinase activity			skin(1)	1																		---	---	---	---
DIRAS2	54769	broad.mit.edu	37	9	93376013	93376013	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93376013G>A	uc004aqx.1	-	2	208	c.97C>T	c.(97-99)CGG>TGG	p.R33W		NM_017594	NP_060064	Q96HU8	DIRA2_HUMAN	Di-Ras2	33	GTP.				small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|GTPase activity				0																		---	---	---	---
SYK	6850	broad.mit.edu	37	9	93650880	93650880	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93650880C>T	uc004aqz.2	+	13	2011	c.1806C>T	c.(1804-1806)TAC>TAT	p.Y602Y	SYK_uc004ara.2_Silent_p.Y579Y|SYK_uc004arb.2_Silent_p.Y579Y|SYK_uc004arc.2_Silent_p.Y602Y|SYK_uc011ltr.1_RNA|SYK_uc011lts.1_RNA|SYK_uc011ltt.1_RNA	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1	602	Protein kinase.				cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5								T	ETV6|ITK	MDS|peripheral T-cell lymphoma								---	---	---	---
AUH	549	broad.mit.edu	37	9	93978376	93978376	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93978376T>C	uc004arf.3	-	9	942	c.907A>G	c.(907-909)ACA>GCA	p.T303A	AUH_uc004arg.3_Missense_Mutation_p.T274A	NM_001698	NP_001689	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-Coenzyme A	303					branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0																		---	---	---	---
OGN	4969	broad.mit.edu	37	9	95152347	95152347	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95152347A>G	uc004asa.2	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|OGN_uc004asb.2_Intron|OGN_uc011ltx.1_Intron	NM_014057	NP_054776			osteoglycin preproprotein							extracellular space|proteinaceous extracellular matrix	growth factor activity				0																		---	---	---	---
WNK2	65268	broad.mit.edu	37	9	95997117	95997117	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95997117T>C	uc004ati.1	+	4	1103	c.1103T>C	c.(1102-1104)ATG>ACG	p.M368T	WNK2_uc011lud.1_Missense_Mutation_p.M368T|WNK2_uc004atj.2_Missense_Mutation_p.M368T|WNK2_uc004atk.2_Missense_Mutation_p.M5T|WNK2_uc010mrc.1_Missense_Mutation_p.M368T|WNK2_uc010mrd.1_Missense_Mutation_p.M5T	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	368	Protein kinase.				intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12																		---	---	---	---
FAM120A	23196	broad.mit.edu	37	9	96233460	96233460	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96233460T>C	uc004atw.2	+	2	537	c.512T>C	c.(511-513)ATT>ACT	p.I171T	FAM120A_uc004atv.2_Missense_Mutation_p.I171T|FAM120A_uc004atx.2_5'UTR|FAM120A_uc004aty.2_5'UTR	NM_014612	NP_055427	Q9NZB2	F120A_HUMAN	oxidative stress-associated Src activator	171						cytoplasm|plasma membrane	RNA binding				0																		---	---	---	---
FAM120A	23196	broad.mit.edu	37	9	96320179	96320179	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96320179G>T	uc004atw.2	+	14	2580	c.2555G>T	c.(2554-2556)AGC>ATC	p.S852I	FAM120A_uc004aty.2_Missense_Mutation_p.S633I|FAM120A_uc004atz.2_Missense_Mutation_p.S501I|FAM120A_uc010mrg.2_Missense_Mutation_p.S165I	NM_014612	NP_055427	Q9NZB2	F120A_HUMAN	oxidative stress-associated Src activator	852	RNA binding.					cytoplasm|plasma membrane	RNA binding				0																		---	---	---	---
C9orf102	375748	broad.mit.edu	37	9	98685665	98685665	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98685665A>G	uc004avt.3	+						C9orf102_uc010mrx.1_Intron|C9orf102_uc011lum.1_Intron|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.2_Intron|C9orf102_uc004avu.2_Intron	NM_001010895	NP_001010895			RAD26L hypothetical protein						DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
C9orf102	375748	broad.mit.edu	37	9	98728851	98728851	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98728851A>G	uc004avt.3	+	14	2376	c.1988A>G	c.(1987-1989)CAC>CGC	p.H663R	C9orf102_uc011lum.1_Missense_Mutation_p.H365R|C9orf102_uc010mry.1_Missense_Mutation_p.H365R|C9orf102_uc010mrz.2_Missense_Mutation_p.H474R|C9orf102_uc004avu.2_5'UTR	NM_001010895	NP_001010895	Q5T890	RAD26_HUMAN	RAD26L hypothetical protein	663	Helicase C-terminal.				DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
ZNF510	22869	broad.mit.edu	37	9	99537116	99537116	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99537116C>T	uc004awn.1	-	3	272	c.83G>A	c.(82-84)CGG>CAG	p.R28Q	ZNF510_uc004awo.1_Missense_Mutation_p.R28Q	NM_014930	NP_055745	Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	28					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
INVS	27130	broad.mit.edu	37	9	103009041	103009041	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103009041T>C	uc004bap.1	+	8	1262	c.1050T>C	c.(1048-1050)ATT>ATC	p.I350I	INVS_uc010mta.1_Silent_p.I254I|INVS_uc011lve.1_Silent_p.I254I|INVS_uc004bao.1_Silent_p.I350I|INVS_uc004baq.1_Silent_p.I254I|INVS_uc004bar.1_Silent_p.I254I|INVS_uc010mtb.1_Silent_p.I24I	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a	350	ANK 10.				negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|membrane|microtubule|nucleus|spindle	calmodulin binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.056)																---	---	---	---
MRPL50	54534	broad.mit.edu	37	9	104160781	104160781	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104160781A>G	uc004bbe.2	-						MRPL50_uc011lvj.1_Intron|ZNF189_uc004bbg.1_5'Flank|ZNF189_uc004bbh.1_5'Flank|ZNF189_uc004bbi.1_5'Flank|ZNF189_uc011lvk.1_5'Flank	NM_019051	NP_061924			mitochondrial ribosomal protein L50							mitochondrion|ribosome					0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109746489	109746489	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109746489A>C	uc004bcz.2	+	10	7144	c.6855A>C	c.(6853-6855)GAA>GAC	p.E2285D	ZNF462_uc010mto.2_Missense_Mutation_p.E2194D|ZNF462_uc004bda.2_Missense_Mutation_p.E2193D|ZNF462_uc011lvz.1_Missense_Mutation_p.E242D|uc004bdc.1_Intron	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	2285					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
RAD23B	5887	broad.mit.edu	37	9	110081036	110081036	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110081036C>T	uc004bde.2	+	6	924	c.557C>T	c.(556-558)ACG>ATG	p.T186M	RAD23B_uc011lwa.1_Missense_Mutation_p.T186M|RAD23B_uc011lwb.1_Missense_Mutation_p.T165M	NM_002874	NP_002865	P54727	RD23B_HUMAN	UV excision repair protein RAD23 homolog B	186					nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1													Direct_reversal_of_damage|NER					---	---	---	---
ACTL7B	10880	broad.mit.edu	37	9	111617896	111617896	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111617896C>T	uc004bdi.2	-	1	380	c.315G>A	c.(313-315)ACG>ACA	p.T105T		NM_006686	NP_006677	Q9Y614	ACL7B_HUMAN	actin-like 7B	105						actin cytoskeleton|cytoplasm	structural constituent of cytoskeleton			pancreas(1)	1																		---	---	---	---
ACTL7A	10881	broad.mit.edu	37	9	111625773	111625773	+	Missense_Mutation	SNP	G	T	T	rs142768089	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111625773G>T	uc004bdj.1	+	1	1171	c.1171G>T	c.(1171-1173)GTG>TTG	p.V391L		NM_006687	NP_006678	Q9Y615	ACL7A_HUMAN	actin-like 7A	391						cytoplasm|cytoskeleton|protein complex	structural constituent of cytoskeleton				0																		---	---	---	---
CTNNAL1	8727	broad.mit.edu	37	9	111734947	111734947	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111734947T>C	uc004bdo.1	-						CTNNAL1_uc010mts.1_Intron|CTNNAL1_uc010mtt.1_Intron|CTNNAL1_uc004bdp.1_Intron|CTNNAL1_uc004bdq.1_Intron	NM_003798	NP_003789			catenin, alpha-like 1						cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)														---	---	---	---
LPAR1	1902	broad.mit.edu	37	9	113637698	113637698	+	3'UTR	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113637698G>A	uc004bfa.2	-	5					LPAR1_uc011lwm.1_3'UTR|LPAR1_uc004bfb.2_3'UTR|LPAR1_uc004bfc.2_3'UTR|LPAR1_uc011lwn.1_3'UTR|LPAR1_uc011lwo.1_3'UTR|LPAR1_uc010mub.2_3'UTR	NM_057159	NP_476500			lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2																		---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115166397	115166397	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115166397A>G	uc004bga.1	+	2	233	c.140A>G	c.(139-141)CAT>CGT	p.H47R	HSDL2_uc011lwv.1_Intron|HSDL2_uc004bgb.1_5'UTR|HSDL2_uc004bgc.1_Missense_Mutation_p.H47R|HSDL2_uc011lww.1_5'UTR	NM_032303	NP_115679	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	47						peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
ZNF883	169834	broad.mit.edu	37	9	115759687	115759687	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115759687T>G	uc011lwy.1	-	5	2092	c.853A>C	c.(853-855)AAA>CAA	p.K285Q		NM_001101338	NP_001094808	P0CG24	ZN883_HUMAN	hypothetical protein LOC169834	285	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117062942	117062942	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117062942G>C	uc011lxl.1	+	51	4676	c.4676G>C	c.(4675-4677)GGC>GCC	p.G1559A	COL27A1_uc004bii.2_RNA	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	1559	Collagen-like 15.|Pro-rich.|Triple-helical region.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																		---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	118950337	118950337	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118950337C>G	uc004bjn.2	+	2	1701	c.1320C>G	c.(1318-1320)TGC>TGG	p.C440W	PAPPA_uc011lxp.1_Missense_Mutation_p.C233W|PAPPA_uc011lxq.1_Missense_Mutation_p.C233W	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	440	Metalloprotease.				cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	119124994	119124994	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119124994C>A	uc004bjn.2	+	18	4852	c.4471C>A	c.(4471-4473)CAG>AAG	p.Q1491K	PAPPA_uc011lxq.1_Missense_Mutation_p.Q866K	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	1491	Sushi 5.				cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119413813	119413813	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119413813T>C	uc004bjs.1	-	17	3167	c.3066A>G	c.(3064-3066)ACA>ACG	p.T1022T	ASTN2_uc004bjr.1_Silent_p.T1018T|ASTN2_uc004bjt.1_Silent_p.T971T|ASTN2_uc004bjp.1_Silent_p.T115T|ASTN2_uc004bjq.1_Silent_p.T74T|ASTN2_uc011lxr.1_Silent_p.T74T|ASTN2_uc011lxs.1_Silent_p.T74T|ASTN2_uc011lxt.1_Silent_p.T74T|ASTN2_uc004bjv.1_Silent_p.T74T	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	1022	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
TRIM32	22954	broad.mit.edu	37	9	119461051	119461051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119461051C>T	uc004bjx.2	+	2	1188	c.1030C>T	c.(1030-1032)CGG>TGG	p.R344W	ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjs.1_Intron|ASTN2_uc004bjt.1_Intron|TRIM32_uc004bjw.2_Missense_Mutation_p.R344W	NM_001099679	NP_001093149	Q13049	TRI32_HUMAN	tripartite motif-containing 32	344					fat cell differentiation|innate immune response|negative regulation of apoptosis|negative regulation of fibroblast proliferation|positive regulation of cell cycle|positive regulation of cell growth|positive regulation of cell migration|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein catabolic process|positive regulation of proteolysis|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to tumor necrosis factor|response to UV	nucleus	myosin binding|protein self-association|RNA binding|Tat protein binding|transcription coactivator activity|translation initiation factor binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(2)|kidney(1)	3														Bardet-Biedl_syndrome				---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119976991	119976991	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119976991G>C	uc004bjs.1	-	3	762	c.661C>G	c.(661-663)CTG>GTG	p.L221V	ASTN2_uc004bjr.1_Missense_Mutation_p.L221V|ASTN2_uc004bjt.1_Missense_Mutation_p.L221V	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	221	Helical; (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
DBC1	1620	broad.mit.edu	37	9	121929568	121929568	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121929568G>A	uc004bkc.2	-	8	2536	c.2080C>T	c.(2080-2082)CTC>TTC	p.L694F		NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	694					cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
DBC1	1620	broad.mit.edu	37	9	121929812	121929812	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121929812G>A	uc004bkc.2	-	8	2292	c.1836C>T	c.(1834-1836)TTC>TTT	p.F612F		NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	612					cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
DBC1	1620	broad.mit.edu	37	9	121971057	121971057	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121971057T>C	uc004bkc.2	-	7	1541	c.1085A>G	c.(1084-1086)AAG>AGG	p.K362R		NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	362					cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123210224	123210224	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123210224C>T	uc004bkf.2	-	22	3155	c.2974G>A	c.(2974-2976)GCT>ACT	p.A992T	CDK5RAP2_uc010mvi.2_Missense_Mutation_p.A42T|CDK5RAP2_uc004bke.2_Missense_Mutation_p.A277T|CDK5RAP2_uc004bkg.2_Missense_Mutation_p.A992T|CDK5RAP2_uc011lxw.1_Missense_Mutation_p.A257T|CDK5RAP2_uc011lxx.1_RNA|CDK5RAP2_uc011lxy.1_RNA|CDK5RAP2_uc011lxz.1_Missense_Mutation_p.A257T|CDK5RAP2_uc011lya.1_Missense_Mutation_p.A257T|CDK5RAP2_uc004bkh.1_Missense_Mutation_p.A762T|CDK5RAP2_uc004bki.2_Missense_Mutation_p.A759T	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	992	Interaction with MAPRE1.				brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
C5	727	broad.mit.edu	37	9	123794459	123794459	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123794459G>A	uc004bkv.2	-	6	629	c.599C>T	c.(598-600)ACG>ATG	p.T200M	C5_uc010mvm.1_Missense_Mutation_p.T200M|C5_uc010mvn.1_Missense_Mutation_p.T200M	NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein	200					activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
STOM	2040	broad.mit.edu	37	9	124111494	124111494	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124111494G>T	uc004blh.2	-	5	509	c.429C>A	c.(427-429)ACC>ACA	p.T143T	STOM_uc011lyk.1_Silent_p.T92T|STOM_uc004bli.2_Intron	NM_004099	NP_004090	P27105	STOM_HUMAN	stomatin isoform a	143	Cytoplasmic (Potential).				protein homooligomerization	cytoskeleton|integral to plasma membrane|melanosome|membrane raft	protein binding				0				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)														---	---	---	---
STOM	2040	broad.mit.edu	37	9	124116898	124116898	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124116898T>C	uc004blh.2	-	3	299	c.219A>G	c.(217-219)CAA>CAG	p.Q73Q	STOM_uc011lyk.1_Silent_p.Q22Q|STOM_uc004bli.2_Intron	NM_004099	NP_004090	P27105	STOM_HUMAN	stomatin isoform a	73	Cytoplasmic (Potential).				protein homooligomerization	cytoskeleton|integral to plasma membrane|melanosome|membrane raft	protein binding				0				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)														---	---	---	---
PTGS1	5742	broad.mit.edu	37	9	125154583	125154583	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125154583T>C	uc004bmg.1	+	11	1695	c.1560T>C	c.(1558-1560)AGT>AGC	p.S520S	PTGS1_uc011lys.1_Silent_p.S458S|PTGS1_uc010mwb.1_Silent_p.S374S|PTGS1_uc004bmf.1_Silent_p.S483S|PTGS1_uc004bmh.1_Silent_p.S411S|PTGS1_uc011lyt.1_Silent_p.S411S	NM_000962	NP_000953	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 isoform 1	520					cyclooxygenase pathway|hormone biosynthetic process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)|skin(1)	2					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)													---	---	---	---
STRBP	55342	broad.mit.edu	37	9	125909141	125909141	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125909141G>A	uc004bns.2	-	13	1761	c.1331C>T	c.(1330-1332)GCG>GTG	p.A444V	STRBP_uc004bnt.2_Missense_Mutation_p.A262V|STRBP_uc004bnu.2_Missense_Mutation_p.A430V|STRBP_uc004bnv.2_Missense_Mutation_p.A444V|STRBP_uc004bnr.2_Missense_Mutation_p.A56V	NM_018387	NP_060857	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	444	DRBM 1.				multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
ZNF79	7633	broad.mit.edu	37	9	130197442	130197442	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130197442G>A	uc004bqw.3	+	3	593	c.179G>A	c.(178-180)CGG>CAG	p.R60Q	ZNF79_uc011maf.1_Missense_Mutation_p.R36Q|ZNF79_uc011mag.1_Missense_Mutation_p.R36Q	NM_007135	NP_009066	Q15937	ZNF79_HUMAN	zinc finger protein 79	60	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
FAM129B	64855	broad.mit.edu	37	9	130280190	130280190	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130280190G>T	uc004brh.2	-	6	822	c.620C>A	c.(619-621)CCT>CAT	p.P207H	FAM129B_uc004bri.2_Missense_Mutation_p.P194H|FAM129B_uc004brj.3_Missense_Mutation_p.P207H	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	207							protein binding				0																		---	---	---	---
DNM1	1759	broad.mit.edu	37	9	130986540	130986540	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130986540T>C	uc011mau.1	+	10	1294	c.1207T>C	c.(1207-1209)TTT>CTT	p.F403L	DNM1_uc010mxr.2_Intron|DNM1_uc011mat.1_Missense_Mutation_p.F403L	NM_004408	NP_004399	Q05193	DYN1_HUMAN	dynamin 1 isoform 1	403					receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
TRUB2	26995	broad.mit.edu	37	9	131076121	131076121	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131076121A>G	uc004buq.1	-	5	436	c.426T>C	c.(424-426)CGT>CGC	p.R142R		NM_015679	NP_056494	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase homolog 2	142					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(1)	1																		---	---	---	---
SLC27A4	10999	broad.mit.edu	37	9	131110839	131110839	+	Missense_Mutation	SNP	A	G	G	rs148956936		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131110839A>G	uc004but.2	+	4	856	c.572A>G	c.(571-573)CAT>CGT	p.H191R	SLC27A4_uc004buu.2_Intron	NM_005094	NP_005085	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid	191					long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0																		---	---	---	---
ODF2	4957	broad.mit.edu	37	9	131222848	131222848	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131222848G>A	uc011mbd.1	+						ODF2_uc011maz.1_Intron|ODF2_uc011mba.1_5'UTR|ODF2_uc010myb.2_Missense_Mutation_p.R4H|ODF2_uc011mbb.1_Intron|ODF2_uc011mbc.1_Missense_Mutation_p.R4H|ODF2_uc004bva.2_Intron|ODF2_uc004bvb.2_Missense_Mutation_p.R4H|ODF2_uc011mbe.1_Missense_Mutation_p.R4H|ODF2_uc004bvc.2_Missense_Mutation_p.R4H|ODF2_uc010myc.2_Intron|ODF2_uc011mbf.1_Intron|ODF2_uc004bvd.3_Intron|ODF2_uc004bve.2_Intron	NM_002540	NP_002531			outer dense fiber of sperm tails 2 isoform 1						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1																		---	---	---	---
PKN3	29941	broad.mit.edu	37	9	131468079	131468079	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131468079G>A	uc004bvw.2	+	3	725	c.332G>A	c.(331-333)CGG>CAG	p.R111Q	PKN3_uc010myh.2_Missense_Mutation_p.R111Q|PKN3_uc011mbk.1_5'UTR	NM_013355	NP_037487	Q6P5Z2	PKN3_HUMAN	protein kinase PKNbeta	111	REM 2.				signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			stomach(2)|lung(2)	4																		---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132671268	132671268	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132671268G>A	uc004byw.1	-	12	1415	c.1196C>T	c.(1195-1197)CCG>CTG	p.P399L	FNBP1_uc011mbv.1_Missense_Mutation_p.P389L|FNBP1_uc011mbw.1_Missense_Mutation_p.P394L|FNBP1_uc004bza.2_Missense_Mutation_p.P333L|FNBP1_uc004byz.1_Missense_Mutation_p.P370L|FNBP1_uc011mbu.1_Missense_Mutation_p.P27L|FNBP1_uc004byx.1_Missense_Mutation_p.P315L|FNBP1_uc004byy.1_Missense_Mutation_p.P305L	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1	399	Required for self-association and induction of membrane tubulation.				endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
ABL1	25	broad.mit.edu	37	9	133759579	133759579	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133759579C>T	uc004bzw.2	+	11	1905	c.1902C>T	c.(1900-1902)GGC>GGT	p.G634G	ABL1_uc004bzv.2_Silent_p.G653G	NM_005157	NP_005148	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase	634					actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133944392	133944392	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133944392A>G	uc004caa.1	+	16	2943	c.2845A>G	c.(2845-2847)AGG>GGG	p.R949G		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	949	Laminin EGF-like 10.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)														---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134357813	134357813	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134357813G>A	uc004can.3	+	20	5094	c.5039G>A	c.(5038-5040)CGG>CAG	p.R1680Q	BAT2L1_uc004cao.3_Missense_Mutation_p.R1037Q|BAT2L1_uc004cap.3_5'Flank	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	1680							protein binding				0																		---	---	---	---
RALGDS	5900	broad.mit.edu	37	9	135982497	135982497	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135982497A>G	uc004cco.2	-	7	1408	c.1388T>C	c.(1387-1389)GTG>GCG	p.V463A	RALGDS_uc004ccp.2_RNA|RALGDS_uc004ccq.2_Missense_Mutation_p.V451A|RALGDS_uc004ccr.2_Missense_Mutation_p.V462A|RALGDS_uc011mcv.1_Missense_Mutation_p.V434A|RALGDS_uc004ccs.2_Missense_Mutation_p.V408A|RALGDS_uc011mcw.1_Missense_Mutation_p.V534A|RALGDS_uc004ccv.1_Missense_Mutation_p.V232A|RALGDS_uc004ccu.1_Missense_Mutation_p.V232A	NM_006266	NP_006257	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	463	Ras-GEF.				nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	Ral guanyl-nucleotide exchange factor activity			large_intestine(1)|lung(1)|ovary(1)	3				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)				T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136251429	136251429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136251429C>T	uc004cdk.2	+	4	309	c.248C>T	c.(247-249)GCC>GTC	p.A83V	C9orf96_uc004cdl.2_RNA	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436	83	Protein kinase.						ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
C9orf7	11094	broad.mit.edu	37	9	136328610	136328610	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136328610G>A	uc011mdg.1	+	2	229	c.127G>A	c.(127-129)GCG>ACG	p.A43T	C9orf7_uc004cec.2_Missense_Mutation_p.A43T|C9orf7_uc011mdh.1_Missense_Mutation_p.A43T|C9orf7_uc011mdi.1_Missense_Mutation_p.A43T|C9orf7_uc010nan.2_RNA	NM_017586	NP_060056	Q9UGQ2	FLOWR_HUMAN	hypothetical protein LOC11094 isoform a	43	Helical; (Potential).					integral to membrane					0				GBM - Glioblastoma multiforme(294;5.7e-39)|all cancers(34;1.83e-23)|OV - Ovarian serous cystadenocarcinoma(145;8.94e-08)|Epithelial(140;1.01e-06)														---	---	---	---
C9orf7	11094	broad.mit.edu	37	9	136328658	136328658	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136328658G>A	uc011mdg.1	+	2	277	c.175G>A	c.(175-177)GCG>ACG	p.A59T	C9orf7_uc004cec.2_Missense_Mutation_p.A59T|C9orf7_uc011mdh.1_Missense_Mutation_p.A59T|C9orf7_uc011mdi.1_Missense_Mutation_p.A59T|C9orf7_uc010nan.2_RNA	NM_017586	NP_060056	Q9UGQ2	FLOWR_HUMAN	hypothetical protein LOC11094 isoform a	59	Helical; (Potential).					integral to membrane					0				GBM - Glioblastoma multiforme(294;5.7e-39)|all cancers(34;1.83e-23)|OV - Ovarian serous cystadenocarcinoma(145;8.94e-08)|Epithelial(140;1.01e-06)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137622201	137622201	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137622201G>A	uc004cfe.2	+	7	1426	c.1044G>A	c.(1042-1044)ACG>ACA	p.T348T		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	348	Nonhelical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137644495	137644495	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137644495A>C	uc004cfe.2	+							NM_000093	NP_000084			alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
FCN2	2220	broad.mit.edu	37	9	137777737	137777737	+	Missense_Mutation	SNP	G	A	A	rs55860122		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137777737G>A	uc004cfg.1	+	6	563	c.553G>A	c.(553-555)GCC>ACC	p.A185T	FCN2_uc004cfh.1_Missense_Mutation_p.A147T	NM_004108	NP_004099	Q15485	FCN2_HUMAN	ficolin 2 isoform a precursor	185	Fibrinogen C-terminal.				complement activation, lectin pathway|opsonization|signal transduction	collagen|extracellular space	antigen binding|calcium ion binding|calcium-dependent protein binding|receptor binding|sugar binding			large_intestine(1)	1		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)														---	---	---	---
KCNT1	57582	broad.mit.edu	37	9	138649027	138649027	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138649027G>A	uc011mdq.1	+	8	700	c.626G>A	c.(625-627)CGC>CAC	p.R209H	KCNT1_uc011mdr.1_Missense_Mutation_p.R36H|KCNT1_uc010nbf.2_Missense_Mutation_p.R161H|KCNT1_uc004cgo.1_5'UTR	NM_020822	NP_065873	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	209						membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)														---	---	---	---
CAMSAP1	157922	broad.mit.edu	37	9	138712780	138712780	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138712780C>G	uc004cgr.3	-	11	3727	c.3727G>C	c.(3727-3729)GCC>CCC	p.A1243P	CAMSAP1_uc004cgq.3_Missense_Mutation_p.A1133P|CAMSAP1_uc010nbg.2_Missense_Mutation_p.A965P	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	1243						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)														---	---	---	---
UBAC1	10422	broad.mit.edu	37	9	138847166	138847166	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138847166G>A	uc004cgt.2	-	2	452	c.234C>T	c.(232-234)ATC>ATT	p.I78I	UBAC1_uc004cgs.1_Silent_p.I78I|UBAC1_uc004cgu.2_RNA	NM_016172	NP_057256	Q9BSL1	UBAC1_HUMAN	ubiquitin associated domain containing 1	78	Ubiquitin-like.					Golgi apparatus|plasma membrane	protein binding			skin(2)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)														---	---	---	---
CARD9	64170	broad.mit.edu	37	9	139264338	139264338	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139264338C>T	uc004chg.3	-						CARD9_uc011mdw.1_Intron|CARD9_uc011mdx.1_Intron	NM_052813	NP_434700			caspase recruitment domain protein 9 isoform 1						positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of stress-activated MAPK cascade|regulation of apoptosis	cytoplasm	CARD domain binding|protein homodimerization activity			pancreas(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)														---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139396735	139396735	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139396735G>A	uc004chz.2	-	28	5373	c.5373C>T	c.(5371-5373)TCC>TCT	p.S1791S		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	1791	Cytoplasmic (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)				T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			---	---	---	---
LCN8	138307	broad.mit.edu	37	9	139649870	139649870	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139649870A>G	uc004cjb.1	-	4	674	c.325T>C	c.(325-327)TAC>CAC	p.Y109H	LCN8_uc004cja.2_RNA	NM_178469	NP_848564	Q6JVE9	LCN8_HUMAN	lipocalin 8	132					transport	extracellular region	binding			pancreas(1)	1	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)														---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139911742	139911742	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139911742A>G	uc011mem.1	-	17	2604	c.2456T>C	c.(2455-2457)ATC>ACC	p.I819T	ABCA2_uc011mel.1_Missense_Mutation_p.I820T|ABCA2_uc004ckl.1_Missense_Mutation_p.I750T|ABCA2_uc004ckm.1_Missense_Mutation_p.I850T|ABCA2_uc004ckn.1_RNA	NM_001606	NP_001597	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	819	Helical; (Potential).				cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139912463	139912463	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139912463G>A	uc011mem.1	-	14	2203	c.2055C>T	c.(2053-2055)TAC>TAT	p.Y685Y	ABCA2_uc011mel.1_Silent_p.Y686Y|ABCA2_uc004ckl.1_Silent_p.Y616Y|ABCA2_uc004ckm.1_Silent_p.Y716Y|ABCA2_uc004ckn.1_RNA	NM_001606	NP_001597	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	685					cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
MAN1B1	11253	broad.mit.edu	37	9	140002104	140002104	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140002104G>A	uc004cld.2	+	12	1921	c.1886G>A	c.(1885-1887)CGA>CAA	p.R629Q	MAN1B1_uc011mep.1_Missense_Mutation_p.R629Q|MAN1B1_uc010ncc.2_RNA|MAN1B1_uc004clf.1_Missense_Mutation_p.R302Q|MAN1B1_uc004clg.1_RNA	NM_016219	NP_057303	Q9UKM7	MA1B1_HUMAN	alpha 1,2-mannosidase	629	Lumenal (Potential).				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|endoplasmic reticulum quality control compartment|integral to membrane	alpha-mannosidase activity|calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)														---	---	---	---
GRIN1	2902	broad.mit.edu	37	9	140058119	140058119	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140058119C>T	uc004clk.2	+	17	2772	c.2442C>T	c.(2440-2442)GCC>GCT	p.A814A	GRIN1_uc004cli.1_Silent_p.A489A|GRIN1_uc004clj.1_Silent_p.A811A|GRIN1_uc004cll.2_Silent_p.A814A|GRIN1_uc004clm.2_Silent_p.A814A|GRIN1_uc004cln.2_Silent_p.A832A|GRIN1_uc004clo.2_Silent_p.A832A	NM_007327	NP_015566	Q05586	NMDZ1_HUMAN	NMDA receptor 1 isoform NR1-3 precursor	814	Helical; (Potential).				ionotropic glutamate receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|regulation of excitatory postsynaptic membrane potential|response to ethanol|visual learning	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane|synaptic vesicle|synaptosome	calcium ion binding|calmodulin binding|extracellular-glutamate-gated ion channel activity|glutamate binding|glycine binding			skin(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)													---	---	---	---
NELF	26012	broad.mit.edu	37	9	140348239	140348239	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140348239C>T	uc004cna.2	-	8	1098	c.866G>A	c.(865-867)CGG>CAG	p.R289Q	C9orf167_uc011mew.1_Intron|NELF_uc011mex.1_Missense_Mutation_p.R86Q|NELF_uc010nci.2_Intron|NELF_uc011mey.1_Intron|NELF_uc011mez.1_Missense_Mutation_p.R266Q|NELF_uc004cmz.2_Missense_Mutation_p.R287Q|NELF_uc004cnc.2_Missense_Mutation_p.R264Q|NELF_uc004cnb.2_Intron	NM_001130969	NP_001124441	Q6X4W1	NELF_HUMAN	nasal embryonic LHRH factor isoform a	289						nucleus|plasma membrane					0	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000222)|Epithelial(140;0.000888)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140611142	140611142	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140611142G>A	uc011mfc.1	+	3	187	c.150G>A	c.(148-150)GCG>GCA	p.A50A	EHMT1_uc004coa.2_Silent_p.A50A|EHMT1_uc004cob.1_Silent_p.A19A	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	50					DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)														---	---	---	---
IL2RA	3559	broad.mit.edu	37	10	6061429	6061429	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6061429A>G	uc001iiz.1	-	6	848	c.689T>C	c.(688-690)ATG>ACG	p.M230T	IL2RA_uc009xih.1_Missense_Mutation_p.M158T|IL2RA_uc001ija.1_Missense_Mutation_p.M96T	NM_000417	NP_000408	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha chain precursor	230	Extracellular (Potential).				cell proliferation	integral to membrane	interleukin-2 receptor activity			ovary(1)|skin(1)	2					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)													---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7618459	7618459	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7618459G>A	uc001ijq.2	-	10	2014	c.1935C>T	c.(1933-1935)CCC>CCT	p.P645P	ITIH5_uc001ijp.2_Silent_p.P431P|ITIH5_uc001ijr.1_Silent_p.P645P	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	645					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7618934	7618934	+	Missense_Mutation	SNP	C	T	T	rs112992012	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7618934C>T	uc001ijq.2	-	10	1539	c.1460G>A	c.(1459-1461)CGC>CAC	p.R487H	ITIH5_uc001ijp.2_Missense_Mutation_p.R273H|ITIH5_uc001ijr.1_Missense_Mutation_p.R487H	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	487					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	8055793	8055793	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8055793T>C	uc010qbd.1	+	6	2668	c.2668T>C	c.(2668-2670)TAC>CAC	p.Y890H		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	890	PHD-type.				maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
MCM10	55388	broad.mit.edu	37	10	13231078	13231078	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13231078A>G	uc001ima.2	+	10	1517	c.1416A>G	c.(1414-1416)TCA>TCG	p.S472S	MCM10_uc001imb.2_Silent_p.S471S|MCM10_uc001imc.2_Silent_p.S471S	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	472					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
RPP38	10557	broad.mit.edu	37	10	15145991	15145991	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15145991C>A	uc001iny.3	+	3	1391	c.678C>A	c.(676-678)AGC>AGA	p.S226R	RPP38_uc009xjm.2_Missense_Mutation_p.S226R|RPP38_uc001inx.3_Missense_Mutation_p.S226R	NM_183005	NP_892117	P78345	RPP38_HUMAN	ribonuclease P/MRP 38 subunit	226					tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity			ovary(1)	1																		---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15255974	15255974	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15255974T>C	uc001iob.2	-	8	1620	c.1613A>G	c.(1612-1614)GAA>GGA	p.E538G		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	538	Cytoplasmic (Potential).					integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17113457	17113457	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17113457T>G	uc001ioo.2	-	19	2645	c.2593A>C	c.(2593-2595)AGT>CGT	p.S865R		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	865	CUB 4.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
STAM	8027	broad.mit.edu	37	10	17756586	17756586	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17756586C>T	uc001ipj.1	+	14	1646	c.1430C>T	c.(1429-1431)GCG>GTG	p.A477V	STAM_uc009xjw.1_Missense_Mutation_p.A135V	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1	477					cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
SLC39A12	221074	broad.mit.edu	37	10	18292281	18292281	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18292281T>C	uc001ipo.2	+	12	2214	c.1941T>C	c.(1939-1941)GTT>GTC	p.V647V	SLC39A12_uc001ipn.2_Silent_p.V610V|SLC39A12_uc001ipp.2_Silent_p.V646V|SLC39A12_uc010qck.1_Silent_p.V513V|uc001ipq.1_RNA	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	647	Helical; (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2																		---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	22021968	22021968	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22021968G>A	uc001iqs.2	+	19	2755	c.2407G>A	c.(2407-2409)GCA>ACA	p.A803T	MLLT10_uc001iqt.2_Missense_Mutation_p.A787T|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Missense_Mutation_p.A787T|MLLT10_uc001ira.2_Missense_Mutation_p.A244T|MLLT10_uc001irb.2_RNA	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	803					positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24880871	24880871	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24880871T>C	uc001isb.2	-	22	4434	c.3947A>G	c.(3946-3948)CAC>CGC	p.H1316R	ARHGAP21_uc010qdb.1_RNA	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1315	Rho-GAP.				signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8																		---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27066140	27066140	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27066140G>A	uc001isx.2	-	3	483	c.316C>T	c.(316-318)CGA>TGA	p.R106*	ABI1_uc001ite.2_Nonsense_Mutation_p.R106*|ABI1_uc010qdh.1_Nonsense_Mutation_p.R106*|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Nonsense_Mutation_p.R106*|ABI1_uc001ita.2_Nonsense_Mutation_p.R106*|ABI1_uc001isz.2_Nonsense_Mutation_p.R106*|ABI1_uc001itb.2_Nonsense_Mutation_p.R123*|ABI1_uc001itc.2_Nonsense_Mutation_p.R106*|ABI1_uc010qdj.1_Nonsense_Mutation_p.R106*|ABI1_uc001itd.2_Nonsense_Mutation_p.R106*|ABI1_uc010qdk.1_Nonsense_Mutation_p.R106*|ABI1_uc010qdg.1_Translation_Start_Site	NM_005470	NP_005461	Q8IZP0	ABI1_HUMAN	abl-interactor 1 isoform a	106	t-SNARE coiled-coil homology.				actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1																		---	---	---	---
ACBD5	91452	broad.mit.edu	37	10	27512341	27512341	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27512341A>G	uc010qdp.1	-	5	607	c.416T>C	c.(415-417)TTG>TCG	p.L139S	ACBD5_uc010qdm.1_Missense_Mutation_p.L137S|ACBD5_uc010qdn.1_Missense_Mutation_p.L30S|ACBD5_uc010qdo.1_Missense_Mutation_p.L30S|ACBD5_uc001ito.2_Missense_Mutation_p.L104S|ACBD5_uc001itp.2_Missense_Mutation_p.L30S|ACBD5_uc001itq.2_Missense_Mutation_p.L30S|ACBD5_uc001itr.1_5'UTR	NM_145698	NP_663736	Q5T8D3	ACBD5_HUMAN	acyl-Coenzyme A binding domain containing 5	137					transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding				0																		---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30316940	30316940	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30316940G>A	uc001iux.2	-	2	2196	c.2137C>T	c.(2137-2139)CCG>TCG	p.P713S	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Missense_Mutation_p.P575S|KIAA1462_uc009xle.1_Missense_Mutation_p.P713S	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	713										ovary(4)	4																		---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33491868	33491868	+	Silent	SNP	G	A	A	rs148913335		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33491868G>A	uc001iwx.3	-	11	2338	c.1815C>T	c.(1813-1815)GAC>GAT	p.D605D	NRP1_uc001iwv.3_Silent_p.D605D|NRP1_uc009xlz.2_Silent_p.D605D|NRP1_uc001iww.3_Silent_p.D424D|NRP1_uc001iwy.3_Silent_p.D605D|NRP1_uc001iwz.2_Silent_p.D605D|NRP1_uc001ixa.2_Intron|NRP1_uc001ixb.1_Silent_p.D605D	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	605	Extracellular (Potential).				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)													---	---	---	---
CREM	1390	broad.mit.edu	37	10	35468210	35468210	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35468210T>C	uc001iyb.2	+						CREM_uc001ixx.2_Missense_Mutation_p.Y123H|CREM_uc001ixy.2_Intron|CREM_uc001ixz.2_Intron|CREM_uc001iya.2_Intron|CREM_uc001iyc.2_Intron|CREM_uc001iyd.2_Intron|CREM_uc001iye.2_Intron|CREM_uc001iyf.2_Intron|CREM_uc001iyg.2_Intron|CREM_uc001iyh.2_Intron|CREM_uc001iyi.2_Intron|CREM_uc001iyj.2_Intron|CREM_uc001iyk.2_Intron	NM_181571	NP_853549			cAMP responsive element modulator isoform a						cell differentiation|multicellular organismal development|signal transduction|spermatogenesis	nucleus	cAMP response element binding protein binding|protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
ZNF33B	7582	broad.mit.edu	37	10	43089408	43089408	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43089408T>C	uc001jaf.1	-	5	1105	c.990A>G	c.(988-990)GAA>GAG	p.E330E	ZNF33B_uc009xmg.1_Intron|ZNF33B_uc001jae.1_Intron|ZNF33B_uc001jag.1_Silent_p.E218E|ZNF33B_uc001jad.2_Intron	NM_006955	NP_008886	Q06732	ZN33B_HUMAN	zinc finger protein 33B	330	C2H2-type 1.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
SYT15	83849	broad.mit.edu	37	10	46968730	46968730	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46968730A>G	uc001jea.2	-						SYT15_uc001jdz.2_Intron|SYT15_uc001jeb.2_Intron|SYT15_uc010qfp.1_5'Flank	NM_031912	NP_114118			synaptotagmin XV isoform a							integral to membrane|plasma membrane					0																		---	---	---	---
C10orf71	118461	broad.mit.edu	37	10	50530925	50530925	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50530925A>G	uc010qgp.1	+	3	674	c.335A>G	c.(334-336)TAC>TGC	p.Y112C		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	112											0																		---	---	---	---
ERCC6	2074	broad.mit.edu	37	10	50678712	50678712	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50678712A>G	uc001jhs.3	-	18	3448	c.3294T>C	c.(3292-3294)AGT>AGC	p.S1098S	ERCC6_uc009xod.2_Silent_p.S258S|ERCC6_uc010qgr.1_Silent_p.S468S|ERCC6_uc001jhr.3_Silent_p.S466S	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	1098					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16													Direct_reversal_of_damage|NER					---	---	---	---
CSTF2T	23283	broad.mit.edu	37	10	53458101	53458101	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53458101C>A	uc001jjp.2	-	1	1255	c.1209G>T	c.(1207-1209)AGG>AGT	p.R403S	PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit	403	Gly-rich.				mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)														---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55782925	55782925	+	Missense_Mutation	SNP	T	G	G	rs74905541		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55782925T>G	uc001jju.1	-	19	2648	c.2253A>C	c.(2251-2253)CAA>CAC	p.Q751H	PCDH15_uc010qhq.1_Missense_Mutation_p.Q756H|PCDH15_uc010qhr.1_Missense_Mutation_p.Q751H|PCDH15_uc010qhs.1_Missense_Mutation_p.Q763H|PCDH15_uc010qht.1_Missense_Mutation_p.Q758H|PCDH15_uc010qhu.1_Missense_Mutation_p.Q751H|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.Q751H|PCDH15_uc010qhw.1_Missense_Mutation_p.Q714H|PCDH15_uc010qhx.1_Missense_Mutation_p.Q680H|PCDH15_uc010qhy.1_Missense_Mutation_p.Q756H|PCDH15_uc010qhz.1_Missense_Mutation_p.Q751H|PCDH15_uc010qia.1_Missense_Mutation_p.Q729H|PCDH15_uc010qib.1_Missense_Mutation_p.Q729H|PCDH15_uc001jjw.2_Missense_Mutation_p.Q751H	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	751	Extracellular (Potential).|Cadherin 7.				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
ANK3	288	broad.mit.edu	37	10	61831056	61831056	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61831056C>A	uc001jky.2	-	37	9775	c.9583G>T	c.(9583-9585)GGC>TGC	p.G3195C	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	3195					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63759903	63759903	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63759903C>T	uc001jlt.1	+	4	582	c.556C>T	c.(556-558)CGG>TGG	p.R186W	ARID5B_uc010qil.1_Missense_Mutation_p.R186W	NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	186					liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64967949	64967949	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64967949T>C	uc001jmn.2	-	10	3780	c.3480A>G	c.(3478-3480)GTA>GTG	p.V1160V	JMJD1C_uc001jml.2_Silent_p.V941V|JMJD1C_uc001jmm.2_Silent_p.V872V|JMJD1C_uc010qiq.1_Silent_p.V978V|JMJD1C_uc009xpi.2_Silent_p.V978V|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc009xpk.1_Silent_p.V197V	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	1160					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64979741	64979741	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64979741G>A	uc001jmn.2	-	4	750	c.450C>T	c.(448-450)GAC>GAT	p.D150D	JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Translation_Start_Site|JMJD1C_uc010qiq.1_Translation_Start_Site|JMJD1C_uc009xpi.2_Translation_Start_Site|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc001jmp.1_Intron	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	150					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
DNA2	1763	broad.mit.edu	37	10	70225564	70225564	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70225564A>G	uc001jof.2	-	4	705	c.705T>C	c.(703-705)TCT>TCC	p.S235S	DNA2_uc001jog.1_Silent_p.S149S|DNA2_uc001joh.1_RNA	NM_001080449	NP_001073918	P51530	DNA2L_HUMAN	DNA replication helicase 2 homolog	149					base-excision repair|DNA replication, removal of RNA primer|mitochondrial DNA repair|mitochondrial DNA replication|positive regulation of DNA replication|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	mitochondrial nucleoid|nucleoplasm	5'-flap endonuclease activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|site-specific endodeoxyribonuclease activity, specific for altered base				0																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71158430	71158430	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71158430G>A	uc001jpl.3	+	17	2556	c.2455G>A	c.(2455-2457)GTC>ATC	p.V819I	HK1_uc001jpg.3_Missense_Mutation_p.V807I|HK1_uc001jph.3_Missense_Mutation_p.V823I|HK1_uc001jpi.3_Missense_Mutation_p.V823I|HK1_uc001jpj.3_Missense_Mutation_p.V854I|HK1_uc001jpk.3_Missense_Mutation_p.V818I	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI	819	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
UNC5B	219699	broad.mit.edu	37	10	73059019	73059019	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73059019C>T	uc001jro.2	+	17	3268	c.2823C>T	c.(2821-2823)ACC>ACT	p.T941T	UNC5B_uc001jrp.2_Silent_p.T930T|UNC5B_uc001jrq.1_5'Flank	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor	941	Cytoplasmic (Potential).|Death.				apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3																		---	---	---	---
NUDT13	25961	broad.mit.edu	37	10	74890516	74890516	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74890516T>A	uc001jtj.2	+	9	1039	c.914T>A	c.(913-915)GTA>GAA	p.V305E	NUDT13_uc010qkc.1_Missense_Mutation_p.V179E|NUDT13_uc010qkd.1_Missense_Mutation_p.V108E|NUDT13_uc009xqw.2_RNA|NUDT13_uc001jtk.2_3'UTR|NUDT13_uc010qke.1_Missense_Mutation_p.V108E|NUDT13_uc001jtl.2_Missense_Mutation_p.V216E	NM_015901	NP_056985	Q86X67	NUD13_HUMAN	nudix-type motif 13	305	Nudix hydrolase.						hydrolase activity|metal ion binding				0	Prostate(51;0.0119)																	---	---	---	---
PLAU	5328	broad.mit.edu	37	10	75676249	75676249	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75676249G>A	uc001jwa.2	+	11	1368	c.1222G>A	c.(1222-1224)GTC>ATC	p.V408I	C10orf55_uc001jvz.1_Intron|PLAU_uc010qkw.1_Missense_Mutation_p.V391I|PLAU_uc010qkx.1_Missense_Mutation_p.V322I|PLAU_uc001jwb.2_RNA|PLAU_uc001jwc.2_Missense_Mutation_p.V408I|PLAU_uc009xrq.1_Missense_Mutation_p.V372I	NM_002658	NP_002649	P00749	UROK_HUMAN	plasminogen activator, urokinase isoform 1	408	Peptidase S1.				blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(2)|kidney(1)	3	Prostate(51;0.0112)				Amiloride(DB00594)|Urokinase(DB00013)													---	---	---	---
VCL	7414	broad.mit.edu	37	10	75871668	75871668	+	Missense_Mutation	SNP	C	T	T	rs143321584		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75871668C>T	uc001jwd.2	+	19	2841	c.2747C>T	c.(2746-2748)CCG>CTG	p.P916L	VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Missense_Mutation_p.P823L|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706	P18206	VINC_HUMAN	vinculin isoform meta-VCL	916	C-terminal tail.				adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76781836	76781836	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76781836G>A	uc001jwn.1	+	16	3712	c.3219G>A	c.(3217-3219)GAG>GAA	p.E1073E	MYST4_uc001jwm.1_Silent_p.E781E|MYST4_uc001jwo.1_Silent_p.E781E|MYST4_uc001jwp.1_Silent_p.E890E	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1073	Poly-Glu.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML						OREG0020273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76789488	76789488	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76789488A>G	uc001jwn.1	+	18	5399	c.4906A>G	c.(4906-4908)ATC>GTC	p.I1636V	MYST4_uc001jwo.1_Missense_Mutation_p.I1344V|MYST4_uc001jwp.1_Missense_Mutation_p.I1453V	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1636	Ser-rich.|Interaction with RUNX1 and RUNX2.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76789800	76789800	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76789800A>C	uc001jwn.1	+	18	5711	c.5218A>C	c.(5218-5220)ATC>CTC	p.I1740L	MYST4_uc001jwo.1_Missense_Mutation_p.I1448L|MYST4_uc001jwp.1_Missense_Mutation_p.I1557L	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1740	Ser-rich.|Interaction with RUNX1 and RUNX2.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
DUSP13	51207	broad.mit.edu	37	10	76863832	76863832	+	3'UTR	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76863832C>A	uc001jws.2	-	4					DUSP13_uc001jwu.2_Missense_Mutation_p.M1I|DUSP13_uc001jww.2_Intron|DUSP13_uc009xrs.2_Missense_Mutation_p.M1I|DUSP13_uc001jwt.2_Missense_Mutation_p.M1I|DUSP13_uc001jwv.2_Intron	NM_001007271	NP_001007272			muscle-restricted dual specificity phosphatase							cytoplasm	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)																	---	---	---	---
SAMD8	142891	broad.mit.edu	37	10	76910314	76910314	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76910314C>T	uc001jwx.1	+	2	131	c.28C>T	c.(28-30)CGC>TGC	p.R10C	SAMD8_uc001jwy.1_Missense_Mutation_p.R10C	NM_144660	NP_653261	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8	10					sphingomyelin biosynthetic process	integral to membrane					0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)																	---	---	---	---
SH2D4B	387694	broad.mit.edu	37	10	82331288	82331288	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82331288G>A	uc001kck.1	+	3	879	c.449G>A	c.(448-450)CGC>CAC	p.R150H	SH2D4B_uc001kcl.1_Missense_Mutation_p.R101H	NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B isoform 1	149	Glu-rich.										0			Colorectal(32;0.229)															---	---	---	---
ACTA2	59	broad.mit.edu	37	10	90697858	90697858	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90697858T>G	uc001kfp.2	-	8	1066	c.950A>C	c.(949-951)AAG>ACG	p.K317T	STAMBPL1_uc010qmx.1_Intron|ACTA2_uc010qmy.1_Missense_Mutation_p.K272T|ACTA2_uc001kfq.2_Missense_Mutation_p.K317T|uc001kfo.1_Intron	NM_001613	NP_001604	P62736	ACTA_HUMAN	alpha 2 actin	317					response to virus	cytosol	ATP binding				0		Colorectal(252;0.0161)		Colorectal(12;0.000123)|COAD - Colon adenocarcinoma(12;0.00018)														---	---	---	---
IFIT2	3433	broad.mit.edu	37	10	91066183	91066183	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91066183C>T	uc009xts.2	+	2	645	c.470C>T	c.(469-471)GCG>GTG	p.A157V	LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|uc001kgd.2_Intron	NM_001547	NP_001538	P09913	IFIT2_HUMAN	interferon-induced protein with	157	TPR 2.				negative regulation of protein binding|response to virus|type I interferon-mediated signaling pathway		protein binding			ovary(1)|skin(1)	2		Colorectal(252;0.0161)																---	---	---	---
HTR7	3363	broad.mit.edu	37	10	92617193	92617193	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92617193A>G	uc001kha.2	-	1	479	c.236T>C	c.(235-237)GTC>GCC	p.V79A	HTR7_uc001kgz.2_Missense_Mutation_p.V79A|HTR7_uc001khb.2_Missense_Mutation_p.V79A	NM_019859	NP_062873	P34969	5HT7R_HUMAN	5-hydroxytryptamine receptor 7 isoform d	79	Extracellular (By similarity).				blood circulation|circadian rhythm	integral to plasma membrane	protein binding|serotonin receptor activity			ovary(1)	1					Eletriptan(DB00216)|Methysergide(DB00247)|Ziprasidone(DB00246)													---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95111577	95111577	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95111577G>T	uc001kin.2	-	33	3631	c.3508C>A	c.(3508-3510)CAT>AAT	p.H1170N	MYOF_uc001kio.2_Missense_Mutation_p.H1157N|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	1170	Cytoplasmic (Potential).|C2 4.				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95211875	95211875	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95211875A>G	uc001kin.2	-	3	291	c.168T>C	c.(166-168)GGT>GGC	p.G56G	MYOF_uc001kio.2_Silent_p.G56G|MYOF_uc001kip.3_Silent_p.G56G|MYOF_uc009xuf.2_Silent_p.G38G	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	56	C2 1.|Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
NOC3L	64318	broad.mit.edu	37	10	96098412	96098412	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96098412A>G	uc001kjq.1	-	18	2132	c.2044T>C	c.(2044-2046)TAC>CAC	p.Y682H		NM_022451	NP_071896	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog	682						nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)																---	---	---	---
PDLIM1	9124	broad.mit.edu	37	10	97050611	97050611	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97050611C>T	uc001kkh.2	-	1	171	c.62G>A	c.(61-63)GGC>GAC	p.G21D	PDLIM1_uc001kki.2_Missense_Mutation_p.G21D|PDLIM1_uc009xuv.2_Missense_Mutation_p.G21D|PDLIM1_uc001kkj.1_Missense_Mutation_p.G21D	NM_020992	NP_066272	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	21	PDZ.			G -> R (in Ref. 1; AAC05580).	response to oxidative stress	cytoplasm|cytoskeleton	zinc ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)														---	---	---	---
ZDHHC16	84287	broad.mit.edu	37	10	99212022	99212022	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99212022C>T	uc001knj.2	+	4	768	c.419C>T	c.(418-420)CCG>CTG	p.P140L	ZDHHC16_uc001knp.2_Missense_Mutation_p.P140L|ZDHHC16_uc001knk.2_Missense_Mutation_p.P140L|ZDHHC16_uc001knl.2_Missense_Mutation_p.P140L|ZDHHC16_uc001knm.2_Intron|ZDHHC16_uc001knn.2_Missense_Mutation_p.P140L|ZDHHC16_uc010qow.1_Missense_Mutation_p.P140L|ZDHHC16_uc009xvq.2_RNA|ZDHHC16_uc001kno.2_Missense_Mutation_p.P140L|ZDHHC16_uc009xvr.2_Missense_Mutation_p.P140L	NM_198046	NP_932163	Q969W1	ZDH16_HUMAN	Abl-philin 2 isoform 1	140	Cytoplasmic (Potential).				apoptosis	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		Colorectal(252;0.0846)		Epithelial(162;5.81e-10)|all cancers(201;4.19e-08)														---	---	---	---
PI4K2A	55361	broad.mit.edu	37	10	99416585	99416585	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99416585C>T	uc001kog.1	+	4	833	c.776C>T	c.(775-777)TCA>TTA	p.S259L	PI4K2A_uc010qoy.1_Missense_Mutation_p.S229L|PI4K2A_uc009xvw.1_5'UTR	NM_018425	NP_060895	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	259	PI3K/PI4K.				phosphatidylinositol biosynthetic process	cytoplasm|integral to plasma membrane|membrane raft	1-phosphatidylinositol 4-kinase activity|ATP binding|magnesium ion binding			lung(1)|skin(1)	2		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)														---	---	---	---
CRTAC1	55118	broad.mit.edu	37	10	99664470	99664470	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99664470G>T	uc001kou.1	-	7	1308	c.952C>A	c.(952-954)CGC>AGC	p.R318S	CRTAC1_uc001kov.2_Missense_Mutation_p.R307S|CRTAC1_uc001kot.1_Missense_Mutation_p.R108S	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	318	FG-GAP 3; atypical.					proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)														---	---	---	---
NKX2-3	159296	broad.mit.edu	37	10	101294811	101294811	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101294811C>T	uc009xwj.2	+	2	627	c.428C>T	c.(427-429)CCG>CTG	p.P143L		NM_145285	NP_660328	Q8TAU0	NKX23_HUMAN	NK2 transcription factor related, locus 3	143						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.45e-08)														---	---	---	---
CWF19L1	55280	broad.mit.edu	37	10	102013291	102013291	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102013291T>C	uc001kqq.1	-	6	597	c.510A>G	c.(508-510)GAA>GAG	p.E170E	CWF19L1_uc001kqs.1_5'UTR|CWF19L1_uc001kqr.1_Silent_p.E170E|CWF19L1_uc001kqt.1_5'UTR|CWF19L1_uc010qpn.1_Silent_p.E33E	NM_018294	NP_060764	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control	170							catalytic activity				0		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)														---	---	---	---
KCNIP2	30819	broad.mit.edu	37	10	103599518	103599518	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103599518A>C	uc001kub.2	-						KCNIP2_uc001ktz.2_Missense_Mutation_p.L27R|KCNIP2_uc009xwu.2_Intron|KCNIP2_uc009xwv.2_Intron|KCNIP2_uc001kuc.2_Intron|KCNIP2_uc001kue.2_Intron|KCNIP2_uc001kud.2_Intron|KCNIP2_uc001kuf.2_Intron|KCNIP2_uc001kua.2_Intron|KCNIP2_uc009xww.2_Intron|KCNIP2_uc010qqh.1_Missense_Mutation_p.L27R|KCNIP2_uc010qqi.1_Intron	NM_173191	NP_775283			Kv channel interacting protein 2 isoform 2						clustering of voltage-gated potassium channels|detection of calcium ion|muscle contraction|regulation of heart contraction|signal transduction|synaptic transmission	cytoplasm|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|calcium ion binding|ER retention sequence binding|identical protein binding|protein N-terminus binding				0		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)														---	---	---	---
LDB1	8861	broad.mit.edu	37	10	103867901	103867901	+	Silent	SNP	C	T	T	rs146408312		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103867901C>T	uc009xwz.2	-	11	1528	c.1185G>A	c.(1183-1185)CCG>CCA	p.P395P	LDB1_uc001kuk.3_Silent_p.P359P	NM_001113407	NP_001106878	Q86U70	LDB1_HUMAN	LIM domain binding 1 isoform 1	395					histone H3-K4 acetylation|negative regulation of erythrocyte differentiation|negative regulation of transcription, DNA-dependent|positive regulation of hemoglobin biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription elongation, DNA-dependent|transcription, DNA-dependent|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	nuclear chromatin|protein complex	LIM domain binding|protein homodimerization activity|transcription corepressor activity			large_intestine(1)	1		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)														---	---	---	---
PSD	5662	broad.mit.edu	37	10	104176760	104176760	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104176760G>A	uc001kvg.1	-	2	563	c.36C>T	c.(34-36)GGC>GGT	p.G12G	PSD_uc001kvh.1_Intron|PSD_uc009xxd.1_Silent_p.G12G|PSD_uc001kvi.1_Silent_p.G12G|FBXL15_uc001kvj.1_5'Flank|FBXL15_uc001kvk.2_5'Flank	NM_002779	NP_002770	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	12					regulation of ARF protein signal transduction	cytoplasm|plasma membrane|ruffle	ARF guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|urinary_tract(1)	3				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)														---	---	---	---
PCGF6	84108	broad.mit.edu	37	10	105107192	105107192	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105107192T>C	uc001kwt.2	-	4	641	c.573A>G	c.(571-573)TTA>TTG	p.L191L	PCGF6_uc001kwu.2_Intron|PCGF6_uc009xxk.2_RNA|PCGF6_uc009xxl.2_RNA|PCGF6_uc009xxm.2_Intron	NM_001011663	NP_001011663	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6 isoform a	191					negative regulation of transcription, DNA-dependent	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			kidney(1)	1		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)														---	---	---	---
C10orf78	119392	broad.mit.edu	37	10	105885351	105885351	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105885351T>C	uc001kxu.2	+	4	640	c.627T>C	c.(625-627)GCT>GCC	p.A209A	C10orf78_uc001kxs.2_Silent_p.A196A|C10orf78_uc001kxt.2_Silent_p.A163A|C10orf78_uc001kxv.2_Silent_p.A271A	NM_001002759	NP_001002759	Q86XK3	SFR1_HUMAN	hypothetical protein LOC119392 isoform a	209					double-strand break repair via homologous recombination	Swi5-Sfr1 complex	protein binding				0		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;1.31e-09)|all cancers(201;3.84e-08)|BRCA - Breast invasive adenocarcinoma(275;0.014)														---	---	---	---
GSTO2	119391	broad.mit.edu	37	10	106039129	106039129	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106039129T>C	uc001kyb.2	+	5	996	c.368T>C	c.(367-369)GTC>GCC	p.V123A	GSTO2_uc010qqw.1_Missense_Mutation_p.V123A|GSTO2_uc010qqx.1_Intron|GSTO2_uc001kyc.2_Missense_Mutation_p.V95A|GSTO2_uc010qqy.1_Intron	NM_183239	NP_899062	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	123	GST C-terminal.				water-soluble vitamin metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)													---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108489836	108489836	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108489836C>T	uc001kym.2	-	6	1004	c.996G>A	c.(994-996)GTG>GTA	p.V332V	SORCS1_uc001kyl.2_Silent_p.V332V|SORCS1_uc009xxs.2_Silent_p.V332V|SORCS1_uc001kyn.1_Silent_p.V332V|SORCS1_uc001kyo.2_Silent_p.V332V	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	332	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
HABP2	3026	broad.mit.edu	37	10	115340373	115340373	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115340373A>C	uc001lai.3	+	8	863	c.760A>C	c.(760-762)AAG>CAG	p.K254Q	HABP2_uc010qrz.1_RNA	NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	254	Kringle.				cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)														---	---	---	---
HABP2	3026	broad.mit.edu	37	10	115341710	115341710	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115341710A>G	uc001lai.3	+	9	1017	c.914A>G	c.(913-915)GAG>GGG	p.E305G	HABP2_uc010qrz.1_Intron	NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	305					cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)														---	---	---	---
C10orf118	55088	broad.mit.edu	37	10	115910861	115910861	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115910861C>T	uc001lbb.1	-	4	1530	c.878G>A	c.(877-879)CGG>CAG	p.R293Q	C10orf118_uc001lbc.1_Missense_Mutation_p.R293Q|C10orf118_uc009xye.1_RNA	NM_018017	NP_060487	Q7Z3E2	CJ118_HUMAN	CTCL tumor antigen L14-2	293	Potential.									ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)														---	---	---	---
VWA2	340706	broad.mit.edu	37	10	116038514	116038514	+	Missense_Mutation	SNP	C	T	T	rs149756313		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116038514C>T	uc001lbl.1	+	8	1058	c.737C>T	c.(736-738)ACG>ATG	p.T246M	VWA2_uc001lbk.1_Missense_Mutation_p.T246M|VWA2_uc009xyf.1_Translation_Start_Site	NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	246						extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)														---	---	---	---
KIAA1598	57698	broad.mit.edu	37	10	118738812	118738812	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118738812G>A	uc009xyw.2	-	2	564	c.66C>T	c.(64-66)GGC>GGT	p.G22G	KIAA1598_uc001lcz.3_Silent_p.G22G|KIAA1598_uc010qso.1_Intron|KIAA1598_uc010qsp.1_Silent_p.G22G|KIAA1598_uc010qsq.1_5'UTR	NM_001127211	NP_001120683	A0MZ66	SHOT1_HUMAN	shootin1 isoform a	22	Potential.				axon guidance	axon					0				all cancers(201;0.00494)														---	---	---	---
FAM45A	404636	broad.mit.edu	37	10	120889037	120889037	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120889037T>C	uc001ldw.2	+	7	749	c.705T>C	c.(703-705)GCT>GCC	p.A235A	FAM45A_uc010qsv.1_Silent_p.A227A|FAM45A_uc010qsw.1_Silent_p.A84A|FAM45A_uc010qsx.1_RNA|FAM45A_uc010qsy.1_Silent_p.A162A|FAM45A_uc010qsz.1_Silent_p.A124A	NM_207009	NP_996892	Q8TCE6	FA45A_HUMAN	hypothetical protein LOC404636	235										ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)														---	---	---	---
PRDX3	10935	broad.mit.edu	37	10	120928817	120928817	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120928817G>A	uc001lec.2	-	6	632	c.589C>T	c.(589-591)CAT>TAT	p.H197Y		NM_006793	NP_006784	P30048	PRDX3_HUMAN	peroxiredoxin 3 isoform a precursor	197	Thioredoxin.				cell redox homeostasis|hydrogen peroxide catabolic process|mitochondrion organization|myeloid cell differentiation|negative regulation of kinase activity|positive regulation of cell proliferation|positive regulation of NF-kappaB transcription factor activity|regulation of mitochondrial membrane potential|response to lipopolysaccharide	early endosome|mitochondrion	alkyl hydroperoxide reductase activity|caspase inhibitor activity|peroxidase activity|peroxiredoxin activity|protein C-terminus binding|protein kinase binding				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)														---	---	---	---
PLEKHA1	59338	broad.mit.edu	37	10	124189429	124189429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124189429C>T	uc001lge.1	+	12	1313	c.1190C>T	c.(1189-1191)GCG>GTG	p.A397V	PLEKHA1_uc001lgf.1_3'UTR|PLEKHA1_uc001lgg.1_Missense_Mutation_p.A397V	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A	397					B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
HMX2	3167	broad.mit.edu	37	10	124909354	124909354	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124909354C>T	uc001lhc.1	+	2	794	c.537C>T	c.(535-537)CGC>CGT	p.R179R		NM_005519	NP_005510	A2RU54	HMX2_HUMAN	H6 family homeobox 2	179	Homeobox.				cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_neural(114;0.169)|Colorectal(57;0.207)|Glioma(114;0.222)		Colorectal(40;0.123)|COAD - Colon adenocarcinoma(40;0.141)														---	---	---	---
C10orf137	26098	broad.mit.edu	37	10	127451935	127451935	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127451935C>T	uc001liq.1	+	25	3904	c.3611C>T	c.(3610-3612)GCA>GTA	p.A1204V	C10orf137_uc001lio.1_Missense_Mutation_p.A1170V|C10orf137_uc001lip.1_Missense_Mutation_p.A908V|C10orf137_uc001lis.1_Missense_Mutation_p.A530V|C10orf137_uc001lit.1_Missense_Mutation_p.A114V	NM_015608	NP_056423	Q3B7T1	EDRF1_HUMAN	erythroid differentiation-related factor 1	1204					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	binding			ovary(5)|large_intestine(3)|lung(2)	10		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)																---	---	---	---
BCCIP	56647	broad.mit.edu	37	10	127516153	127516153	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127516153T>C	uc001ljb.3	+	3	290	c.267T>C	c.(265-267)ACT>ACC	p.T89T	BCCIP_uc001ljd.3_Silent_p.T89T|BCCIP_uc010qui.1_Silent_p.T89T|BCCIP_uc001ljc.3_Silent_p.T89T|BCCIP_uc010quj.1_Silent_p.T89T	NM_078468	NP_510868	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A-interacting protein isoform	89	Interaction with BRCA2.				cell cycle|DNA repair|neuroendocrine cell differentiation|regulation of cyclin-dependent protein kinase activity	nuclear cyclin-dependent protein kinase holoenzyme complex	kinase regulator activity|protein binding			ovary(1)|breast(1)	2		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)																---	---	---	---
FAM196A	642938	broad.mit.edu	37	10	128973736	128973736	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128973736T>C	uc001lju.1	-	1	965	c.924A>G	c.(922-924)TCA>TCG	p.S308S	DOCK1_uc001ljt.2_Intron|DOCK1_uc010qun.1_Intron|FAM196A_uc010quo.1_Silent_p.S308S|FAM196A_uc001ljv.1_Silent_p.S308S|FAM196A_uc009yap.1_Silent_p.S308S	NM_001039762	NP_001034851	Q6ZSG2	F196A_HUMAN	hypothetical protein LOC642938	308										ovary(2)	2																		---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132944832	132944832	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132944832G>A	uc001lkp.2	-	7	1212	c.1126C>T	c.(1126-1128)CGC>TGC	p.R376C	TCERG1L_uc009yax.1_RNA	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	376										large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
GPR123	84435	broad.mit.edu	37	10	134884565	134884565	+	Missense_Mutation	SNP	C	T	T	rs112805112		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134884565C>T	uc001llw.2	+	1	133	c.133C>T	c.(133-135)CGG>TGG	p.R45W				Q86SQ6	GP123_HUMAN	RecName: Full=Probable G-protein coupled receptor 123;	Error:Variant_position_missing_in_Q86SQ6_after_alignment						integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)														---	---	---	---
GPR123	84435	broad.mit.edu	37	10	134942136	134942136	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134942136C>T	uc001llx.3	+	7	1240	c.804C>T	c.(802-804)GCC>GCT	p.A268A	GPR123_uc001llw.2_Silent_p.A987A	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	268	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)														---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135106532	135106532	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135106532C>T	uc001lmg.1	-						TUBGCP2_uc001lmf.1_5'Flank|TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650			tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
NLRP6	171389	broad.mit.edu	37	11	281443	281443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:281443G>A	uc010qvs.1	+	4	1709	c.1709G>A	c.(1708-1710)CGT>CAT	p.R570H	NLRP6_uc010qvt.1_Missense_Mutation_p.R570H	NM_138329	NP_612202	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	570						cytoplasm	ATP binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
NLRP6	171389	broad.mit.edu	37	11	281721	281721	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:281721G>A	uc010qvs.1	+	4	1987	c.1987G>A	c.(1987-1989)GTG>ATG	p.V663M	NLRP6_uc010qvt.1_Missense_Mutation_p.V663M	NM_138329	NP_612202	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	663						cytoplasm	ATP binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	490481	490481	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:490481G>C	uc001lpj.2	+	12	1539	c.1363G>C	c.(1363-1365)GGC>CGC	p.G455R		NM_030783	NP_110410	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	455	Cytoplasmic (Potential).					integral to membrane					0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)													---	---	---	---
C11orf35	256329	broad.mit.edu	37	11	556926	556926	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:556926G>A	uc001lpx.2	-	8	948	c.885C>T	c.(883-885)TTC>TTT	p.F295F	uc001lpy.2_5'Flank|uc001lpz.2_5'Flank	NM_173573	NP_775844	Q8IXW0	CK035_HUMAN	hypothetical protein LOC256329	295										pancreas(1)	1		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
DEAF1	10522	broad.mit.edu	37	11	686886	686886	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:686886G>A	uc001lqq.1	-	5	1469	c.776C>T	c.(775-777)GCG>GTG	p.A259V	DEAF1_uc009ycf.1_RNA	NM_021008	NP_066288	O75398	DEAF1_HUMAN	deformed epidermal autoregulatory factor 1	259	SAND.				embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1018712	1018712	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1018712A>G	uc001lsw.2	-	31	4140	c.4089T>C	c.(4087-4089)CGT>CGC	p.R1363R		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1363	Pro-rich.|Thr-rich.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1025193	1025193	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1025193G>T	uc001lsw.2	-	23	3025	c.2974C>A	c.(2974-2976)CGT>AGT	p.R992S		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	992	VWFD 3.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1027354	1027354	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1027354A>G	uc001lsw.2	-	17	2196	c.2145T>C	c.(2143-2145)TGT>TGC	p.C715C		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	715					maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC2	4583	broad.mit.edu	37	11	1088727	1088727	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1088727G>T	uc001lsx.1	+	26	3539	c.3512G>T	c.(3511-3513)AGG>ATG	p.R1171M		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	1171						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)													---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1263838	1263838	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1263838C>A	uc009ycr.1	+	47	7933	c.7807C>A	c.(7807-7809)CCG>ACG	p.P2603T	MUC5B_uc001ltb.2_Missense_Mutation_p.P1913T	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1910	7 X Cys-rich subdomain repeats.|11 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
BRSK2	9024	broad.mit.edu	37	11	1464708	1464708	+	Intron	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1464708G>C	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron|BRSK2_uc001ltn.2_Intron|BRSK2_uc010qwx.1_Intron	NM_003957	NP_003948			BR serine/threonine kinase 2						establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)														---	---	---	---
KRTAP5-5	439915	broad.mit.edu	37	11	1651484	1651484	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1651484C>A	uc001lty.2	+	1	452	c.414C>A	c.(412-414)GGC>GGA	p.G138G		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	138	8 X 4 AA repeats of C-C-X-P.					keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)														---	---	---	---
CD81	975	broad.mit.edu	37	11	2417204	2417204	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2417204C>T	uc001lwf.1	+						CD81_uc001lwg.1_Intron|CD81_uc001lwh.1_5'Flank	NM_004356	NP_004347			CD81 antigen						activation of MAPK activity|cell proliferation|phosphatidylinositol biosynthetic process|positive regulation of 1-phosphatidylinositol 4-kinase activity|positive regulation of cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|protein localization|regulation of immune response|virion attachment, binding of host cell surface receptor	integral to plasma membrane	protein binding				0		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)														---	---	---	---
TSSC4	10078	broad.mit.edu	37	11	2424179	2424179	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2424179C>T	uc001lwj.2	+	4	677	c.316C>T	c.(316-318)CGG>TGG	p.R106W	TSSC4_uc001lwi.2_Missense_Mutation_p.R42W|TSSC4_uc001lwk.2_Missense_Mutation_p.R106W|TSSC4_uc001lwl.2_Missense_Mutation_p.R106W	NM_005706	NP_005697	Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	106											0		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
CHRNA10	57053	broad.mit.edu	37	11	3687702	3687702	+	Missense_Mutation	SNP	G	A	A	rs147793274	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3687702G>A	uc001lyf.2	-	5	1060	c.988C>T	c.(988-990)CGC>TGC	p.R330C	CHRNA10_uc010qxt.1_Missense_Mutation_p.R124C|CHRNA10_uc010qxu.1_Missense_Mutation_p.R124C	NM_020402	NP_065135	Q9GZZ6	ACH10_HUMAN	cholinergic receptor, nicotinic, alpha 10	330	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|regulation of cell proliferation|synaptic transmission, cholinergic	cell junction|postsynaptic membrane	calcium channel activity|receptor activity|receptor binding			ovary(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577)		BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192)	Chloroprocaine(DB01161)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Procaine(DB00721)|Trimethaphan(DB01116)													---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3744527	3744527	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3744527T>C	uc001lyh.2	-	16	2297	c.2006A>G	c.(2005-2007)GAT>GGT	p.D669G	NUP98_uc001lyi.2_Missense_Mutation_p.D669G|NUP98_uc001lyj.1_Missense_Mutation_p.D669G|NUP98_uc001lyk.1_Missense_Mutation_p.D686G	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	686					carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)				T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								---	---	---	---
PGAP2	27315	broad.mit.edu	37	11	3845180	3845180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3845180G>A	uc001lys.2	+	4	542	c.416G>A	c.(415-417)CGT>CAT	p.R139H	PGAP2_uc001lyl.2_Missense_Mutation_p.R96H|PGAP2_uc010qxw.1_Missense_Mutation_p.R196H|PGAP2_uc010qxx.1_Silent_p.A119A|PGAP2_uc001lyp.3_Intron|PGAP2_uc010qxy.1_Missense_Mutation_p.R135H|PGAP2_uc010qxz.1_Missense_Mutation_p.R135H|PGAP2_uc001lyn.3_Silent_p.A31A|PGAP2_uc010qya.1_RNA|PGAP2_uc001lyr.2_Missense_Mutation_p.R78H|PGAP2_uc010qyb.1_Silent_p.A81A|PGAP2_uc001lyt.2_5'UTR	NM_014489	NP_055304	Q9UHJ9	PGAP2_HUMAN	FGF receptor activating protein 1 isoform 1	139					GPI anchor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein transporter activity				0																		---	---	---	---
OR52K2	119774	broad.mit.edu	37	11	4470665	4470665	+	Silent	SNP	T	C	C	rs146883984		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4470665T>C	uc001lyz.1	+	1	96	c.96T>C	c.(94-96)CCT>CCC	p.P32P		NM_001005172	NP_001005172	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K,	32	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.P32P(1)		skin(2)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR52K2	119774	broad.mit.edu	37	11	4470698	4470698	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4470698A>C	uc001lyz.1	+	1	129	c.129A>C	c.(127-129)GGA>GGC	p.G43G		NM_001005172	NP_001005172	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K,	43	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.G43E(1)		skin(2)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR52E8	390079	broad.mit.edu	37	11	5878374	5878374	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5878374G>A	uc010qzr.1	-	1	559	c.559C>T	c.(559-561)CAC>TAC	p.H187Y	TRIM5_uc001mbq.1_Intron	NM_001005168	NP_001005168	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E,	187	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR52L1	338751	broad.mit.edu	37	11	6007283	6007283	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6007283A>T	uc001mcd.2	-	1	933	c.878T>A	c.(877-879)CTT>CAT	p.L293H		NM_001005173	NP_001005173	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L,	293	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR52L1	338751	broad.mit.edu	37	11	6007474	6007474	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6007474A>G	uc001mcd.2	-	1	742	c.687T>C	c.(685-687)GTT>GTC	p.V229V		NM_001005173	NP_001005173	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L,	229	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
CNGA4	1262	broad.mit.edu	37	11	6265475	6265475	+	Missense_Mutation	SNP	G	A	A	rs149747380		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6265475G>A	uc001mco.2	+	6	1671	c.1564G>A	c.(1564-1566)GCA>ACA	p.A522T	CNGA4_uc010raa.1_3'UTR|CNGA4_uc001mcn.2_3'UTR	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	522	Cytoplasmic (Potential).				response to stimulus|sensory perception of smell		cAMP binding			skin(1)	1		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6645998	6645998	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6645998A>C	uc001mem.1	-	20	7658	c.7248T>G	c.(7246-7248)GCT>GCG	p.A2416A		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	2416	Cadherin 23.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6655431	6655431	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6655431C>A	uc001mem.1	-	3	2314	c.1904G>T	c.(1903-1905)AGC>ATC	p.S635I		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	635	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7324420	7324420	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7324420T>G	uc001mfe.2	+	2	533	c.296T>G	c.(295-297)CTT>CGT	p.L99R	SYT9_uc001mfd.2_RNA|SYT9_uc009yfi.2_RNA	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX	99	Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	9983568	9983568	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9983568T>G	uc001mib.2	-	16	1934	c.1796A>C	c.(1795-1797)AAC>ACC	p.N599T	SBF2_uc001mif.3_Missense_Mutation_p.N355T|SBF2_uc001mih.3_Missense_Mutation_p.N128T	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2	599					myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10022471	10022471	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10022471A>T	uc001mib.2	-	8	989	c.851T>A	c.(850-852)GTC>GAC	p.V284D	SBF2_uc001mif.3_Missense_Mutation_p.V40D	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2	284	DENN.				myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
GALNTL4	374378	broad.mit.edu	37	11	11354360	11354360	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11354360C>A	uc001mjo.2	-	8	1718	c.1297G>T	c.(1297-1299)GGG>TGG	p.G433W		NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	433	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)														---	---	---	---
USP47	55031	broad.mit.edu	37	11	11926990	11926990	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11926990C>T	uc001mjq.1	+	9	1687	c.924C>T	c.(922-924)TAC>TAT	p.Y308Y	USP47_uc001mjr.2_Silent_p.Y220Y|USP47_uc001mjs.2_Silent_p.Y288Y	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	308					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
USP47	55031	broad.mit.edu	37	11	11977643	11977643	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11977643T>C	uc001mjs.2	+	28	4752	c.3989T>C	c.(3988-3990)GTA>GCA	p.V1330A	USP47_uc001mjr.2_Missense_Mutation_p.V1262A|USP47_uc009ygi.2_Missense_Mutation_p.V132A	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	1350					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
C11orf58	10944	broad.mit.edu	37	11	16769659	16769659	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16769659C>T	uc001mmk.2	+	3	341	c.163C>T	c.(163-165)CGT>TGT	p.R55C	C11orf58_uc010rct.1_Missense_Mutation_p.R11C	NM_014267	NP_055082	O00193	SMAP_HUMAN	small acidic protein isoform a	55											0																		---	---	---	---
GTF2H1	2965	broad.mit.edu	37	11	18369452	18369452	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18369452C>T	uc001moi.2	+	10	1733	c.1039C>T	c.(1039-1041)CCA>TCA	p.P347S	GTF2H1_uc001moh.2_Missense_Mutation_p.P347S|GTF2H1_uc009yhm.2_Missense_Mutation_p.P231S|GTF2H1_uc001moj.2_Missense_Mutation_p.P35S	NM_001142307	NP_001135779	P32780	TF2H1_HUMAN	general transcription factor IIH, polypeptide 1,	347					mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	protein binding				0													NER					---	---	---	---
SPTY2D1	144108	broad.mit.edu	37	11	18637193	18637193	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18637193G>A	uc001moy.2	-	3	844	c.628C>T	c.(628-630)CGA>TGA	p.R210*	SPTY2D1_uc010rdi.1_Nonsense_Mutation_p.R210*	NM_194285	NP_919261	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1	210										breast(1)	1																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19955098	19955098	+	Silent	SNP	C	T	T	rs113762718		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19955098C>T	uc010rdm.1	+	8	1738	c.1377C>T	c.(1375-1377)TTC>TTT	p.F459F	NAV2_uc001mpp.2_Silent_p.F372F|NAV2_uc001mpr.3_Silent_p.F436F	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	459						nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
PRMT3	10196	broad.mit.edu	37	11	20424486	20424486	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20424486T>C	uc001mqb.2	+	8	944	c.727T>C	c.(727-729)TAC>CAC	p.Y243H	PRMT3_uc001mqc.2_Missense_Mutation_p.Y166H|PRMT3_uc010rdn.1_Missense_Mutation_p.Y181H	NM_005788	NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3 isoform 1	243							zinc ion binding				0																		---	---	---	---
ANO5	203859	broad.mit.edu	37	11	22296189	22296189	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22296189A>G	uc001mqi.2	+	20	2627	c.2310A>G	c.(2308-2310)ACA>ACG	p.T770T	ANO5_uc001mqj.2_Silent_p.T769T	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	770	Extracellular (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32635417	32635417	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32635417T>A	uc001mtv.2	-	16	2491	c.2447A>T	c.(2446-2448)AAT>ATT	p.N816I		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	816										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
QSER1	79832	broad.mit.edu	37	11	32953933	32953933	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32953933G>T	uc001mty.2	+	4	1009	c.742G>T	c.(742-744)GGA>TGA	p.G248*	QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_5'Flank	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	248	Ser-rich.									ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)																	---	---	---	---
DEPDC7	91614	broad.mit.edu	37	11	33050184	33050184	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33050184C>T	uc001mub.2	+	4	720	c.628C>T	c.(628-630)CGT>TGT	p.R210C	DEPDC7_uc001muc.2_Missense_Mutation_p.R201C	NM_001077242	NP_001070710	Q96QD5	DEPD7_HUMAN	novel 58.3 KDA protein isoform 1	210					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|skin(1)	2																		---	---	---	---
NAT10	55226	broad.mit.edu	37	11	34145925	34145925	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34145925G>A	uc001mvk.2	+	11	1329	c.1085G>A	c.(1084-1086)CGA>CAA	p.R362Q	NAT10_uc010ren.1_Missense_Mutation_p.R290Q	NM_024662	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 isoform a	362						nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)																---	---	---	---
ABTB2	25841	broad.mit.edu	37	11	34181842	34181842	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34181842G>T	uc001mvl.1	-	12	2128	c.1898C>A	c.(1897-1899)CCC>CAC	p.P633H		NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing	633							DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)																---	---	---	---
SLC1A2	6506	broad.mit.edu	37	11	35333945	35333945	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35333945T>C	uc001mwd.2	-	4	953	c.361A>G	c.(361-363)ATG>GTG	p.M121V	SLC1A2_uc001mwe.2_Missense_Mutation_p.M112V|SLC1A2_uc010rev.1_Missense_Mutation_p.M121V	NM_004171	NP_004162	P43004	EAA2_HUMAN	excitatory amino acid transporter 2	121	Helical; (Potential).				D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)													---	---	---	---
ACCSL	390110	broad.mit.edu	37	11	44074571	44074571	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44074571C>T	uc001mxw.1	+	7	957	c.901C>T	c.(901-903)CTC>TTC	p.L301F	ACCSL_uc009ykr.2_Missense_Mutation_p.L120F	NM_001031854	NP_001027025	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase	301							1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(5)	5																		---	---	---	---
CD82	3732	broad.mit.edu	37	11	44626950	44626950	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44626950G>A	uc001myc.2	+	6	555	c.307G>A	c.(307-309)GGG>AGG	p.G103R	CD82_uc001myd.2_Intron	NM_002231	NP_002222	P27701	CD82_HUMAN	CD82 antigen isoform 1	103	Helical; (Potential).					integral to plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45671304	45671304	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45671304C>T	uc001mys.1	-	4	1841	c.1170G>A	c.(1168-1170)TCG>TCA	p.S390S		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	390	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			skin(4)|pancreas(1)	5				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)														---	---	---	---
CREB3L1	90993	broad.mit.edu	37	11	46334005	46334005	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46334005C>T	uc001ncf.2	+	6	1318	c.883C>T	c.(883-885)CGG>TGG	p.R295W		NM_052854	NP_443086	Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like	295	Cytoplasmic (Potential).|Basic motif.				response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L1(6)	soft_tissue(6)|ovary(2)	8				GBM - Glioblastoma multiforme(35;0.0285)				T	FUS	myxofibrosarcoma								---	---	---	---
CHRM4	1132	broad.mit.edu	37	11	46407256	46407256	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46407256C>T	uc001nct.1	-	1	852	c.852G>A	c.(850-852)CCG>CCA	p.P284P		NM_000741	NP_000732	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	284	Cytoplasmic (By similarity).				cell proliferation	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity				0				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)|Tropicamide(DB00809)													---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46419427	46419427	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46419427T>C	uc010rgu.1	-	18	3830	c.3470A>G	c.(3469-3471)GAG>GGG	p.E1157G	AMBRA1_uc010rgt.1_3'UTR|AMBRA1_uc009ylc.1_Missense_Mutation_p.E1128G|AMBRA1_uc001ncu.1_Missense_Mutation_p.E1067G|AMBRA1_uc001ncv.2_Missense_Mutation_p.E1160G|AMBRA1_uc001ncw.2_Missense_Mutation_p.E1038G|AMBRA1_uc001ncx.2_Missense_Mutation_p.E1097G	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	1157					autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
ARHGAP1	392	broad.mit.edu	37	11	46702288	46702288	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46702288G>A	uc001ndd.2	-	8	714	c.645C>T	c.(643-645)GAC>GAT	p.D215D		NM_004308	NP_004299	Q07960	RHG01_HUMAN	Rho GTPase activating protein 1	215	CRAL-TRIO.				Rho protein signal transduction	cytosol|intracellular membrane-bounded organelle	SH3 domain binding|SH3/SH2 adaptor activity			skin(1)	1		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)														---	---	---	---
MADD	8567	broad.mit.edu	37	11	47336824	47336824	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47336824G>T	uc001ner.1	+	30	4514	c.4323G>T	c.(4321-4323)CAG>CAT	p.Q1441H	MADD_uc001neq.2_Missense_Mutation_p.Q1382H|MADD_uc001nev.1_Missense_Mutation_p.Q1339H|MADD_uc001nes.1_Missense_Mutation_p.Q1359H|MADD_uc001net.1_Missense_Mutation_p.Q1402H|MADD_uc009yln.1_Missense_Mutation_p.Q1335H|MADD_uc001neu.1_Missense_Mutation_p.Q1339H|MADD_uc001nex.2_Missense_Mutation_p.Q1441H|MADD_uc001nez.2_Missense_Mutation_p.Q1338H|MADD_uc001new.2_Missense_Mutation_p.Q1381H|MADD_uc009ylo.2_Missense_Mutation_p.Q355H	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	1441					activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)														---	---	---	---
PSMC3	5702	broad.mit.edu	37	11	47441881	47441881	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47441881A>G	uc001nfh.2	-	10	1255	c.1061T>C	c.(1060-1062)TTC>TCC	p.F354S	PSMC3_uc009ylr.1_Missense_Mutation_p.F312S	NM_002804	NP_002795	P17980	PRS6A_HUMAN	proteasome 26S ATPase subunit 3	354					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|interspecies interaction between organisms|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|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|nucleoside-triphosphatase activity|protein binding|transcription coactivator activity|transcription corepressor activity			ovary(4)	4				Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
AGBL2	79841	broad.mit.edu	37	11	47711972	47711972	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47711972T>C	uc001ngg.2	-	9	1387	c.1287A>G	c.(1285-1287)CTA>CTG	p.L429L	AGBL2_uc001ngf.2_RNA|AGBL2_uc010rhq.1_Silent_p.L391L|AGBL2_uc001ngh.1_Silent_p.L373L	NM_024783	NP_079059	Q5U5Z8	CBPC2_HUMAN	carboxypeptidase 2, cytosolic	429					proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
OR4A5	81318	broad.mit.edu	37	11	51412117	51412117	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51412117T>C	uc001nhi.1	-	1	279	c.279A>G	c.(277-279)CAA>CAG	p.Q93Q		NM_001005272	NP_001005272	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A,	93	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(304;0.236)																---	---	---	---
OR5L1	219437	broad.mit.edu	37	11	55579099	55579099	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55579099T>C	uc001nhw.1	+	1	157	c.157T>C	c.(157-159)TCT>CCT	p.S53P		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	53	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)																---	---	---	---
DTX4	23220	broad.mit.edu	37	11	58956242	58956242	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58956242T>G	uc001nns.2	+	3	1227	c.970T>G	c.(970-972)TCC>GCC	p.S324A	DTX4_uc001nnr.2_Missense_Mutation_p.S218A	NM_015177	NP_055992	Q9Y2E6	DTX4_HUMAN	deltex 4 homolog	324					Notch signaling pathway	cytoplasm	zinc ion binding			lung(2)|central_nervous_system(1)	3		all_epithelial(135;0.125)																---	---	---	---
TMEM132A	54972	broad.mit.edu	37	11	60696229	60696229	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60696229C>T	uc001nqj.2	+	4	856	c.663C>T	c.(661-663)TCC>TCT	p.S221S	TMEM132A_uc001nqi.2_Silent_p.S221S|TMEM132A_uc001nqk.2_Silent_p.S234S|TMEM132A_uc001nql.1_Silent_p.S234S	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	221	Extracellular (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1																		---	---	---	---
CD5	921	broad.mit.edu	37	11	60889125	60889125	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60889125G>A	uc009ynk.2	+	6	951	c.848G>A	c.(847-849)AGC>AAC	p.S283N		NM_014207	NP_055022	P06127	CD5_HUMAN	CD5 molecule precursor	283	Extracellular (Potential).|SRCR 3.				cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)														---	---	---	---
DAGLA	747	broad.mit.edu	37	11	61511463	61511463	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61511463C>T	uc001nsa.2	+	20	2742	c.2631C>T	c.(2629-2631)GAC>GAT	p.D877D		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	877	Cytoplasmic (Potential).				cell death|lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3				READ - Rectum adenocarcinoma(4;0.219)														---	---	---	---
RAB3IL1	5866	broad.mit.edu	37	11	61675603	61675603	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61675603G>A	uc001nso.2	-	2	345	c.187C>T	c.(187-189)CGC>TGC	p.R63C	RAB3IL1_uc001nsp.2_Missense_Mutation_p.R110C	NM_013401	NP_037533	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	63							protein binding			skin(2)|central_nervous_system(1)	3																		---	---	---	---
EML3	256364	broad.mit.edu	37	11	62375291	62375291	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62375291A>G	uc001ntu.1	-	11	1517	c.1209T>C	c.(1207-1209)AGT>AGC	p.S403S	EML3_uc001ntr.1_Silent_p.S375S|EML3_uc001nts.1_Silent_p.S375S|EML3_uc001ntt.1_Silent_p.S287S|EML3_uc010rly.1_Silent_p.S403S|EML3_uc009yny.1_Silent_p.S186S	NM_153265	NP_694997	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like	403	WD 3.					cytoplasm|microtubule	protein binding			ovary(1)	1																		---	---	---	---
SNHG1	23642	broad.mit.edu	37	11	62620803	62620803	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62620803T>C	uc001nvp.2	-						SLC3A2_uc001nwb.2_5'Flank|SLC3A2_uc001nwc.2_5'Flank|SLC3A2_uc001nwd.2_5'Flank|SLC3A2_uc001nwe.2_5'Flank|SLC3A2_uc001nwf.2_5'Flank|SNHG1_uc001nvo.2_Intron|SNHG1_uc001nvq.2_Intron|SNHG1_uc001nvs.2_Intron|SNHG1_uc001nvr.2_Intron|SNHG1_uc001nvt.2_RNA|SNHG1_uc001nvu.2_Intron|SNORD22_uc001nvv.2_5'Flank|SNORD31_uc009yoj.1_RNA					Homo sapiens cDNA FLJ38530 fis, clone HCHON2001039.												0																		---	---	---	---
PRDX5	25824	broad.mit.edu	37	11	64088156	64088156	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64088156G>A	uc001nzu.2	+	3	449	c.330G>A	c.(328-330)GAG>GAA	p.E110E	PRDX5_uc001nzv.2_Intron|PRDX5_uc001nzw.2_Intron|PRDX5_uc001nzx.2_RNA	NM_012094	NP_036226	P30044	PRDX5_HUMAN	peroxiredoxin 5 isoform a precursor	110	Thioredoxin.				cell redox homeostasis|cellular response to reactive oxygen species|inflammatory response|negative regulation of apoptosis	cytosolic part|mitochondrion|peroxisome	caspase inhibitor activity|peroxidase activity|peroxiredoxin activity			breast(1)	1					Auranofin(DB00995)													---	---	---	---
CCDC88B	283234	broad.mit.edu	37	11	64108903	64108903	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64108903G>A	uc001nzy.2	+	6	502	c.458G>A	c.(457-459)CGG>CAG	p.R153Q	CCDC88B_uc009ypo.1_Missense_Mutation_p.R150Q|CCDC88B_uc001nzz.1_5'Flank	NM_032251	NP_115627	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88	153					microtubule cytoskeleton organization	cytoplasm	microtubule binding			ovary(3)|skin(1)	4																		---	---	---	---
RASGRP2	10235	broad.mit.edu	37	11	64502579	64502579	+	Intron	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64502579C>A	uc009ypu.2	-						RASGRP2_uc001oat.2_Intron|RASGRP2_uc001oau.2_Intron|RASGRP2_uc009ypv.2_Intron|RASGRP2_uc009ypw.2_Intron	NM_001098671	NP_001092141			RAS guanyl releasing protein 2						platelet activation|Ras protein signal transduction|regulation of cell growth|regulation of small GTPase mediated signal transduction	cell junction|cytosol|ruffle membrane|synapse|synaptosome	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity				0																		---	---	---	---
ATG2A	23130	broad.mit.edu	37	11	64678326	64678326	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64678326G>A	uc001obx.2	-	11	1682	c.1567C>T	c.(1567-1569)CTG>TTG	p.L523L		NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	523							protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SLC22A20	440044	broad.mit.edu	37	11	65000689	65000689	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65000689T>C	uc010roc.1	+	8	1115	c.1112T>C	c.(1111-1113)CTG>CCG	p.L371P		NM_001004326	NP_001004326	A6NK97	S22AK_HUMAN	solute carrier family 22, member 20	371	Extracellular (Potential).				ion transport	integral to membrane	transmembrane transporter activity			central_nervous_system(1)	1																		---	---	---	---
KDM2A	22992	broad.mit.edu	37	11	67010480	67010480	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67010480A>G	uc001ojw.2	+	13	2344	c.1480A>G	c.(1480-1482)ATT>GTT	p.I494V	KDM2A_uc001ojx.2_RNA|KDM2A_uc001ojy.2_Missense_Mutation_p.I188V|KDM2A_uc010rpn.1_Missense_Mutation_p.I55V|KDM2A_uc001ojz.1_5'Flank	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11	494					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	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|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
ANKRD13D	338692	broad.mit.edu	37	11	67068551	67068551	+	Silent	SNP	C	T	T	rs148986056	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67068551C>T	uc001okc.1	+	12	1414	c.903C>T	c.(901-903)AAC>AAT	p.N301N	ANKRD13D_uc001okd.1_Silent_p.N388N|ANKRD13D_uc001oke.1_Silent_p.N301N|ANKRD13D_uc001okg.1_Silent_p.N84N|ANKRD13D_uc001okh.1_Silent_p.N84N|ANKRD13D_uc001oki.1_Silent_p.N38N|SSH3_uc001okj.2_5'Flank|SSH3_uc001okk.2_5'Flank|SSH3_uc001okl.2_5'Flank	NM_207354	NP_997237	Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	301										ovary(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)															---	---	---	---
CARNS1	57571	broad.mit.edu	37	11	67190978	67190978	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67190978G>A	uc009yrp.2	+	9	1842	c.1390G>A	c.(1390-1392)GGC>AGC	p.G464S	PPP1CA_uc001okx.1_5'Flank|CARNS1_uc001olc.3_Missense_Mutation_p.G603S	NM_020811	NP_065862	A5YM72	CRNS1_HUMAN	ATP-grasp domain containing 1	464					carnosine biosynthetic process		ATP binding|carnosine synthase activity|metal ion binding				0																		---	---	---	---
TBX10	347853	broad.mit.edu	37	11	67399140	67399140	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67399140G>A	uc001omp.2	-	8	1182	c.1094C>T	c.(1093-1095)CCA>CTA	p.P365L	NUDT8_uc001omn.2_5'Flank|NUDT8_uc001omo.1_5'Flank	NM_005995	NP_005986	O75333	TBX10_HUMAN	T-box 10	365					anatomical structure morphogenesis|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
SAPS3	55291	broad.mit.edu	37	11	68370949	68370949	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68370949G>A	uc001onw.2	+	22	2706	c.2439G>A	c.(2437-2439)GCG>GCA	p.A813A	SAPS3_uc001onv.2_Silent_p.A813A|SAPS3_uc001ony.3_Silent_p.A784A|SAPS3_uc001onx.2_Silent_p.A807A|SAPS3_uc009ysh.2_Silent_p.A733A|SAPS3_uc001onu.2_Silent_p.A733A|SAPS3_uc010rqc.1_Silent_p.A581A|SAPS3_uc010rqd.1_Silent_p.A496A|SAPS3_uc001onz.2_Silent_p.A141A|SAPS3_uc001ooa.2_Silent_p.A263A	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6	813					regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)															---	---	---	---
P2RY6	5031	broad.mit.edu	37	11	73008237	73008237	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73008237C>A	uc001otm.2	+	4	1079	c.674C>A	c.(673-675)CCG>CAG	p.P225Q	P2RY6_uc001otn.2_Missense_Mutation_p.P225Q|P2RY6_uc001oto.2_Missense_Mutation_p.P225Q|P2RY6_uc001otp.2_Missense_Mutation_p.P225Q|P2RY6_uc001otq.2_Missense_Mutation_p.P225Q|P2RY6_uc001otr.2_Missense_Mutation_p.P225Q|P2RY6_uc001ots.2_Missense_Mutation_p.P225Q	NM_176796	NP_789766	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y6	225	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1																		---	---	---	---
DNAJB13	374407	broad.mit.edu	37	11	73677268	73677268	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73677268G>A	uc001ouo.2	+	5	1329	c.578G>A	c.(577-579)CGC>CAC	p.R193H		NM_153614	NP_705842	P59910	DJB13_HUMAN	testis spermatogenesis apoptosis-related protein	193					apoptosis|protein folding|spermatogenesis		heat shock protein binding|unfolded protein binding				0	Breast(11;7.42e-05)																	---	---	---	---
SERPINH1	871	broad.mit.edu	37	11	75282937	75282937	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75282937G>A	uc001owr.2	+	5	1295	c.1066G>A	c.(1066-1068)GCC>ACC	p.A356T	SERPINH1_uc009yug.2_Missense_Mutation_p.A356T|SERPINH1_uc001ows.2_Missense_Mutation_p.A356T|SERPINH1_uc001owt.2_Missense_Mutation_p.A139T	NM_001235	NP_001226	P50454	SERPH_HUMAN	serine (or cysteine) proteinase inhibitor, clade	356					regulation of proteolysis|response to unfolded protein	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	collagen binding|serine-type endopeptidase inhibitor activity			ovary(2)	2	Ovarian(111;0.11)																	---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77378348	77378348	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77378348C>T	uc001oyn.2	-	16	4060	c.3940G>A	c.(3940-3942)GCT>ACT	p.A1314T	RSF1_uc001oym.2_Missense_Mutation_p.A1062T	NM_016578	NP_057662	Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1314					CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77394826	77394826	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77394826T>C	uc001oyn.2	-	11	3114	c.2994A>G	c.(2992-2994)AAA>AAG	p.K998K	RSF1_uc001oym.2_Silent_p.K746K	NM_016578	NP_057662	Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	998	Potential.				CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77639378	77639378	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77639378A>G	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron	NM_033547	NP_291025			integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)															---	---	---	---
FAM181B	220382	broad.mit.edu	37	11	82444597	82444597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82444597C>T	uc001ozp.2	-	1	310	c.175G>A	c.(175-177)GTG>ATG	p.V59M		NM_175885	NP_787081	A6NEQ2	F181B_HUMAN	hypothetical protein LOC220382	59										large_intestine(1)	1																		---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83770417	83770417	+	Missense_Mutation	SNP	C	T	T	rs150156552		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83770417C>T	uc001paj.2	-	6	848	c.545G>A	c.(544-546)CGT>CAT	p.R182H	DLG2_uc001pai.2_Missense_Mutation_p.R131H|DLG2_uc010rsy.1_Missense_Mutation_p.R149H|DLG2_uc010rsz.1_Missense_Mutation_p.R182H|DLG2_uc010rta.1_Missense_Mutation_p.R182H|DLG2_uc001pak.2_Missense_Mutation_p.R287H|DLG2_uc010rtb.1_Missense_Mutation_p.R149H|DLG2_uc001pal.1_Missense_Mutation_p.R182H|DLG2_uc001pam.1_Missense_Mutation_p.R221H	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2	182	PDZ 1.					cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
TMEM126A	84233	broad.mit.edu	37	11	85367435	85367435	+	Silent	SNP	T	C	C	rs11556796		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85367435T>C	uc001par.2	+	5	574	c.478T>C	c.(478-480)TTA>CTA	p.L160L		NM_032273	NP_115649	Q9H061	T126A_HUMAN	transmembrane protein 126A	160						integral to membrane|mitochondrion				ovary(2)	2		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)																---	---	---	---
CCDC89	220388	broad.mit.edu	37	11	85396776	85396776	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85396776T>G	uc001pau.1	-	1	545	c.398A>C	c.(397-399)CAC>CCC	p.H133P		NM_152723	NP_689936	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	133	Potential.					cytoplasm|nucleus					0		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)																---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85694973	85694973	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85694973G>T	uc001pbm.2	-	14	1738	c.1452C>A	c.(1450-1452)GGC>GGA	p.G484G	PICALM_uc001pbl.2_Silent_p.G434G|PICALM_uc001pbn.2_Silent_p.G477G|PICALM_uc010rtl.1_Silent_p.G383G|PICALM_uc001pbk.2_5'Flank|PICALM_uc010rtk.1_Silent_p.G66G|PICALM_uc001pbo.1_Silent_p.G116G	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly	484					clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)						T	MLLT10|MLL	TALL|AML|								---	---	---	---
FZD4	8322	broad.mit.edu	37	11	86663069	86663069	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86663069G>A	uc001pce.2	-	2	1035	c.729C>T	c.(727-729)ATC>ATT	p.I243I	PRSS23_uc001pcc.1_RNA	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4 precursor	243	Helical; Name=1; (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
CTSC	1075	broad.mit.edu	37	11	88068203	88068203	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88068203C>T	uc001pck.3	-	2	321	c.220G>A	c.(220-222)GCA>ACA	p.A74T	CTSC_uc001pcl.3_5'UTR|CTSC_uc001pcm.3_Missense_Mutation_p.A74T|CTSC_uc001pcn.3_Missense_Mutation_p.A74T	NM_001814	NP_001805	P53634	CATC_HUMAN	cathepsin C isoform a preproprotein	74			Missing (in PLS).		immune response	lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88258487	88258487	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88258487T>G	uc001pcq.2	-	8	2916	c.2716A>C	c.(2716-2718)ACA>CCA	p.T906P	GRM5_uc009yvm.2_Intron	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	906	Cytoplasmic (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89173856	89173856	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89173856C>A	uc001pct.2	-	6	714	c.475G>T	c.(475-477)GTT>TTT	p.V159F	NOX4_uc009yvr.2_Missense_Mutation_p.V134F|NOX4_uc001pcu.2_Missense_Mutation_p.V85F|NOX4_uc001pcw.2_Intron|NOX4_uc001pcx.2_Intron|NOX4_uc001pcv.2_Missense_Mutation_p.V159F|NOX4_uc009yvo.2_RNA|NOX4_uc010rtu.1_Intron|NOX4_uc009yvp.2_Missense_Mutation_p.V159F|NOX4_uc010rtv.1_Missense_Mutation_p.V135F|NOX4_uc009yvq.2_Missense_Mutation_p.V135F|NOX4_uc009yvs.1_RNA	NM_016931	NP_058627	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform a	159	Ferric oxidoreductase.|Helical; (Potential).				cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)																---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92577541	92577541	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92577541C>T	uc001pdj.3	+	18	11025	c.11008C>T	c.(11008-11010)CGG>TGG	p.R3670W	FAT3_uc001pdi.3_Missense_Mutation_p.R110W	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	3670	Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
GPR83	10888	broad.mit.edu	37	11	94113477	94113477	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94113477C>T	uc001pet.2	-	4	1282	c.1110G>A	c.(1108-1110)CAG>CAA	p.Q370Q		NM_016540	NP_057624	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83 precursor	370	Cytoplasmic (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			central_nervous_system(2)|ovary(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
JRKL	8690	broad.mit.edu	37	11	96124882	96124882	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96124882T>C	uc009ywu.2	+	2	1321	c.1069T>C	c.(1069-1071)TGG>CGG	p.W357R	CCDC82_uc001pfx.3_5'Flank|CCDC82_uc009ywr.2_5'Flank|CCDC82_uc009ywt.1_5'Flank|JRKL_uc001pfy.2_Missense_Mutation_p.W357R	NM_003772	NP_003763	Q9Y4A0	JERKL_HUMAN	jerky homolog-like	357	DDE.				central nervous system development|regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)		BRCA - Breast invasive adenocarcinoma(274;0.148)														---	---	---	---
PGR	5241	broad.mit.edu	37	11	100996890	100996890	+	Splice_Site	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100996890C>T	uc001pgh.2	-	2	2381	c.1638_splice	c.e2-1	p.R546_splice	PGR_uc001pgi.2_Splice_Site_p.R546_splice|PGR_uc009yww.1_Splice_Site|PGR_uc001pgj.2_Splice_Site|PGR_uc009ywx.1_Splice_Site|uc010rum.1_5'Flank	NM_000926	NP_000917			progesterone receptor						cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)													---	---	---	---
TRPC6	7225	broad.mit.edu	37	11	101362460	101362460	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101362460T>G	uc001pgk.3	-	3	1380	c.955A>C	c.(955-957)AAA>CAA	p.K319Q	TRPC6_uc009ywy.2_Intron|TRPC6_uc009ywz.1_Missense_Mutation_p.K319Q	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	319	Cytoplasmic (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)														---	---	---	---
BIRC3	330	broad.mit.edu	37	11	102196012	102196012	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102196012C>T	uc001pgx.2	+	3	994	c.772C>T	c.(772-774)CGC>TGC	p.R258C		NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3	258	BIR 3.				anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)				T	MALT1	MALT								---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103070064	103070064	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103070064T>C	uc001pho.2	+	49	8091	c.7947T>C	c.(7945-7947)GGT>GGC	p.G2649G	DYNC2H1_uc001phn.1_Silent_p.G2649G|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2649	AAA 4 (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DDI1	414301	broad.mit.edu	37	11	103908639	103908639	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103908639G>T	uc001phr.2	+	1	1332	c.1089G>T	c.(1087-1089)GAG>GAT	p.E363D	PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	363					proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|upper_aerodigestive_tract(1)|pancreas(1)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)														---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105732740	105732740	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105732740T>C	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc001piv.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820			glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
ALKBH8	91801	broad.mit.edu	37	11	107427686	107427686	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107427686C>T	uc010rvr.1	-	3	248	c.173G>A	c.(172-174)CGG>CAG	p.R58Q	ALKBH8_uc010rvq.1_5'UTR|ALKBH8_uc009yxp.2_Missense_Mutation_p.R58Q|ALKBH8_uc001pjl.2_RNA	NM_138775	NP_620130	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8	58	RRM.				response to DNA damage stimulus	cytosol|nucleus	metal ion binding|nucleotide binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|protein binding|RNA binding|tRNA (uracil) methyltransferase activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)														---	---	---	---
C11orf65	160140	broad.mit.edu	37	11	108277568	108277568	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108277568A>G	uc001pkh.2	-	5	421	c.351T>C	c.(349-351)AAT>AAC	p.N117N	C11orf65_uc010rvx.1_Silent_p.N68N|C11orf65_uc009yxu.1_RNA	NM_152587	NP_689800	Q8NCR3	CK065_HUMAN	hypothetical protein LOC160140	117										ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)														---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108383615	108383615	+	Silent	SNP	C	T	T	rs114840330	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108383615C>T	uc001pkk.2	-	6	2730	c.2619G>A	c.(2617-2619)TCG>TCA	p.S873S	EXPH5_uc010rvy.1_Silent_p.S685S|EXPH5_uc010rvz.1_Silent_p.S717S|EXPH5_uc010rwa.1_Silent_p.S797S	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	873					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
FDXACB1	91893	broad.mit.edu	37	11	111747699	111747699	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111747699G>A	uc001pmc.3	-	3	663	c.366C>T	c.(364-366)CAC>CAT	p.H122H	ALG9_uc010rwo.1_Translation_Start_Site|FDXACB1_uc009yyi.2_Translation_Start_Site|C11orf1_uc001pmd.2_5'Flank	NM_138378	NP_612387	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain	122					phenylalanyl-tRNA aminoacylation|tRNA processing		ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0																		---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114112978	114112978	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114112978G>A	uc001pop.2	+	5	1807	c.1543G>A	c.(1543-1545)GTG>ATG	p.V515M	ZBTB16_uc001poq.2_Missense_Mutation_p.V515M	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein	515					apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
APOC3	345	broad.mit.edu	37	11	116701502	116701502	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116701502C>T	uc001ppt.1	+	3	115	c.69C>T	c.(67-69)GCC>GCT	p.A23A		NM_000040	NP_000031	P02656	APOC3_HUMAN	apolipoprotein C-III precursor	23					Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|chylomicron remnant clearance|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol import|negative regulation of fatty acid biosynthetic process|negative regulation of high-density lipoprotein particle clearance|negative regulation of lipoprotein lipase activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor-mediated endocytosis|negative regulation of triglyceride catabolic process|negative regulation of very-low-density lipoprotein particle clearance|negative regulation of very-low-density lipoprotein particle remodeling|phospholipid efflux|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle assembly	chylomicron|intermediate-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	high-density lipoprotein particle receptor binding|lipase inhibitor activity|phospholipid binding				0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)														---	---	---	---
PAFAH1B2	5049	broad.mit.edu	37	11	117030719	117030719	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117030719C>T	uc001pqe.1	+	3	253	c.151C>T	c.(151-153)CAG>TAG	p.Q51*	PAFAH1B2_uc009yzk.1_Nonsense_Mutation_p.Q51*|PAFAH1B2_uc009yzl.1_Nonsense_Mutation_p.Q51*|PAFAH1B2_uc009yzm.2_RNA|PAFAH1B2_uc009yzn.2_RNA|PAFAH1B2_uc009yzj.1_Intron	NM_002572	NP_002563	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase,	51					lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)				T	IGH@	MLCLS								---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117241945	117241945	+	Silent	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117241945A>T	uc001prc.2	+	9	1062	c.915A>T	c.(913-915)GGA>GGT	p.G305G	CEP164_uc001prb.2_Silent_p.G305G|CEP164_uc010rxk.1_Silent_p.G279G|CEP164_uc001prf.2_RNA|CEP164_uc009yzp.1_RNA	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	305					cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117391893	117391893	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117391893T>C	uc001prh.1	-	6	1347	c.1345A>G	c.(1345-1347)ACC>GCC	p.T449A	DSCAML1_uc001pri.1_Missense_Mutation_p.T253A	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	389	Extracellular (Potential).|Ig-like C2-type 4.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
AMICA1	120425	broad.mit.edu	37	11	118081424	118081424	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118081424C>T	uc001psk.2	-	4	376	c.202G>A	c.(202-204)GAA>AAA	p.E68K	AMICA1_uc001psh.2_Missense_Mutation_p.E29K|AMICA1_uc009yzw.1_RNA|AMICA1_uc001psi.2_Missense_Mutation_p.E58K|AMICA1_uc001psj.2_Missense_Mutation_p.E68K|AMICA1_uc010rxw.1_Missense_Mutation_p.E29K|AMICA1_uc010rxx.1_Missense_Mutation_p.E68K|AMICA1_uc001psl.1_Missense_Mutation_p.E24K	NM_001098526	NP_001091996	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen	68	Ig-like V-type 1.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)														---	---	---	---
MPZL3	196264	broad.mit.edu	37	11	118110974	118110974	+	Silent	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118110974A>T	uc001psm.2	-	2	194	c.192T>A	c.(190-192)CTT>CTA	p.L64L	MPZL3_uc010rxy.1_Silent_p.L52L|MPZL3_uc010rxz.1_RNA|MPZL3_uc009yzy.2_Intron	NM_198275	NP_938016	Q6UWV2	MPZL3_HUMAN	myelin protein zero-like 3 precursor	64	Ig-like V-type.				cell adhesion	integral to membrane					0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)														---	---	---	---
MLL	4297	broad.mit.edu	37	11	118374596	118374596	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118374596A>G	uc001pta.2	+	27	8003	c.7980A>G	c.(7978-7980)TCA>TCG	p.S2660S	MLL_uc001ptb.2_Silent_p.S2663S	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2660					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
TTC36	143941	broad.mit.edu	37	11	118399486	118399486	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118399486G>A	uc001ptg.1	+	2	287	c.287G>A	c.(286-288)CGA>CAA	p.R96Q	TTC36_uc010ryb.1_RNA|TTC36_uc010ryc.1_Missense_Mutation_p.R37Q|TMEM25_uc010ryd.1_5'Flank|TMEM25_uc001ptk.3_5'Flank|TMEM25_uc010rye.1_5'Flank|TMEM25_uc001pth.2_5'Flank|TMEM25_uc009zad.2_5'Flank|TMEM25_uc001pti.2_5'Flank|TMEM25_uc010ryf.1_5'Flank|TMEM25_uc001ptl.2_5'Flank|TMEM25_uc001ptm.2_5'Flank	NM_001080441	NP_001073910	A6NLP5	TTC36_HUMAN	tetratricopeptide repeat domain 36	96	TPR 2.						binding				0																		---	---	---	---
CBL	867	broad.mit.edu	37	11	119156153	119156153	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119156153T>C	uc001pwe.2	+	11	1956	c.1818T>C	c.(1816-1818)AGT>AGC	p.S606S		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	606	Pro-rich.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)										CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome				---	---	---	---
TECTA	7007	broad.mit.edu	37	11	120996337	120996337	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120996337C>T	uc010rzo.1	+	7	1530	c.1530C>T	c.(1528-1530)TGC>TGT	p.C510C		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	510	VWFD 1.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
TECTA	7007	broad.mit.edu	37	11	121037433	121037433	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121037433G>T	uc010rzo.1	+	17	5530	c.5530G>T	c.(5530-5532)GAT>TAT	p.D1844Y		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1844	ZP.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
TECTA	7007	broad.mit.edu	37	11	121038774	121038774	+	Silent	SNP	G	A	A	rs146930070		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121038774G>A	uc010rzo.1	+	18	5598	c.5598G>A	c.(5596-5598)ACG>ACA	p.T1866T		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1866	ZP.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
OR10G9	219870	broad.mit.edu	37	11	123894160	123894160	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123894160T>C	uc010sad.1	+	1	441	c.441T>C	c.(439-441)ACT>ACC	p.T147T		NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)														---	---	---	---
OR10G7	390265	broad.mit.edu	37	11	123909354	123909354	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123909354A>G	uc001pzq.1	-	1	355	c.355T>C	c.(355-357)TAT>CAT	p.Y119H		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	119	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)														---	---	---	---
VWA5A	4013	broad.mit.edu	37	11	124007961	124007961	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124007961T>C	uc001pzu.2	+	15	2074	c.1865T>C	c.(1864-1866)ATA>ACA	p.I622T	VWA5A_uc001pzt.2_Missense_Mutation_p.I622T	NM_001130142	NP_001123614	O00534	VMA5A_HUMAN	BCSC-1 isoform 1	622										upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
NFRKB	4798	broad.mit.edu	37	11	129745274	129745274	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129745274G>A	uc001qfi.2	-	18	2033	c.1832C>T	c.(1831-1833)GCA>GTA	p.A611V	NFRKB_uc001qfg.2_Missense_Mutation_p.A636V|NFRKB_uc001qfh.2_Missense_Mutation_p.A634V|NFRKB_uc010sbw.1_Missense_Mutation_p.A621V|NFRKB_uc009zcr.2_5'Flank	NM_001143835	NP_001137307	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	611					DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)														---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	420145	420145	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:420145G>A	uc001qif.1	-	21	3485	c.3122C>T	c.(3121-3123)CCG>CTG	p.P1041L	KDM5A_uc001qie.1_Missense_Mutation_p.P1041L|KDM5A_uc010sdn.1_Missense_Mutation_p.P1000L	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	1041					chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
CCDC77	84318	broad.mit.edu	37	12	521059	521059	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:521059A>G	uc001qig.2	+	4	365	c.185A>G	c.(184-186)TAT>TGT	p.Y62C	CCDC77_uc009zdk.2_Missense_Mutation_p.Y30C|CCDC77_uc010sdp.1_Missense_Mutation_p.Y30C|CCDC77_uc010sdq.1_Missense_Mutation_p.Y30C	NM_032358	NP_115734	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77 isoform a	62	Potential.					centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)															---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	662881	662881	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:662881G>T	uc001qii.1	+	14	1792	c.1792G>T	c.(1792-1794)GGC>TGC	p.G598C	B4GALNT3_uc001qij.1_Missense_Mutation_p.G501C|B4GALNT3_uc001qik.1_Missense_Mutation_p.G147C	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	598	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)															---	---	---	---
RAD52	5893	broad.mit.edu	37	12	1025529	1025529	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1025529C>T	uc001qis.1	-	9	960	c.846G>A	c.(844-846)CCG>CCA	p.P282P	RAD52_uc001qit.1_RNA|RAD52_uc010sdt.1_Silent_p.P205P|RAD52_uc001qiu.1_Silent_p.P282P|RAD52_uc001qiv.1_RNA|RAD52_uc001qiw.1_RNA|RAD52_uc010sdu.1_Missense_Mutation_p.V300I	NM_134424	NP_602296	P43351	RAD52_HUMAN	RAD52 homolog	282					DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)										Homologous_recombination					---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6709688	6709688	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6709688A>G	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron	NM_001273	NP_001264			chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
CDCA3	83461	broad.mit.edu	37	12	6954973	6954973	+	3'UTR	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6954973G>A	uc001qre.2	-	5					GNB3_uc001qrc.2_Intron|GNB3_uc001qrd.2_Intron|GNB3_uc009zfe.2_Intron|uc001qrf.1_RNA	NM_031299	NP_112589			cell division cycle associated 3						cell division|mitosis	cytosol					0																		---	---	---	---
USP5	8078	broad.mit.edu	37	12	6972488	6972488	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6972488A>G	uc001qri.3	+	15	1960	c.1901A>G	c.(1900-1902)TAT>TGT	p.Y634C	USP5_uc001qrh.3_Intron	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	634					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			lung(2)|breast(1)|skin(1)	4																		---	---	---	---
PTPN6	5777	broad.mit.edu	37	12	7064594	7064594	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7064594C>A	uc001qsb.2	+	6	935	c.693C>A	c.(691-693)AAC>AAA	p.N231K	PTPN6_uc001qsa.1_Missense_Mutation_p.N233K|PTPN6_uc010sfr.1_Missense_Mutation_p.N192K|PTPN6_uc009zfl.1_Missense_Mutation_p.N231K|PTPN6_uc010sfs.1_Missense_Mutation_p.N219K	NM_002831	NP_002822	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type	231					apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol|membrane|nucleus	protein binding|protein tyrosine phosphatase activity			breast(1)	1																		---	---	---	---
C1RL	51279	broad.mit.edu	37	12	7249730	7249730	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7249730G>A	uc001qsn.2	-	6	738	c.721C>T	c.(721-723)CAG>TAG	p.Q241*	C1RL_uc009zft.2_Silent_p.P256P	NM_016546	NP_057630	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	241					complement activation, classical pathway|innate immune response|proteolysis		serine-type endopeptidase activity			pancreas(1)	1																		---	---	---	---
GDF3	9573	broad.mit.edu	37	12	7848094	7848094	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7848094G>A	uc001qte.2	-	1	267	c.231C>T	c.(229-231)GGC>GGT	p.G77G		NM_020634	NP_065685	Q9NR23	GDF3_HUMAN	growth differentiation factor 3 precursor	77					eye development|growth|skeletal system development	extracellular space	cytokine activity|growth factor activity			skin(3)|ovary(1)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
CLEC4A	50856	broad.mit.edu	37	12	8290779	8290779	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8290779G>A	uc001qtz.1	+	6	857	c.610G>A	c.(610-612)GTT>ATT	p.V204I	CLEC4A_uc009zga.1_Missense_Mutation_p.V165I|CLEC4A_uc001qub.1_Missense_Mutation_p.V171I|CLEC4A_uc001quc.1_Missense_Mutation_p.V132I|CLEC4A_uc009zgb.1_3'UTR	NM_016184	NP_057268	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A isoform	204	Extracellular (Potential).|C-type lectin.				cell adhesion|cell surface receptor linked signaling pathway|innate immune response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0				Kidney(36;0.0915)														---	---	---	---
LOH12CR1	118426	broad.mit.edu	37	12	12514227	12514227	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12514227A>G	uc001ral.2	+	2	512	c.146A>G	c.(145-147)AAC>AGC	p.N49S	LOH12CR1_uc009zhu.2_Intron	NM_058169	NP_477517	Q969J3	L12R1_HUMAN	LOH1CR12	49										ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)														---	---	---	---
DUSP16	80824	broad.mit.edu	37	12	12673799	12673799	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12673799G>A	uc001rao.1	-						DUSP16_uc001ran.1_Intron	NM_030640	NP_085143			dual specificity phosphatase 16						inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)														---	---	---	---
H2AFJ	55766	broad.mit.edu	37	12	14927470	14927470	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14927470G>A	uc009zia.2	+	1	201	c.66G>A	c.(64-66)GCG>GCA	p.A22A	H2AFJ_uc001rch.3_RNA	NM_177925	NP_808760	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	22					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26568326	26568326	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26568326C>T	uc001rhg.2	-	51	7633	c.7216G>A	c.(7216-7218)GTC>ATC	p.V2406I	ITPR2_uc009zjg.1_Missense_Mutation_p.V557I	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	2406	Helical; (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
FGD4	121512	broad.mit.edu	37	12	32760948	32760948	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32760948C>T	uc001rkz.2	+	8	1528	c.1051C>T	c.(1051-1053)CGG>TGG	p.R351W	FGD4_uc001rlc.2_Missense_Mutation_p.R436W|FGD4_uc001rky.2_Missense_Mutation_p.R103W|FGD4_uc001rla.2_Missense_Mutation_p.R7W|FGD4_uc010ske.1_Missense_Mutation_p.R463W|FGD4_uc001rlb.1_RNA	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	351	DH.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)																	---	---	---	---
PKP2	5318	broad.mit.edu	37	12	33031126	33031126	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33031126C>T	uc001rlj.3	-	3	803	c.688G>A	c.(688-690)GTT>ATT	p.V230I	PKP2_uc001rlk.3_Missense_Mutation_p.V230I|PKP2_uc010skj.1_Missense_Mutation_p.V230I	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	230					cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40041751	40041751	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40041751T>G	uc001rmc.2	+	6	709	c.542T>G	c.(541-543)CTT>CGT	p.L181R	C12orf40_uc009zjv.1_RNA	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	181										ovary(6)	6																		---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41365252	41365252	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41365252T>C	uc001rmm.1	+						CNTN1_uc009zjy.1_Silent_p.G607G|CNTN1_uc001rmn.1_Intron|CNTN1_uc001rmo.2_Silent_p.G607G	NM_001843	NP_001834			contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
RAPGEF3	10411	broad.mit.edu	37	12	48134094	48134094	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48134094G>T	uc009zkp.2	-	21	2630	c.2190C>A	c.(2188-2190)ACC>ACA	p.T730T	uc001rpv.2_RNA|RAPGEF3_uc001rpw.2_Silent_p.T65T|RAPGEF3_uc001rpx.2_Silent_p.T187T|RAPGEF3_uc010sln.1_Silent_p.T227T|RAPGEF3_uc001rpy.2_RNA|RAPGEF3_uc009zkq.2_Silent_p.T730T|RAPGEF3_uc001rpz.3_Silent_p.T772T	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	730					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)														---	---	---	---
RAPGEF3	10411	broad.mit.edu	37	12	48144859	48144859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48144859C>T	uc009zkp.2	-	5	957	c.517G>A	c.(517-519)GCC>ACC	p.A173T	RAPGEF3_uc009zkq.2_Missense_Mutation_p.A173T|RAPGEF3_uc001rpz.3_Missense_Mutation_p.A215T|RAPGEF3_uc009zkr.2_Intron|RAPGEF3_uc009zks.2_Missense_Mutation_p.A227T|RAPGEF3_uc001rqb.3_Missense_Mutation_p.A215T	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	173					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)														---	---	---	---
COL2A1	1280	broad.mit.edu	37	12	48391986	48391986	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48391986T>C	uc001rqu.2	-	4	491	c.310_splice	c.e4-1	p.G104_splice	COL2A1_uc001rqv.2_Splice_Site_p.G35_splice	NM_001844	NP_001835			collagen, type II, alpha 1 isoform 1 precursor						axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)													---	---	---	---
ANP32D	23519	broad.mit.edu	37	12	48866788	48866788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48866788A>G	uc010slt.1	+	1	341	c.341A>G	c.(340-342)AAC>AGC	p.N114S		NM_012404	NP_036536	O95626	AN32D_HUMAN	acidic nuclear phosphoprotein 32D	114	LRR 5.									ovary(1)|central_nervous_system(1)	2																		---	---	---	---
OR8S1	341568	broad.mit.edu	37	12	48921860	48921860	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48921860C>T	uc010slu.1	+	2	1054	c.1054C>T	c.(1054-1056)CGC>TGC	p.R352C		NM_001005203	NP_001005203	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S,	352	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
DNAJC22	79962	broad.mit.edu	37	12	49742913	49742913	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49742913A>G	uc001rua.2	+	2	659	c.258A>G	c.(256-258)ATA>ATG	p.I86M	DNAJC22_uc001rub.2_Missense_Mutation_p.I86M	NM_024902	NP_079178	Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	86	Helical; (Potential).				protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
MCRS1	10445	broad.mit.edu	37	12	49954162	49954162	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49954162A>C	uc001ruk.1	-						MCRS1_uc001rui.1_Intron|MCRS1_uc001ruj.1_Intron|MCRS1_uc001rul.1_Intron|MCRS1_uc009zlj.1_Intron|MCRS1_uc001rum.1_Intron	NM_006337	NP_006328			microspherule protein 1 isoform 1						DNA recombination|DNA repair|protein modification process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|MLL1 complex|nucleolus	protein binding			large_intestine(1)	1																		---	---	---	---
NCKAP5L	57701	broad.mit.edu	37	12	50188924	50188924	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50188924C>T	uc009zlk.2	-	8	2921	c.2719G>A	c.(2719-2721)GCC>ACC	p.A907T	NCKAP5L_uc001rvc.3_Missense_Mutation_p.A111T|NCKAP5L_uc001rvb.2_Missense_Mutation_p.A500T	NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	903										central_nervous_system(1)	1																		---	---	---	---
NCKAP5L	57701	broad.mit.edu	37	12	50190190	50190190	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50190190G>A	uc009zlk.2	-	8	1655	c.1453C>T	c.(1453-1455)CGA>TGA	p.R485*	NCKAP5L_uc001rvc.3_5'Flank|NCKAP5L_uc001rvb.2_Nonsense_Mutation_p.R78*	NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	481	Pro-rich.									central_nervous_system(1)	1																		---	---	---	---
TFCP2	7024	broad.mit.edu	37	12	51492670	51492670	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51492670T>C	uc001rxw.2	-	13	1767	c.1308A>G	c.(1306-1308)ACA>ACG	p.T436T	TFCP2_uc001rxv.1_Silent_p.T436T|TFCP2_uc009zlx.1_Silent_p.T385T|TFCP2_uc001rxx.2_Silent_p.T358T|TFCP2_uc009zly.1_Silent_p.T338T	NM_005653	NP_005644	Q12800	TFCP2_HUMAN	transcription factor CP2	436					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
CELA1	1990	broad.mit.edu	37	12	51737527	51737527	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51737527T>C	uc001ryi.1	-							NM_001971	NP_001962			chymotrypsin-like elastase family, member 1						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			breast(1)	1																		---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51865289	51865289	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51865289G>A	uc001rys.1	+	14	2055	c.1877G>A	c.(1876-1878)AGC>AAC	p.S626N	SLC4A8_uc010sni.1_Missense_Mutation_p.S573N|SLC4A8_uc001rym.2_Missense_Mutation_p.S573N|SLC4A8_uc001ryn.2_Missense_Mutation_p.S573N|SLC4A8_uc001ryo.2_Missense_Mutation_p.S573N|SLC4A8_uc010snj.1_Missense_Mutation_p.S653N|SLC4A8_uc001ryq.3_Missense_Mutation_p.S626N|SLC4A8_uc001ryr.2_Missense_Mutation_p.S626N|SLC4A8_uc010snk.1_Missense_Mutation_p.S573N	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate	626	Extracellular (Potential).				bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)														---	---	---	---
KRT85	3891	broad.mit.edu	37	12	52758133	52758133	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52758133G>A	uc001sag.2	-	3	767	c.647C>T	c.(646-648)GCC>GTC	p.A216V		NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85	216	Rod.|Coil 1B.				epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT72	140807	broad.mit.edu	37	12	52981585	52981585	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52981585G>A	uc001sar.2	-	7	1226	c.1140C>T	c.(1138-1140)TGC>TGT	p.C380C	KRT72_uc001saq.2_Silent_p.C380C|KRT72_uc010sns.1_Silent_p.C338C|KRT72_uc010snt.1_Silent_p.C192C	NM_001146225	NP_001139697	Q14CN4	K2C72_HUMAN	keratin 72 isoform 1	380	Coil 2.|Rod.					keratin filament	structural molecule activity			ovary(5)|pancreas(1)	6				BRCA - Breast invasive adenocarcinoma(357;0.195)														---	---	---	---
KRT73	319101	broad.mit.edu	37	12	53009939	53009939	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53009939G>A	uc001sas.2	-							NM_175068	NP_778238			keratin 73							keratin filament	structural molecule activity			large_intestine(2)|ovary(2)|skin(2)	6				BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT2	3849	broad.mit.edu	37	12	53045454	53045454	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53045454C>T	uc001sat.2	-	1	506	c.473G>A	c.(472-474)AGC>AAC	p.S158N		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	158	Head.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)														---	---	---	---
CSAD	51380	broad.mit.edu	37	12	53554090	53554090	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53554090C>T	uc001sby.2	-	13	1106	c.980G>A	c.(979-981)CGC>CAC	p.R327H	CSAD_uc001sbw.2_Missense_Mutation_p.R180H|CSAD_uc009zmt.2_Missense_Mutation_p.R109H|CSAD_uc010snx.1_Missense_Mutation_p.R354H|CSAD_uc001sbz.2_Missense_Mutation_p.R327H|CSAD_uc009zmu.2_Missense_Mutation_p.R180H|CSAD_uc001sca.3_RNA	NM_015989	NP_057073	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	327					carboxylic acid metabolic process		pyridoxal phosphate binding|sulfinoalanine decarboxylase activity			ovary(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)									Hereditary_Prostate_Cancer				---	---	---	---
PFDN5	5204	broad.mit.edu	37	12	53691936	53691936	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53691936T>C	uc001scl.2	+	5	505	c.388_splice	c.e5+2	p.A130_splice	PFDN5_uc001scm.2_Splice_Site_p.A85_splice|PFDN5_uc001scn.2_Splice_Site|PFDN5_uc001sco.2_Splice_Site|C12orf10_uc010sof.1_5'Flank|C12orf10_uc001scp.3_5'Flank|C12orf10_uc009zmx.2_5'Flank|C12orf10_uc001scq.3_5'Flank	NM_002624	NP_002615			prefoldin subunit 5 isoform alpha						'de novo' posttranslational protein folding|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent	nucleus|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
AMHR2	269	broad.mit.edu	37	12	53825046	53825046	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53825046G>A	uc001scx.1	+	11	1589	c.1511G>A	c.(1510-1512)CGC>CAC	p.R504H	AMHR2_uc009zmy.1_3'UTR	NM_020547	NP_065434	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II isoform	504	Cytoplasmic (Potential).|Protein kinase.		R -> C (in PMDS2).		Mullerian duct regression		ATP binding|hormone binding|metal ion binding			ovary(1)|skin(1)	2					Adenosine triphosphate(DB00171)									Persistant_Mullerian_Duct_Syndrome_(type_I_and_II)				---	---	---	---
KIAA0748	9840	broad.mit.edu	37	12	55356217	55356217	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55356217C>T	uc001sgn.3	-	9	1575	c.1465G>A	c.(1465-1467)GAG>AAG	p.E489K	KIAA0748_uc001sgl.3_Missense_Mutation_p.E351K|KIAA0748_uc001sgm.3_Missense_Mutation_p.E236K|KIAA0748_uc010spb.1_Missense_Mutation_p.E236K|KIAA0748_uc010spc.1_Missense_Mutation_p.E351K|KIAA0748_uc010spd.1_Missense_Mutation_p.E489K|KIAA0748_uc001sgo.3_RNA	NM_001098815	NP_001092285	A2RU30	K0748_HUMAN	hypothetical protein LOC9840	489										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DNAJC14	85406	broad.mit.edu	37	12	56221493	56221493	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56221493A>G	uc001shx.1	-	2	1154	c.950T>C	c.(949-951)GTA>GCA	p.V317A	DNAJC14_uc001shu.1_Missense_Mutation_p.V317A|DNAJC14_uc009zob.1_Missense_Mutation_p.V317A|DNAJC14_uc001shy.1_Missense_Mutation_p.V317A	NM_032364	NP_115740	Q6Y2X3	DJC14_HUMAN	dopamine receptor interacting protein	317	Helical; (Potential).				protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
WIBG	84305	broad.mit.edu	37	12	56295983	56295983	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56295983C>G	uc001sif.1	-	3	440	c.288G>C	c.(286-288)AAG>AAC	p.K96N	WIBG_uc001sie.1_Missense_Mutation_p.K95N	NM_032345	NP_115721	Q9BRP8	WIBG_HUMAN	within bgcn homolog isoform 1	96	Potential.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|exon-exon junction complex|nucleolus|nucleoplasm	protein binding|ribosome binding|RNA binding				0																		---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56478854	56478854	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56478854G>A	uc001sjh.2	+	3	503	c.310G>A	c.(310-312)GTG>ATG	p.V104M	ERBB3_uc009zoj.2_RNA|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.V45M|ERBB3_uc001sjg.2_Missense_Mutation_p.V104M	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	104	Extracellular (Potential).		V -> M (in an ovarian mucinous carcinoma sample; somatic mutation).		cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity	p.V104M(1)		lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)															---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56482369	56482369	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56482369C>A	uc001sjh.2	+	8	1110	c.917C>A	c.(916-918)CCT>CAT	p.P306H	ERBB3_uc009zoj.2_RNA|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.P247H|ERBB3_uc001sji.2_5'UTR	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	306	Extracellular (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)															---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56559290	56559290	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56559290T>C	uc001skb.2	-	26	3057	c.2951A>G	c.(2950-2952)CAT>CGT	p.H984R	SMARCC2_uc001skd.2_Missense_Mutation_p.H1015R|SMARCC2_uc001ska.2_Missense_Mutation_p.H1015R|SMARCC2_uc001skc.2_Missense_Mutation_p.H1014R|SMARCC2_uc010sqf.1_Missense_Mutation_p.H904R	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	984	Pro-rich.				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
STAT2	6773	broad.mit.edu	37	12	56749288	56749288	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56749288G>T	uc001slc.2	-	5	488	c.410C>A	c.(409-411)CCT>CAT	p.P137H	STAT2_uc001sld.2_Missense_Mutation_p.P133H|STAT2_uc010sqn.1_Missense_Mutation_p.P133H	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription	137					interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3																		---	---	---	---
ATP5B	506	broad.mit.edu	37	12	57038606	57038606	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57038606A>G	uc001slr.2	-	3	549	c.444T>C	c.(442-444)ATT>ATC	p.I148I	SNORD59B_uc001sls.1_5'Flank	NM_001686	NP_001677	P06576	ATPB_HUMAN	mitochondrial ATP synthase beta subunit	148					angiogenesis|ATP hydrolysis coupled proton transport|regulation of intracellular pH|respiratory electron transport chain	cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)	1																		---	---	---	---
GPR182	11318	broad.mit.edu	37	12	57389924	57389924	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57389924C>G	uc001smk.2	+	2	1025	c.931C>G	c.(931-933)CTG>GTG	p.L311V	RDH16_uc010sqx.1_Intron	NM_007264	NP_009195	O15218	GP182_HUMAN	G protein-coupled receptor 182	311	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(1)	1																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57548011	57548011	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57548011G>A	uc001snd.2	+	7	1328	c.862G>A	c.(862-864)GAC>AAC	p.D288N	LRP1_uc001snc.1_Missense_Mutation_p.D288N	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	288	Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57674225	57674225	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57674225T>C	uc009zpm.1	-	12	1253	c.1218A>G	c.(1216-1218)CAA>CAG	p.Q406Q	R3HDM2_uc010srn.1_RNA|R3HDM2_uc001snu.2_Silent_p.Q67Q|R3HDM2_uc001snr.2_Silent_p.Q133Q|R3HDM2_uc001sns.2_Silent_p.Q406Q|R3HDM2_uc001snt.2_Silent_p.Q420Q|R3HDM2_uc009zpn.1_Silent_p.Q29Q	NM_014925	NP_055740	Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	406	Gln-rich.					nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57864151	57864151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57864151G>A	uc001snx.2	+	12	1706	c.1628G>A	c.(1627-1629)AGC>AAC	p.S543N	GLI1_uc009zpq.2_Missense_Mutation_p.S415N	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	543					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15			GBM - Glioblastoma multiforme(3;3.99e-32)															---	---	---	---
MBD6	114785	broad.mit.edu	37	12	57920920	57920920	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57920920C>T	uc001soj.1	+	7	2216	c.1992C>T	c.(1990-1992)TTC>TTT	p.F664F	MBD6_uc001sok.1_Silent_p.F531F|MBD6_uc001sol.1_RNA	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	664	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
TBK1	29110	broad.mit.edu	37	12	64878159	64878159	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64878159C>T	uc001ssc.1	+	9	1131	c.1069C>T	c.(1069-1071)CGA>TGA	p.R357*		NM_013254	NP_037386	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	357	Ubiquitin-like.				I-kappaB kinase/NF-kappaB cascade|innate immune response|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription from RNA polymerase II promoter|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|large_intestine(1)|breast(1)	5				GBM - Glioblastoma multiforme(28;0.0386)														---	---	---	---
RASSF3	283349	broad.mit.edu	37	12	65088630	65088630	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65088630C>T	uc001ssd.2	+	5	775	c.655C>T	c.(655-657)CGC>TGC	p.R219C	RASSF3_uc009zqn.2_RNA|RASSF3_uc001sse.2_Missense_Mutation_p.R149C	NM_178169	NP_835463	Q86WH2	RASF3_HUMAN	Ras association (RalGDS/AF-6) domain family	219	SARAH.				signal transduction	cytoplasm|microtubule	identical protein binding				0			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)														---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66531769	66531769	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66531769G>A	uc001stc.2	-	7	764	c.688C>T	c.(688-690)CGG>TGG	p.R230W	LLPH_uc010ssx.1_RNA|TMBIM4_uc001std.2_Missense_Mutation_p.R199W|TMBIM4_uc009zqr.2_Missense_Mutation_p.R277W|TMBIM4_uc001ste.2_RNA|TMBIM4_uc001stf.2_3'UTR|TMBIM4_uc009zqs.2_3'UTR	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4	230						integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66856867	66856867	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66856867G>A	uc001stk.2	-	9	1120	c.879C>T	c.(877-879)GGC>GGT	p.G293G	GRIP1_uc010sta.1_Silent_p.G237G|GRIP1_uc001stj.2_Silent_p.G23G|GRIP1_uc001stl.1_Silent_p.G237G|GRIP1_uc001stm.2_Silent_p.G293G	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	293	PDZ 3.				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66909462	66909462	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66909462T>C	uc001stk.2	-	7	902	c.661A>G	c.(661-663)AGT>GGT	p.S221G	GRIP1_uc010sta.1_Missense_Mutation_p.S165G|GRIP1_uc001stl.1_Missense_Mutation_p.S165G|GRIP1_uc001stm.2_Missense_Mutation_p.S221G	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	221	PDZ 2.				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
CAND1	55832	broad.mit.edu	37	12	67696289	67696289	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67696289A>G	uc001stn.2	+	8	1624	c.1187A>G	c.(1186-1188)CAC>CGC	p.H396R	CAND1_uc001sto.2_Missense_Mutation_p.H74R	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	396	HEAT 9.				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)														---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69042539	69042539	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69042539G>A	uc001sub.2	+	2	198	c.35G>A	c.(34-36)CGA>CAA	p.R12Q	RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Missense_Mutation_p.G12E|RAP1B_uc010stf.1_Missense_Mutation_p.G12E|RAP1B_uc010stg.1_Missense_Mutation_p.G12E|RAP1B_uc010sth.1_Missense_Mutation_p.G12E|RAP1B_uc010sti.1_Missense_Mutation_p.G12E	NM_001089704	NP_001083173	P61224	RAP1B_HUMAN	SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;	12	GTP.				blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)														---	---	---	---
NUP107	57122	broad.mit.edu	37	12	69085904	69085904	+	Intron	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69085904T>A	uc001suf.2	+						NUP107_uc001sug.2_Intron|NUP107_uc010stj.1_Intron	NM_020401	NP_065134			nucleoporin 107kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
YEATS4	8089	broad.mit.edu	37	12	69756672	69756672	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69756672A>G	uc001sux.2	+	2	377	c.156A>G	c.(154-156)AAA>AAG	p.K52K		NM_006530	NP_006521	O95619	YETS4_HUMAN	glioma-amplified sequence-41	52	YEATS.				histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)															---	---	---	---
FRS2	10818	broad.mit.edu	37	12	69968485	69968485	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69968485G>A	uc001suy.2	+	10	1787	c.1277G>A	c.(1276-1278)CGC>CAC	p.R426H	FRS2_uc001suz.2_Missense_Mutation_p.R426H|FRS2_uc009zrj.2_Missense_Mutation_p.R426H|FRS2_uc009zrk.2_Missense_Mutation_p.R426H	NM_006654	NP_006645	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	426					activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)															---	---	---	---
PTPRB	5787	broad.mit.edu	37	12	70964915	70964915	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70964915G>A	uc001swb.3	-	11	2637	c.2607C>T	c.(2605-2607)ACC>ACT	p.T869T	PTPRB_uc010sto.1_Silent_p.T869T|PTPRB_uc010stp.1_Silent_p.T779T|PTPRB_uc001swc.3_Silent_p.T1087T|PTPRB_uc001swa.3_Silent_p.T999T|PTPRB_uc001swd.3_Silent_p.T1086T|PTPRB_uc009zrr.1_Silent_p.T966T	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	869	Fibronectin type-III 10.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)															---	---	---	---
TRHDE	29953	broad.mit.edu	37	12	73046163	73046163	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73046163G>A	uc001sxa.2	+	16	2632	c.2602G>A	c.(2602-2604)GTC>ATC	p.V868I		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	868	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76784295	76784295	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76784295A>T	uc001sye.1	-	11	1552	c.1072T>A	c.(1072-1074)TCA>ACA	p.S358T	OSBPL8_uc001syf.1_Missense_Mutation_p.S316T|OSBPL8_uc001syg.1_Missense_Mutation_p.S316T|OSBPL8_uc001syh.1_Missense_Mutation_p.S333T	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform	358					lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
ATP2B1	490	broad.mit.edu	37	12	90028843	90028843	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90028843T>C	uc001tbh.2	-	3	773	c.592A>G	c.(592-594)AGG>GGG	p.R198G	ATP2B1_uc001tbg.2_Missense_Mutation_p.R198G	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b	198	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93206795	93206795	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93206795A>T	uc001tck.2	-	16	2269	c.2004T>A	c.(2002-2004)CAT>CAA	p.H668Q		NM_003566	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1, 162kD	668	Gln/Glu/Lys-rich.|Potential.				early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
PLXNC1	10154	broad.mit.edu	37	12	94642120	94642120	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94642120A>G	uc001tdc.2	+	14	2959	c.2710A>G	c.(2710-2712)ACC>GCC	p.T904A		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	904	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	100166822	100166822	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100166822T>G	uc001tge.1	-	8	1423	c.1006A>C	c.(1006-1008)AAA>CAA	p.K336Q	ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Missense_Mutation_p.K302Q	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a	336						Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
SLC17A8	246213	broad.mit.edu	37	12	100813589	100813589	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100813589T>G	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480			solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101763573	101763573	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101763573G>A	uc001tia.1	+	49	6615	c.6459G>A	c.(6457-6459)GAG>GAA	p.E2153E		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	2153					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101767239	101767239	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101767239G>A	uc001tia.1	+	53	7095	c.6939G>A	c.(6937-6939)ACG>ACA	p.T2313T		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	2313					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102025445	102025445	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102025445G>A	uc001tii.2	+	5	413	c.311G>A	c.(310-312)AGC>AAC	p.S104N	MYBPC1_uc001tif.1_Missense_Mutation_p.S117N|MYBPC1_uc001tig.2_Missense_Mutation_p.S129N|MYBPC1_uc010svq.1_Missense_Mutation_p.S91N|MYBPC1_uc001tih.2_Missense_Mutation_p.S129N|MYBPC1_uc001tij.2_Missense_Mutation_p.S104N|MYBPC1_uc010svr.1_Missense_Mutation_p.S104N|MYBPC1_uc010svs.1_Missense_Mutation_p.S104N|MYBPC1_uc010svt.1_Missense_Mutation_p.S92N|MYBPC1_uc010svu.1_Missense_Mutation_p.S104N|MYBPC1_uc001tik.2_Missense_Mutation_p.S78N	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	104	Ig-like C2-type 1.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
PAH	5053	broad.mit.edu	37	12	103288514	103288514	+	Silent	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103288514T>G	uc001tjq.1	-	4	823	c.351A>C	c.(349-351)ACA>ACC	p.T117T	PAH_uc010swc.1_Silent_p.T117T	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	117					catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)													---	---	---	---
STAB2	55576	broad.mit.edu	37	12	103981261	103981261	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103981261C>T	uc001tjw.2	+	1	193	c.7C>T	c.(7-9)CTA>TTA	p.L3L		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	3					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																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104063344	104063344	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104063344A>G	uc001tjw.2	+	21	2384	c.2198A>G	c.(2197-2199)TAT>TGT	p.Y733C		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	733	Extracellular (Potential).				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																		---	---	---	---
ALDH1L2	160428	broad.mit.edu	37	12	105420320	105420320	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105420320T>C	uc001tlc.2	-						ALDH1L2_uc009zuo.2_Intron|ALDH1L2_uc009zup.2_Intron	NM_001034173	NP_001029345			aldehyde dehydrogenase 1 family, member L2						10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	108013948	108013948	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108013948G>T	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron|BTBD11_uc001tml.1_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
CORO1C	23603	broad.mit.edu	37	12	109042423	109042423	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109042423G>A	uc001tnj.2	-	10	1359	c.1263C>T	c.(1261-1263)GAC>GAT	p.D421D	CORO1C_uc009zva.2_Silent_p.D474D|CORO1C_uc010sxf.1_Silent_p.D384D	NM_014325	NP_055140	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C isoform 1	421					actin cytoskeleton organization|phagocytosis|signal transduction	actin cytoskeleton	actin filament binding			skin(3)	3																		---	---	---	---
USP30	84749	broad.mit.edu	37	12	109523747	109523747	+	3'UTR	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109523747C>T	uc010sxi.1	+	13					USP30_uc001tnu.3_3'UTR|USP30_uc001tnw.3_3'UTR	NM_032663	NP_116052			ubiquitin specific peptidase 30						ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109702967	109702967	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109702967G>T	uc001tob.2	+	51	7114	c.6995G>T	c.(6994-6996)CGC>CTC	p.R2332L	ACACB_uc001toc.2_Missense_Mutation_p.R2332L|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Missense_Mutation_p.R998L	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	2332					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109826650	109826650	+	Splice_Site	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109826650G>A	uc010sxn.1	+	1	126	c.126_splice	c.e1+1	p.Y42_splice		NM_001101421	NP_001094891			myosin 1H							myosin complex	motor activity				0																		---	---	---	---
KCTD10	83892	broad.mit.edu	37	12	109889420	109889420	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109889420G>A	uc001toi.1	-	7	1010	c.922C>T	c.(922-924)CGG>TGG	p.R308W	KCTD10_uc001toh.1_RNA|KCTD10_uc009zvi.1_Missense_Mutation_p.R282W|KCTD10_uc001toj.1_Missense_Mutation_p.R317W|KCTD10_uc001tok.1_Missense_Mutation_p.R127W	NM_031954	NP_114160	Q9H3F6	BACD3_HUMAN	potassium channel tetramerisation domain	308					proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|nucleus|voltage-gated potassium channel complex	voltage-gated potassium channel activity				0																		---	---	---	---
KCTD10	83892	broad.mit.edu	37	12	109889456	109889456	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109889456G>A	uc001toi.1	-	7	974	c.886C>T	c.(886-888)CGC>TGC	p.R296C	KCTD10_uc001toh.1_RNA|KCTD10_uc009zvi.1_Missense_Mutation_p.R270C|KCTD10_uc001toj.1_Missense_Mutation_p.R305C|KCTD10_uc001tok.1_Missense_Mutation_p.R115C	NM_031954	NP_114160	Q9H3F6	BACD3_HUMAN	potassium channel tetramerisation domain	296					proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|nucleus|voltage-gated potassium channel complex	voltage-gated potassium channel activity				0																		---	---	---	---
GLTP	51228	broad.mit.edu	37	12	110290398	110290398	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110290398A>G	uc001tpm.2	-	5	706	c.592T>C	c.(592-594)TAC>CAC	p.Y198H	GLTP_uc010sxt.1_RNA	NM_016433	NP_057517	Q9NZD2	GLTP_HUMAN	glycolipid transfer protein	198						cytoplasm	glycolipid binding|glycolipid transporter activity				0		Lung NSC(355;2.38e-06)|Breast(359;0.00354)|Myeloproliferative disorder(1001;0.0122)		BRCA - Breast invasive adenocarcinoma(302;0.0025)												OREG0022112	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ATP2A2	488	broad.mit.edu	37	12	110734412	110734412	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110734412T>C	uc001tqk.3	+	5	896	c.333T>C	c.(331-333)AAT>AAC	p.N111N	ATP2A2_uc001tql.3_Silent_p.N111N|ATP2A2_uc010sxy.1_Silent_p.N111N	NM_170665	NP_733765	P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, slow twitch 2 isoform	111	Cytoplasmic (By similarity).				ATP biosynthetic process|cell adhesion|epidermis development|platelet activation|sarcoplasmic reticulum calcium ion transport	integral to plasma membrane|microsome|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|protein C-terminus binding|S100 alpha binding			ovary(3)|skin(1)	4																		---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112116963	112116963	+	Missense_Mutation	SNP	G	A	A	rs76800978	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112116963G>A	uc001tsn.3	-	4	819	c.625C>T	c.(625-627)CGT>TGT	p.R209C	BRAP_uc010syh.1_Missense_Mutation_p.R68C|BRAP_uc009zvv.2_Missense_Mutation_p.R179C	NM_006768	NP_006759	Q7Z569	BRAP_HUMAN	BRCA1 associated protein	209					MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1																		---	---	---	---
SLC24A6	80024	broad.mit.edu	37	12	113756814	113756814	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113756814G>A	uc001tvc.2	-	8	967	c.757C>T	c.(757-759)CGG>TGG	p.R253W	SLC24A6_uc001tuz.2_Translation_Start_Site|SLC24A6_uc001tva.2_RNA|SLC24A6_uc001tvb.2_Translation_Start_Site	NM_024959	NP_079235	Q6J4K2	NCKX6_HUMAN	solute carrier family 24 member 6 precursor	253	Cytoplasmic (Potential).				response to stimulus|sodium ion transport	integral to membrane|plasma membrane	calcium:cation antiporter activity			central_nervous_system(1)	1																		---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117627076	117627076	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117627076G>A	uc001twk.2	-	2	370	c.331C>T	c.(331-333)CGG>TGG	p.R111W	FBXO21_uc001twj.2_Missense_Mutation_p.R111W|FBXO21_uc009zwq.2_Missense_Mutation_p.R111W	NM_033624	NP_296373	O94952	FBX21_HUMAN	F-box only protein 21 isoform 1	111					ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)														---	---	---	---
RFC5	5985	broad.mit.edu	37	12	118467637	118467637	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118467637A>G	uc001twq.2	+						RFC5_uc010syx.1_Intron|RFC5_uc010syy.1_Intron|RFC5_uc010syz.1_Intron|RFC5_uc009zwr.2_Intron	NM_007370	NP_031396			replication factor C 5 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SRRM4	84530	broad.mit.edu	37	12	119419710	119419710	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119419710A>G	uc001txa.1	+	1	315	c.23A>G	c.(22-24)GAG>GGG	p.E8G		NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein	8					cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2																		---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120510351	120510351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120510351C>T	uc001txl.1	+	6	1151	c.1126C>T	c.(1126-1128)CGC>TGC	p.R376C	CCDC64_uc001txk.2_Missense_Mutation_p.R376C|CCDC64_uc009zwv.1_Intron|CCDC64_uc010sze.1_Intron|CCDC64_uc010szf.1_Missense_Mutation_p.R25C	NM_207311	NP_997194	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	376	Potential.				Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
MLEC	9761	broad.mit.edu	37	12	121132904	121132904	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121132904T>C	uc001tyy.1	+	4	749	c.598T>C	c.(598-600)TAT>CAT	p.Y200H		NM_014730	NP_055545	Q14165	MLEC_HUMAN	malectin precursor	200	Lumenal (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	carbohydrate binding			ovary(1)	1																		---	---	---	---
CAMKK2	10645	broad.mit.edu	37	12	121678610	121678610	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121678610A>G	uc001tzu.2	-	17	1783	c.1659T>C	c.(1657-1659)AGT>AGC	p.S553S	CAMKK2_uc001tzt.2_Missense_Mutation_p.V539A|CAMKK2_uc001tzv.2_Silent_p.S553S|CAMKK2_uc001tzw.2_Silent_p.S510S|CAMKK2_uc001tzx.2_Missense_Mutation_p.V539A|CAMKK2_uc001tzy.2_Missense_Mutation_p.V496A|CAMKK2_uc001tzz.1_Intron|CAMKK2_uc001uaa.1_Intron	NM_006549	NP_006540	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase	553					calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity	cytoplasm	ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity			lung(1)|large_intestine(1)|stomach(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
RNF34	80196	broad.mit.edu	37	12	121855521	121855521	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121855521T>C	uc001ual.1	+	3	554	c.440T>C	c.(439-441)GTA>GCA	p.V147A	RNF34_uc010szw.1_Missense_Mutation_p.V148A|RNF34_uc001uak.1_Missense_Mutation_p.V148A|RNF34_uc001uam.1_Missense_Mutation_p.V147A	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2	147					apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)														---	---	---	---
ORAI1	84876	broad.mit.edu	37	12	122079058	122079058	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122079058A>G	uc010szz.1	+	3	608	c.415A>G	c.(415-417)ATG>GTG	p.M139V		NM_032790	NP_116179	Q96D31	CRCM1_HUMAN	calcium release-activated calcium channel	139	Helical; (Potential).				platelet activation|positive regulation of calcium ion transport	integral to plasma membrane	protein binding|store-operated calcium channel activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122826190	122826190	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122826190A>G	uc001ucg.1	-	10	1667	c.1561T>C	c.(1561-1563)TTG>CTG	p.L521L	CLIP1_uc001uch.1_Silent_p.L510L|CLIP1_uc001uci.1_Silent_p.L475L|CLIP1_uc001ucj.1_Silent_p.L211L|CLIP1_uc009zxo.1_Silent_p.L77L	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a	521	Potential.				mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123060120	123060120	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123060120T>C	uc001ucv.2	+	28	2576	c.2413T>C	c.(2413-2415)TAT>CAT	p.Y805H	KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	805					cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
HIP1R	9026	broad.mit.edu	37	12	123334461	123334461	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123334461T>G	uc001udj.1	+	5	456	c.397T>G	c.(397-399)TAC>GAC	p.Y133D	HIP1R_uc001udg.1_Missense_Mutation_p.Y121D|HIP1R_uc001udi.1_Missense_Mutation_p.Y133D|HIP1R_uc001udh.2_Missense_Mutation_p.Y133D	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related	133	ENTH.				receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)														---	---	---	---
EIF2B1	1967	broad.mit.edu	37	12	124111688	124111688	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124111688C>T	uc001ufm.2	-	5	528	c.385G>A	c.(385-387)GCC>ACC	p.A129T	EIF2B1_uc001ufn.2_Missense_Mutation_p.A129T|EIF2B1_uc010tat.1_Missense_Mutation_p.A129T	NM_001414	NP_001405	Q14232	EI2BA_HUMAN	eukaryotic translation initiation factor 2B,	129					cellular response to stimulus|oligodendrocyte development|regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex|membrane fraction|plasma membrane	protein binding|translation initiation factor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.67e-05)|Epithelial(86;0.000353)|all cancers(50;0.00489)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124409638	124409638	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124409638G>T	uc001uft.3	+	67	11479	c.11454G>T	c.(11452-11454)TTG>TTT	p.L3818F	DNAH10_uc001ufu.3_5'UTR	NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3818	TPR 4.				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124419276	124419276	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124419276A>C	uc001uft.3	+	77	13257	c.13232A>C	c.(13231-13233)AAG>ACG	p.K4411T	DNAH10_uc001ufu.3_Missense_Mutation_p.K324T	NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4411					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124915170	124915170	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124915170C>T	uc010tba.1	-	9	1163	c.1046G>A	c.(1045-1047)CGC>CAC	p.R349H	NCOR2_uc010tay.1_Missense_Mutation_p.R349H|NCOR2_uc010taz.1_Missense_Mutation_p.R349H|NCOR2_uc010tbb.1_Missense_Mutation_p.R349H|NCOR2_uc010tbc.1_Missense_Mutation_p.R349H|NCOR2_uc001ugj.1_Missense_Mutation_p.R349H|NCOR2_uc001ugk.1_Missense_Mutation_p.R349H	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2	349					cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124968140	124968140	+	Splice_Site	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124968140A>G	uc010tba.1	-	3	528	c.411_splice	c.e3+1	p.K137_splice	NCOR2_uc010tay.1_Splice_Site_p.K137_splice|NCOR2_uc010taz.1_Splice_Site_p.K137_splice|NCOR2_uc010tbb.1_Splice_Site_p.K137_splice|NCOR2_uc010tbc.1_Splice_Site_p.K137_splice|NCOR2_uc001ugj.1_Splice_Site_p.K137_splice|NCOR2_uc001ugk.1_Splice_Site_p.K137_splice|uc001ugl.2_5'Flank	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
UBC	7316	broad.mit.edu	37	12	125397600	125397600	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125397600T>C	uc001ugs.3	-	2	1166	c.718A>G	c.(718-720)ACC>GCC	p.T240A	UBC_uc001ugr.2_5'Flank|UBC_uc001ugu.1_Missense_Mutation_p.T240A|UBC_uc001ugt.2_Missense_Mutation_p.T240A|UBC_uc001ugv.2_Intron|UBC_uc001ugw.2_Missense_Mutation_p.T88A	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	240	Ubiquitin-like 4.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130912893	130912893	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130912893A>C	uc001uil.2	-							NM_015347	NP_056162			RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132491389	132491389	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132491389A>T	uc001ujn.2	+	14	3306	c.3271A>T	c.(3271-3273)ATT>TTT	p.I1091F	EP400_uc001ujl.2_Missense_Mutation_p.I1090F|EP400_uc001ujm.2_Missense_Mutation_p.I1091F	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1127	Interactions with RUVBL1 and RUVBL2.|Helicase ATP-binding.				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)														---	---	---	---
P2RX2	22953	broad.mit.edu	37	12	133197136	133197136	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133197136G>T	uc001ukj.1	+	7	741	c.741G>T	c.(739-741)AAG>AAT	p.K247N	P2RX2_uc001uki.1_Missense_Mutation_p.K247N|P2RX2_uc001ukk.1_Missense_Mutation_p.K247N|P2RX2_uc001ukl.1_Missense_Mutation_p.K223N|P2RX2_uc001ukm.1_Missense_Mutation_p.K175N|P2RX2_uc001ukn.1_Missense_Mutation_p.K155N|P2RX2_uc009zyt.1_Missense_Mutation_p.K247N|P2RX2_uc001uko.1_Missense_Mutation_p.G212C	NM_170682	NP_733782	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X2 isoform A	247	Extracellular (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|protein homooligomerization	integral to membrane	ATP binding|extracellular ATP-gated cation channel activity|identical protein binding|purinergic nucleotide receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)														---	---	---	---
POLE	5426	broad.mit.edu	37	12	133254211	133254211	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133254211C>T	uc001uks.1	-	7	717	c.673G>A	c.(673-675)GAT>AAT	p.D225N	POLE_uc010tbq.1_RNA|POLE_uc009zyu.1_Missense_Mutation_p.D198N	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	225					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
PXMP2	5827	broad.mit.edu	37	12	133266939	133266939	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133266939G>T	uc001ukt.2	+	2	278	c.213G>T	c.(211-213)GGG>GGT	p.G71G	POLE_uc001uks.1_5'Flank|POLE_uc010tbq.1_5'Flank|POLE_uc009zyu.1_5'Flank|PGAM5_uc010tbr.1_RNA	NM_018663	NP_061133	Q9NR77	PXMP2_HUMAN	peroxisomal membrane protein 2, 22kDa	71	Peroxisomal (Potential).					integral to membrane|peroxisomal membrane	protein binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.86e-08)|Epithelial(86;2.47e-07)|all cancers(50;6.85e-06)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20638643	20638643	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20638643C>T	uc001umr.2	+	20	3388	c.3090C>T	c.(3088-3090)GGC>GGT	p.G1030G	ZMYM2_uc001ums.2_Silent_p.G1030G|ZMYM2_uc001umt.2_Silent_p.G1030G|ZMYM2_uc001umv.2_Silent_p.G410G|ZMYM2_uc001umw.2_Silent_p.G483G	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	1030					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)														---	---	---	---
LATS2	26524	broad.mit.edu	37	13	21563416	21563416	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21563416G>A	uc009zzs.2	-	4	868	c.503C>T	c.(502-504)ACG>ATG	p.T168M	LATS2_uc001unr.3_Missense_Mutation_p.T168M	NM_014572	NP_055387	Q9NRM7	LATS2_HUMAN	LATS, large tumor suppressor, homolog 2	168					cell division|G1/S transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|intracellular protein kinase cascade|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity	microtubule organizing center|nucleus|spindle pole	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(3)|ovary(2)|breast(1)|pancreas(1)	10		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)														---	---	---	---
SGCG	6445	broad.mit.edu	37	13	23853606	23853606	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23853606T>G	uc001uom.2	+	5	649	c.494T>G	c.(493-495)CTT>CGT	p.L165R	SGCG_uc009zzv.2_Missense_Mutation_p.L165R|SGCG_uc009zzw.2_Missense_Mutation_p.L165R	NM_000231	NP_000222	Q13326	SGCG_HUMAN	gamma sarcoglycan	165	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	23912055	23912055	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23912055G>A	uc001uon.2	-	10	6549	c.5960C>T	c.(5959-5961)TCC>TTC	p.S1987F	SACS_uc001uoo.2_Missense_Mutation_p.S1840F|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	1987					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	23929676	23929676	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23929676A>G	uc001uon.2	-	8	1664	c.1075T>C	c.(1075-1077)TAT>CAT	p.Y359H	SACS_uc001uoo.2_Missense_Mutation_p.Y212H|SACS_uc001uop.1_Missense_Mutation_p.Y146H|SACS_uc001uoq.1_Missense_Mutation_p.Y212H	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	359					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
RNF17	56163	broad.mit.edu	37	13	25367423	25367423	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25367423A>G	uc001upr.2	+	10	1220	c.1179A>G	c.(1177-1179)TTA>TTG	p.L393L	RNF17_uc010tdd.1_Silent_p.L252L|RNF17_uc010aab.2_RNA|RNF17_uc010tde.1_Silent_p.L393L|RNF17_uc001ups.2_Silent_p.L332L|RNF17_uc001upq.1_Silent_p.L393L	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	393					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)														---	---	---	---
NUPL1	9818	broad.mit.edu	37	13	25887102	25887102	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25887102C>T	uc001uqi.2	+	4	614	c.368C>T	c.(367-369)GCT>GTT	p.A123V	NUPL1_uc001uqg.1_Missense_Mutation_p.A123V|NUPL1_uc001uqj.2_Missense_Mutation_p.A111V	NM_014089	NP_054808	Q9BVL2	NUPL1_HUMAN	nucleoporin like 1 isoform a	123	14 X 2 AA repeats of F-G.				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore					0		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.0092)|Epithelial(112;0.0477)|OV - Ovarian serous cystadenocarcinoma(117;0.165)|GBM - Glioblastoma multiforme(144;0.244)														---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32913117	32913117	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32913117T>C	uc001uub.1	+	11	4852	c.4625T>C	c.(4624-4626)GTG>GCG	p.V1542A		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	1542	BRCA2 4.				cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
KL	9365	broad.mit.edu	37	13	33628375	33628375	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33628375A>G	uc001uus.2	+	2	1299	c.1291A>G	c.(1291-1293)ATG>GTG	p.M431V	KL_uc001uur.1_Missense_Mutation_p.M124V	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor	431	Glycosyl hydrolase-1 1.|Extracellular (Potential).				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)														---	---	---	---
KL	9365	broad.mit.edu	37	13	33628382	33628382	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33628382A>G	uc001uus.2	+	2	1306	c.1298A>G	c.(1297-1299)TAC>TGC	p.Y433C	KL_uc001uur.1_Missense_Mutation_p.Y126C	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor	433	Glycosyl hydrolase-1 1.|Extracellular (Potential).				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33703571	33703571	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33703571G>T	uc001uuw.2	-	5	1369	c.1243C>A	c.(1243-1245)CTC>ATC	p.L415I	STARD13_uc001uuu.2_Missense_Mutation_p.L407I|STARD13_uc001uuv.2_Missense_Mutation_p.L297I|STARD13_uc001uux.2_Missense_Mutation_p.L380I|STARD13_uc010tec.1_RNA|STARD13_uc010abh.1_Missense_Mutation_p.L400I	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain	415					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36686055	36686055	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36686055T>G	uc001uvf.2	-	3	907	c.674A>C	c.(673-675)AAG>ACG	p.K225T		NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1	225	Doublecortin 2.				cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37607598	37607598	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37607598C>T	uc001uwg.2	-	10	943	c.695G>A	c.(694-696)CGC>CAC	p.R232H	FAM48A_uc010abt.2_Missense_Mutation_p.R233H|FAM48A_uc001uwh.2_Missense_Mutation_p.R233H|FAM48A_uc001uwi.2_Missense_Mutation_p.R232H|FAM48A_uc001uwj.2_Missense_Mutation_p.R233H|FAM48A_uc001uwk.2_Missense_Mutation_p.R232H|FAM48A_uc010tes.1_Missense_Mutation_p.R220H|FAM48A_uc001uwl.1_Missense_Mutation_p.R232H	NM_001014286	NP_001014308	Q8NEM7	FA48A_HUMAN	family with sequence similarity 48, member A	232					autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39264653	39264653	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39264653A>G	uc001uwv.2	+	1	3481	c.3172A>G	c.(3172-3174)ACC>GCC	p.T1058A		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1058	Extracellular (Potential).|CSPG 7.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39343783	39343783	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39343783C>T	uc001uwv.2	+	4	5788	c.5479C>T	c.(5479-5481)CAG>TAG	p.Q1827*	FREM2_uc001uww.2_5'UTR	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1827	Calx-beta 1.|Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39587233	39587233	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39587233A>G	uc001uwy.2	-	11	3029	c.2156T>C	c.(2155-2157)GTA>GCA	p.V719A	C13orf23_uc001uwz.2_Missense_Mutation_p.V697A	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	719	Ser-rich.									ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42764582	42764582	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42764582G>C	uc001uyl.1	+	16	1977	c.1956G>C	c.(1954-1956)CAG>CAC	p.Q652H	DGKH_uc010tfh.1_Missense_Mutation_p.Q652H|DGKH_uc001uym.1_Missense_Mutation_p.Q652H|DGKH_uc010tfi.1_Missense_Mutation_p.Q407H|DGKH_uc010tfj.1_Missense_Mutation_p.Q507H|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.Q507H|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	652					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
SIAH3	283514	broad.mit.edu	37	13	46358019	46358019	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46358019C>T	uc001vap.2	-	2	391	c.309G>A	c.(307-309)ACG>ACA	p.T103T		NM_198849	NP_942146	Q8IW03	SIAH3_HUMAN	seven in absentia homolog 3	103	SIAH-type; degenerate.				multicellular organismal development|ubiquitin-dependent protein catabolic process	nucleus	metal ion binding			ovary(1)|skin(1)	2																		---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46549464	46549464	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46549464G>A	uc010tfw.1	-	11	2428	c.2422C>T	c.(2422-2424)CGA>TGA	p.R808*	ZC3H13_uc001vas.1_Nonsense_Mutation_p.R808*|ZC3H13_uc001vat.1_Nonsense_Mutation_p.R808*	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	808	Arg/Glu-rich.						nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)														---	---	---	---
SUCLA2	8803	broad.mit.edu	37	13	48562777	48562777	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48562777T>G	uc001vbs.2	-	4	490	c.433A>C	c.(433-435)ACG>CCG	p.T145P	SUCLA2_uc010tgb.1_Missense_Mutation_p.T85P|SUCLA2_uc010tgc.1_Missense_Mutation_p.T11P|SUCLA2_uc010tgd.1_Missense_Mutation_p.T85P|SUCLA2_uc001vbt.1_RNA|SUCLA2_uc001vbu.1_Missense_Mutation_p.T145P	NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	145	ATP-grasp.				succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)													---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49772224	49772224	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49772224A>C	uc001vcm.2	+	22	2902	c.2597A>C	c.(2596-2598)GAG>GCG	p.E866A	FNDC3A_uc001vcn.2_Missense_Mutation_p.E866A|FNDC3A_uc001vco.2_RNA|FNDC3A_uc001vcq.2_Missense_Mutation_p.E810A	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	866	Fibronectin type-III 7.					Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52515321	52515321	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52515321C>T	uc001vfw.2	-	16	3609	c.3452G>A	c.(3451-3453)CGT>CAT	p.R1151H	ATP7B_uc010adv.2_Missense_Mutation_p.R721H|ATP7B_uc001vfx.2_Missense_Mutation_p.R944H|ATP7B_uc001vfy.2_Missense_Mutation_p.R1040H|ATP7B_uc010tgt.1_Missense_Mutation_p.R1086H|ATP7B_uc010tgu.1_Missense_Mutation_p.R1103H|ATP7B_uc010tgv.1_Missense_Mutation_p.R1073H|ATP7B_uc001vfv.2_Missense_Mutation_p.R423H|ATP7B_uc010tgs.1_Missense_Mutation_p.R362H	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1151	Cytoplasmic (Potential).		R -> H (in WD).		ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
UTP14C	9724	broad.mit.edu	37	13	52598544	52598544	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52598544T>C	uc001vgb.2	+						UTP14C_uc001vga.2_Silent_p.N226N|UTP14C_uc001vgc.2_RNA	NM_021645	NP_067677			UTP14, U3 small nucleolar ribonucleoprotein,						cell differentiation|meiosis|multicellular organismal development|rRNA processing|spermatogenesis	nucleolus|small-subunit processome				ovary(3)|large_intestine(1)|breast(1)	5		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)														---	---	---	---
LECT1	11061	broad.mit.edu	37	13	53277901	53277901	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53277901G>A	uc001vhf.2	-	7	945	c.834C>T	c.(832-834)CAC>CAT	p.H278H	LECT1_uc001vhg.2_Silent_p.H277H|LECT1_uc001vhh.2_Silent_p.H267H	NM_007015	NP_008946	O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1 isoform 1	278					cartilage development|proteoglycan metabolic process	endomembrane system|extracellular region|integral to membrane				ovary(2)	2		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67801672	67801672	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67801672T>C	uc001vik.2	-	2	1593	c.901A>G	c.(901-903)AGA>GGA	p.R301G	PCDH9_uc001vil.2_Missense_Mutation_p.R301G|PCDH9_uc010thl.1_Missense_Mutation_p.R301G|PCDH9_uc001vin.3_Missense_Mutation_p.R301G	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	301	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75886963	75886963	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75886963A>G	uc001vjl.1	-	13	2641	c.2294T>C	c.(2293-2295)GTC>GCC	p.V765A	TBC1D4_uc010tht.1_5'UTR|TBC1D4_uc010thu.1_5'UTR|TBC1D4_uc010aer.2_Missense_Mutation_p.V757A|TBC1D4_uc010aes.2_Missense_Mutation_p.V702A	NM_014832	NP_055647	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	765						cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103282504	103282504	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103282504A>G	uc001vpi.3	+	10	1306	c.1203A>G	c.(1201-1203)AAA>AAG	p.K401K		NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II	401					proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109859071	109859071	+	Missense_Mutation	SNP	G	A	A	rs139848765	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109859071G>A	uc001vqt.1	+	35	5590	c.5464G>A	c.(5464-5466)GCT>ACT	p.A1822T	MYO16_uc010agk.1_Missense_Mutation_p.A1844T	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	1822					cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110802784	110802784	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110802784T>C	uc001vqw.3	-	52	5058	c.4936A>G	c.(4936-4938)ACG>GCG	p.T1646A	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	1646	Collagen IV NC1.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
CARKD	55739	broad.mit.edu	37	13	111286940	111286940	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111286940G>A	uc001vrb.2	+	6	558	c.544G>A	c.(544-546)GCG>ACG	p.A182T	CARKD_uc010tji.1_Missense_Mutation_p.A119T|CARKD_uc010tjj.1_Missense_Mutation_p.A164T|CARKD_uc001vqz.2_RNA|CARKD_uc001vra.2_RNA|CARKD_uc010tjk.1_Missense_Mutation_p.A72T|CARKD_uc010tjl.1_Missense_Mutation_p.A51T|CARKD_uc001vrc.2_Missense_Mutation_p.A182T			Q8IW45	CARKD_HUMAN	RecName: Full=Carbohydrate kinase domain-containing protein; Flags: Precursor;	182	YjeF C-terminal.									skin(1)	1																		---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111870075	111870075	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111870075A>G	uc001vrs.2	+	6	831	c.581A>G	c.(580-582)AAC>AGC	p.N194S	ARHGEF7_uc001vrr.2_Missense_Mutation_p.N173S|ARHGEF7_uc001vrt.2_Missense_Mutation_p.N144S|ARHGEF7_uc010tjn.1_RNA|ARHGEF7_uc001vru.1_Missense_Mutation_p.N16S|ARHGEF7_uc001vrv.3_Missense_Mutation_p.N16S|ARHGEF7_uc001vrw.3_Missense_Mutation_p.N16S|ARHGEF7_uc001vrx.3_Missense_Mutation_p.N16S|ARHGEF7_uc010tjo.1_Missense_Mutation_p.N91S	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	194	SH3.				apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
MCF2L	23263	broad.mit.edu	37	13	113718707	113718707	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113718707C>T	uc001vsu.2	+	6	772	c.750C>T	c.(748-750)TGC>TGT	p.C250C	MCF2L_uc001vsq.2_Silent_p.C250C|MCF2L_uc010tjr.1_Silent_p.C193C|MCF2L_uc001vsr.2_Silent_p.C197C|MCF2L_uc001vss.3_Silent_p.C191C|MCF2L_uc010tjs.1_Silent_p.C191C|MCF2L_uc001vst.1_Silent_p.C155C	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming	223	CRAL-TRIO.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)																---	---	---	---
FAM70B	348013	broad.mit.edu	37	13	114507957	114507957	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114507957C>T	uc001vuh.2	+	8	796	c.769C>T	c.(769-771)CCC>TCC	p.P257S		NM_182614	NP_872420	Q8WV15	FA70B_HUMAN	family with sequence similarity 70, member B	257	Pro-rich.					integral to membrane					0	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.123)|all_epithelial(44;0.133)	all cancers(43;0.181)															---	---	---	---
RASA3	22821	broad.mit.edu	37	13	114786967	114786967	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114786967G>A	uc001vui.2	-	9	829	c.698C>T	c.(697-699)GCC>GTC	p.A233V	RASA3_uc010tkk.1_Missense_Mutation_p.A201V|RASA3_uc001vuj.2_5'UTR|RASA3_uc010tkl.1_RNA|RASA3_uc010aha.1_RNA	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	233	C2 2.				intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)															---	---	---	---
CDC16	8881	broad.mit.edu	37	13	115007699	115007699	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115007699A>G	uc001vuk.1	+	6	683	c.485A>G	c.(484-486)TAC>TGC	p.Y162C	CDC16_uc010tkm.1_Missense_Mutation_p.Y162C|CDC16_uc001vul.1_Missense_Mutation_p.Y162C|CDC16_uc001vum.1_Missense_Mutation_p.Y68C|CDC16_uc001vun.1_Missense_Mutation_p.Y161C|CDC16_uc001vuo.1_Missense_Mutation_p.Y161C	NM_003903	NP_003894	Q13042	CDC16_HUMAN	anaphase-promoting complex, subunit 6	162	TPR 1.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|mitosis|mitotic cell cycle spindle assembly checkpoint|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 K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)															---	---	---	---
OR4N2	390429	broad.mit.edu	37	14	20296294	20296294	+	Silent	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20296294T>G	uc010tkv.1	+	1	687	c.687T>G	c.(685-687)TCT>TCG	p.S229S		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	229	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20849766	20849766	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20849766G>A	uc001vxe.2	-	31	4544	c.4504C>T	c.(4504-4506)CGT>TGT	p.R1502C	TEP1_uc010ahk.2_Missense_Mutation_p.R845C|TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Missense_Mutation_p.R1394C|TEP1_uc010tlh.1_Intron	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1502					telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
FLJ10357	55701	broad.mit.edu	37	14	21552988	21552988	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21552988G>A	uc001vzp.2	+	18	3895	c.3866G>A	c.(3865-3867)CGC>CAC	p.R1289H	FLJ10357_uc001vzo.1_Missense_Mutation_p.R368H|FLJ10357_uc010aij.2_RNA|FLJ10357_uc010tln.1_Missense_Mutation_p.R575H	NM_018071	NP_060541	Q8TER5	ARH40_HUMAN	hypothetical protein LOC55701	1289	PH.				regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;5.79e-11)|Epithelial(56;8.35e-09)|all cancers(55;4.23e-08)	GBM - Glioblastoma multiforme(265;0.0197)														---	---	---	---
RPGRIP1	57096	broad.mit.edu	37	14	21792816	21792816	+	Missense_Mutation	SNP	C	T	T	rs3748360	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21792816C>T	uc001wag.2	+	14	1802	c.1802C>T	c.(1801-1803)TCG>TTG	p.S601L	RPGRIP1_uc001wah.2_Missense_Mutation_p.S243L|RPGRIP1_uc001wai.2_Intron|RPGRIP1_uc001waj.1_Missense_Mutation_p.S66L|RPGRIP1_uc001wak.2_Missense_Mutation_p.S76L|RPGRIP1_uc010aim.2_Intron|RPGRIP1_uc001wal.2_Missense_Mutation_p.R10C|RPGRIP1_uc001wam.2_5'UTR	NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator	601					response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
SUPT16H	11198	broad.mit.edu	37	14	21830483	21830483	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21830483T>C	uc001wao.2	-	15	2005	c.1666A>G	c.(1666-1668)AAT>GAT	p.N556D		NM_007192	NP_009123	Q9Y5B9	SP16H_HUMAN	chromatin-specific transcription elongation	556					DNA repair|DNA replication|nucleosome disassembly|positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|nucleoplasm	GTP binding				0	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)														---	---	---	---
CDH24	64403	broad.mit.edu	37	14	23523477	23523477	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23523477C>T	uc001wil.2	-	6	1105	c.845G>A	c.(844-846)CGG>CAG	p.R282Q	CDH24_uc010akf.2_Missense_Mutation_p.R282Q|CDH24_uc001win.3_Missense_Mutation_p.R282Q	NM_022478	NP_071923	Q86UP0	CAD24_HUMAN	cadherin-like 24 isoform 1	282	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|cell-cell adhesion|homophilic cell adhesion	cell-cell junction|cell-cell junction|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|delta-catenin binding			central_nervous_system(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)														---	---	---	---
MYH6	4624	broad.mit.edu	37	14	23853917	23853917	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23853917T>C	uc001wjv.2	-	36	5366	c.5299A>G	c.(5299-5301)ATG>GTG	p.M1767V		NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	1767	Potential.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)														---	---	---	---
DHRS2	10202	broad.mit.edu	37	14	24108526	24108526	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24108526C>T	uc001wkt.3	+	3	726	c.279C>T	c.(277-279)CAC>CAT	p.H93H	DHRS2_uc010aku.1_Silent_p.H93H|DHRS2_uc001wku.3_Silent_p.H93H|DHRS2_uc010akv.2_RNA|DHRS2_uc001wkv.3_Silent_p.H93H	NM_182908	NP_878912	Q13268	DHRS2_HUMAN	dehydrogenase/reductase member 2 isoform 1	71					C21-steroid hormone metabolic process|cellular response to oxidative stress|myeloid dendritic cell differentiation|negative regulation of apoptosis|negative regulation of cell proliferation|response to toxin	mitochondrion|nuclear envelope	binding|carbonyl reductase (NADPH) activity			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00659)														---	---	---	---
RIPK3	11035	broad.mit.edu	37	14	24807621	24807621	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24807621T>C	uc001wpb.2	-						RIPK3_uc001wpa.2_5'UTR|RIPK3_uc010alq.2_Intron|RIPK3_uc010toi.1_Intron|RIPK3_uc010toj.1_3'UTR	NM_006871	NP_006862			receptor-interacting serine-threonine kinase 3						apoptosis|induction of apoptosis by extracellular signals	cytoplasm	ATP binding|protein binding|transcription coactivator activity			central_nervous_system(2)|ovary(1)|lung(1)	4				GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
CTSG	1511	broad.mit.edu	37	14	25044028	25044028	+	Intron	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25044028A>T	uc001wpq.2	-							NM_001911	NP_001902			cathepsin G preproprotein						immune response|proteolysis	cell surface|extracellular space|plasma membrane|stored secretory granule	heparin binding|serine-type endopeptidase activity			ovary(2)	2				GBM - Glioblastoma multiforme(265;0.0269)														---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30068878	30068878	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30068878T>G	uc001wqh.2	-	14	2232	c.2051A>C	c.(2050-2052)AAG>ACG	p.K684T		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	684	Protein kinase.				cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	34269414	34269414	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34269414C>T	uc001wru.2	+	12	1965	c.1901C>T	c.(1900-1902)CCG>CTG	p.P634L	NPAS3_uc001wrs.2_Missense_Mutation_p.P621L|NPAS3_uc001wrt.2_Missense_Mutation_p.P602L|NPAS3_uc001wrv.2_Missense_Mutation_p.P604L	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3	634					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
FBXO33	254170	broad.mit.edu	37	14	39870564	39870564	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39870564A>G	uc001wvk.2	-	3	1550	c.1212T>C	c.(1210-1212)ACT>ACC	p.T404T		NM_203301	NP_976046	Q7Z6M2	FBX33_HUMAN	F-box protein 33	404											0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)														---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42356770	42356770	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42356770T>C	uc001wvm.2	+	3	2140	c.942T>C	c.(940-942)CCT>CCC	p.P314P	LRFN5_uc010ana.2_Silent_p.P314P	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	314	Extracellular (Potential).|Ig-like.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)											HNSCC(30;0.082)			---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42357187	42357187	+	Silent	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42357187T>A	uc001wvm.2	+	3	2557	c.1359T>A	c.(1357-1359)GGT>GGA	p.G453G	LRFN5_uc010ana.2_Silent_p.G453G	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	453	Extracellular (Potential).|Fibronectin type-III.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)											HNSCC(30;0.082)			---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45501482	45501482	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45501482C>T	uc001wvv.2	+	11	3924	c.3715C>T	c.(3715-3717)CAT>TAT	p.H1239Y	FAM179B_uc001wvw.2_Missense_Mutation_p.H1239Y|FAM179B_uc010anc.2_RNA	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	1239							binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45542738	45542738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45542738G>A	uc001wvv.2	+	19	5346	c.5137G>A	c.(5137-5139)GAT>AAT	p.D1713N	FAM179B_uc001wvw.2_Missense_Mutation_p.D1766N|FAM179B_uc010anc.2_RNA	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	1713							binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
RPL10L	140801	broad.mit.edu	37	14	47120878	47120878	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47120878C>T	uc001wwg.2	-	1	151	c.62G>A	c.(61-63)CGT>CAT	p.R21H		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	21					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50904261	50904261	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50904261G>A	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
PYGL	5836	broad.mit.edu	37	14	51387719	51387719	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51387719G>A	uc001wyu.2	-	6	854	c.727C>T	c.(727-729)CGC>TGC	p.R243C	PYGL_uc010tqq.1_Missense_Mutation_p.R209C|PYGL_uc001wyv.2_5'UTR|PYGL_uc010anz.1_Missense_Mutation_p.R46C	NM_002863	NP_002854	P06737	PYGL_HUMAN	liver glycogen phosphorylase isoform 1	243					glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding			skin(1)	1	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)													---	---	---	---
TRIM9	114088	broad.mit.edu	37	14	51448529	51448529	+	Silent	SNP	C	T	T	rs146015079	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51448529C>T	uc001wyx.3	-	8	2661	c.1896G>A	c.(1894-1896)TCG>TCA	p.S632S	TRIM9_uc001wyy.2_Silent_p.S713S	NM_015163	NP_055978	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 1	632	B30.2/SPRY.				proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)																	---	---	---	---
NID2	22795	broad.mit.edu	37	14	52485867	52485867	+	Missense_Mutation	SNP	G	T	T	rs138141385		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52485867G>T	uc001wzo.2	-	14	3174	c.2940C>A	c.(2938-2940)TTC>TTA	p.F980L	NID2_uc010tqs.1_Missense_Mutation_p.F932L|NID2_uc010tqt.1_Missense_Mutation_p.F980L|NID2_uc001wzp.2_Missense_Mutation_p.F980L	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	980	Thyroglobulin type-1 1.					basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)																	---	---	---	---
KIAA0831	22863	broad.mit.edu	37	14	55848812	55848812	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55848812G>A	uc001xbx.1	-	6	781	c.745C>T	c.(745-747)CGA>TGA	p.R249*	FBXO34_uc001xbv.2_Intron|KIAA0831_uc001xbw.1_Nonsense_Mutation_p.R136*	NM_014924	NP_055739	Q6ZNE5	BAKOR_HUMAN	Barkor	249					autophagic vacuole assembly|positive regulation of autophagy	autophagic vacuole|endoplasmic reticulum|pre-autophagosomal structure membrane	protein binding				0																		---	---	---	---
TBPL2	387332	broad.mit.edu	37	14	55903343	55903343	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55903343A>T	uc001xby.2	-	2	544	c.544T>A	c.(544-546)TCC>ACC	p.S182T		NM_199047	NP_950248	Q6SJ96	TBPL2_HUMAN	TATA box binding protein like 2	182					multicellular organismal development|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding				0																		---	---	---	---
PELI2	57161	broad.mit.edu	37	14	56757153	56757153	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56757153G>A	uc001xch.2	+	5	961	c.675G>A	c.(673-675)TCG>TCA	p.S225S		NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2	225					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58604793	58604793	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58604793G>A	uc001xdc.2	-	2	1395	c.1284C>T	c.(1282-1284)AAC>AAT	p.N428N	C14orf37_uc010tro.1_Silent_p.N466N|C14orf37_uc001xdd.2_Silent_p.N428N|C14orf37_uc001xde.2_Silent_p.N428N	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor	428	Extracellular (Potential).					integral to membrane	binding				0																		---	---	---	---
C14orf39	317761	broad.mit.edu	37	14	60903608	60903608	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60903608A>C	uc001xez.3	-	18	1829	c.1719T>G	c.(1717-1719)GGT>GGG	p.G573G	C14orf39_uc010apo.2_Silent_p.G284G	NM_174978	NP_777638	Q08AQ4	Q08AQ4_HUMAN	hypothetical protein LOC317761	573										ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)														---	---	---	---
C14orf39	317761	broad.mit.edu	37	14	60903657	60903657	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60903657A>T	uc001xez.3	-	18	1780	c.1670T>A	c.(1669-1671)TTT>TAT	p.F557Y	C14orf39_uc010apo.2_Missense_Mutation_p.F268Y	NM_174978	NP_777638	Q08AQ4	Q08AQ4_HUMAN	hypothetical protein LOC317761	557										ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)														---	---	---	---
ACTN1	87	broad.mit.edu	37	14	69392309	69392309	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69392309G>A	uc001xkl.2	-	2	496	c.186C>T	c.(184-186)GGC>GGT	p.G62G	ACTN1_uc010ttb.1_5'UTR|ACTN1_uc001xkm.2_Silent_p.G62G|ACTN1_uc001xkn.2_Silent_p.G62G|ACTN1_uc001xko.1_5'UTR|ACTN1_uc010ttd.1_Silent_p.G41G	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b	62	CH 1.|Actin-binding.				focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
KIAA0247	9766	broad.mit.edu	37	14	70171406	70171406	+	Silent	SNP	C	T	T	rs150724393	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70171406C>T	uc001xlk.2	+	4	721	c.405C>T	c.(403-405)CTC>CTT	p.L135L	KIAA0247_uc010aqz.2_Silent_p.L110L	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor	135	Helical; (Potential).					integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)														---	---	---	---
SMOC1	64093	broad.mit.edu	37	14	70346477	70346477	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70346477C>T	uc001xls.1	+	1	335	c.82C>T	c.(82-84)CGC>TGC	p.R28C	SMOC1_uc001xlt.1_Missense_Mutation_p.R28C	NM_022137	NP_071420	Q9H4F8	SMOC1_HUMAN	secreted modular calcium-binding protein 1	28					cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction	basement membrane	calcium ion binding			upper_aerodigestive_tract(1)|pancreas(1)	2				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)														---	---	---	---
SLC8A3	6547	broad.mit.edu	37	14	70634917	70634917	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70634917C>A	uc001xly.2	-	2	977	c.223G>T	c.(223-225)GCC>TCC	p.A75S	SLC8A3_uc001xlw.2_Missense_Mutation_p.A75S|SLC8A3_uc001xlx.2_Missense_Mutation_p.A75S|SLC8A3_uc001xlz.2_Missense_Mutation_p.A75S|SLC8A3_uc010ara.2_RNA	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium	75	Helical; (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)														---	---	---	---
ADAM21	8747	broad.mit.edu	37	14	70924985	70924985	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70924985G>T	uc001xmd.2	+	1	769	c.769G>T	c.(769-771)GGA>TGA	p.G257*		NM_003813	NP_003804	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21 preproprotein	257	Peptidase M12B.|Extracellular (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			pancreas(1)|skin(1)	2				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71462617	71462617	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71462617C>T	uc001xmo.2	+	8	3050	c.2604C>T	c.(2602-2604)GGC>GGT	p.G868G	PCNX_uc001xmn.3_Intron|PCNX_uc010are.1_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	868						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)														---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72924983	72924983	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72924983A>G	uc001xna.3	+	5	763	c.240A>G	c.(238-240)GAA>GAG	p.E80E	RGS6_uc010ttn.1_Silent_p.E80E|RGS6_uc001xmx.3_Silent_p.E80E|RGS6_uc010tto.1_RNA|RGS6_uc001xmy.3_Silent_p.E80E|RGS6_uc010ttp.1_Silent_p.E11E|RGS6_uc001xmz.1_5'Flank|RGS6_uc010arg.2_RNA	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6	80	DEP.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
HEATR4	399671	broad.mit.edu	37	14	73985802	73985802	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73985802G>A	uc010tub.1	-	5	1457	c.1135C>T	c.(1135-1137)CGG>TGG	p.R379W	HEATR4_uc010tua.1_Missense_Mutation_p.R332W	NM_203309	NP_976054			HEAT repeat containing 4											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)														---	---	---	---
FAM161B	145483	broad.mit.edu	37	14	74401052	74401052	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74401052A>G	uc001xpd.1	-	9	1957	c.1851T>C	c.(1849-1851)GGT>GGC	p.G617G		NM_152445	NP_689658			hypothetical protein LOC145483											ovary(1)	1																		---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75130505	75130505	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75130505G>T	uc001xqb.2	-	20	2895	c.2390C>A	c.(2389-2391)CCT>CAT	p.P797H		NM_001039479	NP_001034568	O15033	K0317_HUMAN	hypothetical protein LOC9870	797	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
RPS6KL1	83694	broad.mit.edu	37	14	75373805	75373805	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75373805C>T	uc010tux.1	-	11	2090	c.1562G>A	c.(1561-1563)CGG>CAG	p.R521Q	RPS6KL1_uc001xqx.1_3'UTR|RPS6KL1_uc001xqw.2_Missense_Mutation_p.R490Q|RPS6KL1_uc010asd.1_RNA	NM_031464	NP_113652	Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	521	Protein kinase.					ribosome	ATP binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00658)														---	---	---	---
RPS6KL1	83694	broad.mit.edu	37	14	75376763	75376763	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75376763A>C	uc010tux.1	-	7	1281	c.753T>G	c.(751-753)GCT>GCG	p.A251A	RPS6KL1_uc001xqx.1_Silent_p.A3A|RPS6KL1_uc001xqw.2_Silent_p.A220A|RPS6KL1_uc010asd.1_RNA	NM_031464	NP_113652	Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	251	Protein kinase.					ribosome	ATP binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00658)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75580066	75580066	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75580066C>T	uc001xrl.2	-	8	1068	c.914G>A	c.(913-915)CGC>CAC	p.R305H	NEK9_uc001xrk.2_5'UTR	NM_033116	NP_149107	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	305	Protein kinase.				cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)														---	---	---	---
KIAA1737	85457	broad.mit.edu	37	14	77576173	77576173	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77576173T>C	uc001xtd.2	+	3	334	c.155T>C	c.(154-156)CTG>CCG	p.L52P	KIAA1737_uc001xtc.1_5'UTR	NM_033426	NP_219494	Q9C0C6	K1737_HUMAN	KIAA1737 protein	52											0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)														---	---	---	---
GSTZ1	2954	broad.mit.edu	37	14	77794336	77794336	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77794336C>T	uc001xtj.2	+	5	580	c.298C>T	c.(298-300)CGT>TGT	p.R100C	GSTZ1_uc001xtk.2_Intron|GSTZ1_uc010ass.2_Missense_Mutation_p.R45C|GSTZ1_uc001xtm.2_Missense_Mutation_p.R45C	NM_145870	NP_665877	O43708	MAAI_HUMAN	glutathione transferase zeta 1 isoform 1	100	GST C-terminal.				glutathione metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol|mitochondrion	glutathione peroxidase activity|glutathione transferase activity|maleylacetoacetate isomerase activity|protein homodimerization activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)													---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79175585	79175585	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79175585G>A	uc001xun.2	+	4	619	c.128G>A	c.(127-129)CGT>CAT	p.R43H	NRXN3_uc001xum.1_RNA|NRXN3_uc010asv.1_Missense_Mutation_p.R177H	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	416	Laminin G-like 2.|Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	80164262	80164262	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80164262C>T	uc001xun.2	+	15	3278	c.2787C>T	c.(2785-2787)CGC>CGT	p.R929R	NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_Silent_p.R297R|NRXN3_uc010asw.2_Silent_p.R327R|NRXN3_uc001xur.3_Silent_p.R297R	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1302	Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
EML5	161436	broad.mit.edu	37	14	89091345	89091345	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89091345C>T	uc001xxg.2	-	36	5053	c.4867G>A	c.(4867-4869)GGA>AGA	p.G1623R	EML5_uc001xxf.2_Missense_Mutation_p.G410R|EML5_uc001xxh.1_Missense_Mutation_p.G754R	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	1615	WD 24.					cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
EML5	161436	broad.mit.edu	37	14	89202717	89202717	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89202717C>T	uc001xxg.2	-	8	1226	c.1040G>A	c.(1039-1041)CGT>CAT	p.R347H		NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	347	WD 7.					cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
C14orf102	55051	broad.mit.edu	37	14	90783003	90783003	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90783003C>T	uc001xyi.1	-	3	357	c.326G>A	c.(325-327)AGG>AAG	p.R109K	C14orf102_uc001xyj.1_Intron	NM_017970	NP_060440	Q9H7Z3	CN102_HUMAN	hypothetical protein LOC55051 isoform 1	109	Poly-Ser.|Potential.						protein binding			ovary(2)|lung(1)	3		all_cancers(154;0.118)		COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91642369	91642369	+	Silent	SNP	G	A	A	rs149668017	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91642369G>A	uc001xzb.2	+	9	1452	c.684G>A	c.(682-684)CCG>CCA	p.P228P	C14orf159_uc010atv.1_RNA|C14orf159_uc001xyy.2_Silent_p.P233P|C14orf159_uc001xyx.2_Silent_p.P216P|C14orf159_uc001xyw.2_Silent_p.P233P|C14orf159_uc001xzc.2_Silent_p.P228P|C14orf159_uc001xza.2_Silent_p.P233P|C14orf159_uc001xyv.2_Silent_p.P233P|C14orf159_uc001xyz.2_Silent_p.P104P|C14orf159_uc001xze.2_Silent_p.P228P	NM_001102366	NP_001095836	Q7Z3D6	CN159_HUMAN	hypothetical protein LOC80017 isoform a	228						mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)														---	---	---	---
TC2N	123036	broad.mit.edu	37	14	92258779	92258779	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92258779A>G	uc001xzu.3	-	9	1170	c.979T>C	c.(979-981)TCA>CCA	p.S327P	TC2N_uc001xzt.3_Missense_Mutation_p.S327P|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Missense_Mutation_p.S327P	NM_001128595	NP_001122067	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	327						nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
SLC24A4	123041	broad.mit.edu	37	14	92920235	92920235	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92920235G>A	uc001yak.2	+						SLC24A4_uc001yai.2_Intron|SLC24A4_uc010twm.1_Intron|SLC24A4_uc001yaj.2_Intron|SLC24A4_uc010auj.2_Intron|SLC24A4_uc010twn.1_Intron|SLC24A4_uc001yan.2_5'UTR	NM_153646	NP_705932			solute carrier family 24 member 4 isoform 1							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)														---	---	---	---
IFI27L1	122509	broad.mit.edu	37	14	94568188	94568188	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94568188G>A	uc001ycl.2	+	4	298	c.90G>A	c.(88-90)GCG>GCA	p.A30A	IFI27L1_uc001yck.2_Silent_p.A30A	NM_206949	NP_996832	Q96BM0	I27L1_HUMAN	interferon, alpha-inducible protein 27-like 1	30	Helical; (Potential).					integral to membrane					0																		---	---	---	---
IFI27L2	83982	broad.mit.edu	37	14	94595893	94595893	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94595893A>G	uc001ycq.2	-							NM_032036	NP_114425			TLH29 protein precursor							integral to membrane					0																		---	---	---	---
EML1	2009	broad.mit.edu	37	14	100380551	100380551	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100380551C>T	uc001ygs.2	+	14	1599	c.1530C>T	c.(1528-1530)GCC>GCT	p.A510A	EML1_uc010tww.1_Silent_p.A498A|EML1_uc001ygr.2_Silent_p.A529A	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	510						cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)																---	---	---	---
YY1	7528	broad.mit.edu	37	14	100728744	100728744	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100728744T>C	uc001ygy.1	+	2	1263	c.783T>C	c.(781-783)CCT>CCC	p.P261P		NM_003403	NP_003394	P25490	TYY1_HUMAN	YY1 transcription factor	261	Involved in nuclear matrix association.				cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding				0		Melanoma(154;0.152)																---	---	---	---
MIR665	100126315	broad.mit.edu	37	14	101341422	101341422	+	RNA	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101341422T>C	hsa-mir-665|MI0005563	+			c.53T>C																				0																		---	---	---	---
SNORD114-3	767579	broad.mit.edu	37	14	101418266	101418266	+	5'Flank	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101418266T>C	uc001yit.2	+						SNORD114-2_uc001yis.2_RNA|SNORD114-4_uc001yiu.2_5'Flank	NR_003195				Homo sapiens cDNA FLJ10247 fis, clone HEMBB1000705.												0																		---	---	---	---
ZNF839	55778	broad.mit.edu	37	14	102792994	102792994	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102792994T>C	uc001ylo.2	+	2	963	c.613T>C	c.(613-615)TCA>CCA	p.S205P	ZNF839_uc010awk.1_Missense_Mutation_p.S321P|ZNF839_uc001ylp.2_RNA|ZNF839_uc001ylq.1_Missense_Mutation_p.S205P|ZNF839_uc001ylr.2_Missense_Mutation_p.S205P	NM_018335	NP_060805	A8K0R7	ZN839_HUMAN	zinc finger protein 839	205	C2H2-type.					intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C14orf73	91828	broad.mit.edu	37	14	103571411	103571411	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103571411T>C	uc001ymk.2	+	6	1542	c.1466_splice	c.e6+2	p.R489_splice		NM_001077594	NP_001071062			hypothetical protein LOC91828												0		Melanoma(154;0.155)	Epithelial(46;0.221)													OREG0022947	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C14orf73	91828	broad.mit.edu	37	14	103574861	103574861	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103574861A>G	uc001ymk.2	+							NM_001077594	NP_001071062			hypothetical protein LOC91828												0		Melanoma(154;0.155)	Epithelial(46;0.221)															---	---	---	---
EIF5	1983	broad.mit.edu	37	14	103802217	103802217	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103802217G>T	uc001ymq.2	+	3	542	c.20G>T	c.(19-21)CGC>CTC	p.R7L	EIF5_uc001ymr.2_Missense_Mutation_p.R7L|EIF5_uc001yms.2_Missense_Mutation_p.R7L|EIF5_uc001ymt.2_Missense_Mutation_p.R7L|EIF5_uc001ymu.2_Missense_Mutation_p.R7L|SNORA28_uc001ymv.1_5'Flank	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	7					regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			pancreas(1)|breast(1)|skin(1)	3		Melanoma(154;0.155)	Epithelial(46;0.182)															---	---	---	---
EIF5	1983	broad.mit.edu	37	14	103802238	103802238	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103802238A>G	uc001ymq.2	+	3	563	c.41A>G	c.(40-42)TAT>TGT	p.Y14C	EIF5_uc001ymr.2_Missense_Mutation_p.Y14C|EIF5_uc001yms.2_Missense_Mutation_p.Y14C|EIF5_uc001ymt.2_Missense_Mutation_p.Y14C|EIF5_uc001ymu.2_Missense_Mutation_p.Y14C|SNORA28_uc001ymv.1_5'Flank	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	14					regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			pancreas(1)|breast(1)|skin(1)	3		Melanoma(154;0.155)	Epithelial(46;0.182)															---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104129110	104129110	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104129110A>G	uc001yno.2	+	5	951	c.643A>G	c.(643-645)ACG>GCG	p.T215A	KLC1_uc010tyd.1_Missense_Mutation_p.T374A|KLC1_uc010tye.1_Missense_Mutation_p.T211A|KLC1_uc001ynm.1_Missense_Mutation_p.T215A|KLC1_uc001ynn.1_Missense_Mutation_p.T211A|KLC1_uc010tyf.1_Missense_Mutation_p.T215A	NM_182923	NP_891553	Q07866	KLC1_HUMAN	kinesin light chain 1 isoform 2	215	TPR 1.				blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)																---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105406625	105406625	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105406625C>T	uc010axc.1	-	7	15283	c.15163G>A	c.(15163-15165)GGG>AGG	p.G5055R	AHNAK2_uc001ypx.2_Missense_Mutation_p.G4955R	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5055						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105410125	105410125	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105410125T>G	uc010axc.1	-	7	11783	c.11663A>C	c.(11662-11664)AAG>ACG	p.K3888T	AHNAK2_uc001ypx.2_Missense_Mutation_p.K3788T	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3888						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106091275	106091275	+	RNA	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106091275C>T	uc010tyt.1	-	3647		c.62233G>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106539202	106539202	+	RNA	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106539202G>A	uc010tyt.1	-	1519		c.31491C>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107013089	107013089	+	RNA	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107013089A>G	uc010tyt.1	-	169		c.7968T>C								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20170027	20170027	+	IGR	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20170027T>G								None (None upstream) : GOLGA6L6 (567067 downstream)																																			---	---	---	---
NDN	4692	broad.mit.edu	37	15	23931581	23931581	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23931581A>G	uc001ywk.2	-	1	870	c.784T>C	c.(784-786)TGG>CGG	p.W262R		NM_002487	NP_002478	Q99608	NECD_HUMAN	necdin	262	MAGE.				negative regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perikaryon	DNA binding				0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)										Prader-Willi_syndrome				---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25220628	25220628	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25220628T>C	uc001ywp.1	+	8	1017	c.127T>C	c.(127-129)TGT>CGT	p.C43R	SNRPN_uc001ywq.1_Missense_Mutation_p.C43R|SNRPN_uc001ywr.1_Missense_Mutation_p.C43R|SNRPN_uc001yws.1_Missense_Mutation_p.C43R|SNRPN_uc001ywt.1_Missense_Mutation_p.C43R|SNRPN_uc001ywv.1_Missense_Mutation_p.C46R|SNRPN_uc001yww.1_Missense_Mutation_p.C43R|SNRPN_uc001ywx.1_Missense_Mutation_p.C43R|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_3'UTR	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N	43				Missing (in Ref. 8).	RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)										Prader-Willi_syndrome				---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28202861	28202861	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28202861C>T	uc001zbh.3	-	16	1767	c.1657G>A	c.(1657-1659)GTC>ATC	p.V553I	OCA2_uc010ayv.2_Missense_Mutation_p.V529I	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	553	Cytoplasmic (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										Oculocutaneous_Albinism				---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28211897	28211897	+	Silent	SNP	C	T	T	rs151046206		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28211897C>T	uc001zbh.3	-	15	1685	c.1575G>A	c.(1573-1575)CCG>CCA	p.P525P	OCA2_uc010ayv.2_Silent_p.P501P	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	525	Helical; (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										Oculocutaneous_Albinism				---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28413691	28413691	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28413691C>T	uc001zbj.2	-	67	10381	c.10275G>A	c.(10273-10275)CCG>CCA	p.P3425P		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	3425					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28538101	28538101	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28538101T>G	uc001zbj.2	-	4	361	c.255A>C	c.(253-255)GAA>GAC	p.E85D	HERC2_uc001zbl.1_5'UTR	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	85					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33261050	33261050	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33261050A>C	uc001zhf.3	-	4	2183	c.2183T>G	c.(2182-2184)CTT>CGT	p.L728R		NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	951	FH1.|Pro-rich.				actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	34064222	34064222	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34064222T>G	uc001zhi.2	+	63	8988	c.8918T>G	c.(8917-8919)CTT>CGT	p.L2973R	RYR3_uc010bar.2_Missense_Mutation_p.L2973R	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2973	Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
TMCO5A	145942	broad.mit.edu	37	15	38235602	38235602	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38235602A>G	uc001zjw.2	+						TMCO5A_uc001zjv.1_Intron	NM_152453	NP_689666			transmembrane and coiled-coil domains 5A							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
SPRED1	161742	broad.mit.edu	37	15	38643558	38643558	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38643558A>G	uc001zka.3	+	7	1363	c.1028A>G	c.(1027-1029)AAT>AGT	p.N343S		NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain	343	SPR.				inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)										Legius_syndrome				---	---	---	---
PAK6	56924	broad.mit.edu	37	15	40564623	40564623	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40564623C>T	uc010bbl.2	+	6	1497	c.1057C>T	c.(1057-1059)CGC>TGC	p.R353C	PAK6_uc010bbm.2_Missense_Mutation_p.R353C|PAK6_uc001zky.3_Missense_Mutation_p.R353C|PAK6_uc010bbn.2_Missense_Mutation_p.R353C|PAK6_uc001zlb.2_Missense_Mutation_p.R353C	NM_001128628	NP_001122100	Q9NQU5	PAK6_HUMAN	p21-activated kinase 6	353	Linker.						ATP binding|protein binding|protein serine/threonine kinase activity			lung(5)|large_intestine(1)|ovary(1)|skin(1)	8		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)														---	---	---	---
PLCB2	5330	broad.mit.edu	37	15	40590804	40590804	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40590804T>A	uc001zld.2	-	10	1257	c.956A>T	c.(955-957)AAT>ATT	p.N319I	PLCB2_uc010bbo.2_Missense_Mutation_p.N319I|PLCB2_uc010ucm.1_Missense_Mutation_p.N319I	NM_004573	NP_004564	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	319	PI-PLC X-box.				activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)|breast(3)|kidney(1)|pancreas(1)	8		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)														---	---	---	---
C15orf52	388115	broad.mit.edu	37	15	40630826	40630826	+	Silent	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40630826T>G	uc001zlh.3	-	5	571	c.555A>C	c.(553-555)GCA>GCC	p.A185A	C15orf52_uc001zli.1_Silent_p.A117A|C15orf52_uc010ucn.1_5'Flank	NM_207380	NP_997263	Q6ZUT6	CO052_HUMAN	hypothetical protein LOC388115	185										large_intestine(1)	1		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)												OREG0023060	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40911163	40911163	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40911163A>G	uc010bbs.1	+	10	568	c.407A>G	c.(406-408)AAC>AGC	p.N136S	CASC5_uc010ucq.1_Intron|CASC5_uc001zme.2_Missense_Mutation_p.N110S|CASC5_uc010bbt.1_Missense_Mutation_p.N110S	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1	136	Interaction with BUB1 and BUB1B.				acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)														---	---	---	---
VPS18	57617	broad.mit.edu	37	15	41192619	41192619	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41192619T>A	uc001zne.2	+	4	1942	c.1603T>A	c.(1603-1605)TGG>AGG	p.W535R		NM_020857	NP_065908	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18	535					endosome organization|lysosome organization|protein transport	HOPS complex|late endosome membrane|lysosomal membrane	metal ion binding|protein binding			ovary(2)|large_intestine(1)	3		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)														---	---	---	---
SPTBN5	51332	broad.mit.edu	37	15	42148707	42148707	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42148707G>A	uc001zos.2	-	53	9126	c.8793C>T	c.(8791-8793)GCC>GCT	p.A2931A		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2966	Spectrin 26.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)														---	---	---	---
GANC	2595	broad.mit.edu	37	15	42641615	42641615	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42641615G>A	uc001zpi.2	+	22	2767	c.2453G>A	c.(2452-2454)GGC>GAC	p.G818D	CAPN3_uc001zpk.1_5'UTR|CAPN3_uc001zpl.1_5'UTR	NM_198141	NP_937784	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	818					carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)														---	---	---	---
ZFP106	64397	broad.mit.edu	37	15	42734562	42734562	+	Nonsense_Mutation	SNP	G	A	A	rs141505106	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42734562G>A	uc001zpw.2	-	7	3738	c.3403C>T	c.(3403-3405)CGA>TGA	p.R1135*	ZFP106_uc001zpu.2_Nonsense_Mutation_p.R320*|ZFP106_uc001zpv.2_Nonsense_Mutation_p.R320*|ZFP106_uc001zpx.2_Nonsense_Mutation_p.R363*	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	1135						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43094027	43094027	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43094027A>C	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771			tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)														---	---	---	---
LCMT2	9836	broad.mit.edu	37	15	43622543	43622543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43622543C>T	uc001zrg.2	-	1	349	c.145G>A	c.(145-147)GCA>ACA	p.A49T	LCMT2_uc010udn.1_Intron|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608	O60294	LCMT2_HUMAN	leucine carboxyl methyltransferase 2	49					tRNA processing		methyltransferase activity|protein binding				0		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)													---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44065384	44065384	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44065384T>C	uc001zsw.1	-	11	1527	c.1124A>G	c.(1123-1125)TAC>TGC	p.Y375C	ELL3_uc001zsv.1_Missense_Mutation_p.Y329C|ELL3_uc001zsx.1_Missense_Mutation_p.Y259C	NM_025165	NP_079441	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	375					positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44944003	44944003	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44944003A>G	uc001ztx.2	-	6	1173	c.1142T>C	c.(1141-1143)GTG>GCG	p.V381A	SPG11_uc010ueh.1_Missense_Mutation_p.V381A|SPG11_uc010uei.1_Missense_Mutation_p.V381A|SPG11_uc001zua.1_Missense_Mutation_p.V381A	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	381	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
TRIM69	140691	broad.mit.edu	37	15	45059837	45059837	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45059837A>G	uc001zuf.2	+	8	2265	c.1370A>G	c.(1369-1371)TAC>TGC	p.Y457C	TRIM69_uc001zui.1_Missense_Mutation_p.Y253C|TRIM69_uc010bdy.1_Missense_Mutation_p.Y236C|TRIM69_uc001zug.1_Missense_Mutation_p.Y457C|TRIM69_uc001zuh.1_Missense_Mutation_p.Y298C	NM_182985	NP_892030	Q86WT6	TRI69_HUMAN	tripartite motif-containing 69 isoform a	457	B30.2/SPRY.				apoptosis	nuclear speck	zinc ion binding				0		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)														---	---	---	---
SLC12A1	6557	broad.mit.edu	37	15	48543969	48543969	+	Splice_Site	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48543969T>G	uc001zwn.3	+	15	2158	c.1942_splice	c.e15+2	p.D648_splice	SLC12A1_uc010uew.1_Splice_Site_p.D454_splice|SLC12A1_uc010bem.2_Splice_Site_p.D648_splice|SLC12A1_uc001zwq.3_Splice_Site_p.D419_splice|SLC12A1_uc001zwr.3_Splice_Site_p.D375_splice	NM_000338	NP_000329			sodium potassium chloride cotransporter 2						potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)													---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48725097	48725097	+	Silent	SNP	T	C	C	rs150858138	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48725097T>C	uc001zwx.1	-	55	7033	c.6705A>G	c.(6703-6705)GGA>GGG	p.G2235G	FBN1_uc010beo.1_RNA	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	2235	EGF-like 38; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48936816	48936816	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48936816C>T	uc001zwx.1	-	2	479	c.151G>A	c.(151-153)GAC>AAC	p.D51N		NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	51					heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
KIAA1370	56204	broad.mit.edu	37	15	52901974	52901974	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52901974T>C	uc002acg.3	-	6	1290	c.1137A>G	c.(1135-1137)CAA>CAG	p.Q379Q	KIAA1370_uc002ach.3_RNA|KIAA1370_uc010bfg.1_Silent_p.Q291Q|KIAA1370_uc010ugf.1_Silent_p.Q386Q	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204	379											0				all cancers(107;0.0803)														---	---	---	---
ONECUT1	3175	broad.mit.edu	37	15	53081473	53081473	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53081473C>T	uc002aci.1	-	1	737	c.609G>A	c.(607-609)CCG>CCA	p.P203P		NM_004498	NP_004489	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	203					endocrine pancreas development	nucleus	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding				0				all cancers(107;0.0708)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55657475	55657475	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55657475C>G	uc002acv.1	-	7	904	c.739G>C	c.(739-741)GTC>CTC	p.V247L	CCPG1_uc002acy.2_Missense_Mutation_p.V247L|CCPG1_uc002acu.1_Missense_Mutation_p.V103L|CCPG1_uc002acw.1_Intron|CCPG1_uc002acx.2_Missense_Mutation_p.V247L|CCPG1_uc010bfk.1_Missense_Mutation_p.V247L|CCPG1_uc002acz.1_Missense_Mutation_p.V247L	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2	247	Lumenal (Potential).|Interaction with MCF2L and SRC (By similarity).				cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56393577	56393577	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56393577A>G	uc010bfn.2	-	7	791	c.791T>C	c.(790-792)GTA>GCA	p.V264A	RFX7_uc010ugk.1_RNA|RFX7_uc002adn.1_Missense_Mutation_p.V78A	NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	167					regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
ANXA2	302	broad.mit.edu	37	15	60641385	60641385	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60641385C>T	uc002agn.2	-	13	1009	c.849G>A	c.(847-849)ACG>ACA	p.T283T	ANXA2_uc002agk.2_Silent_p.T283T|ANXA2_uc002agl.2_Silent_p.T283T|ANXA2_uc002agm.2_Silent_p.T301T|ANXA2_uc010uhd.1_Intron	NM_001136015	NP_001129487	P07355	ANXA2_HUMAN	annexin A2 isoform 2	283	Annexin 4.				angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)													---	---	---	---
RORA	6095	broad.mit.edu	37	15	60907207	60907207	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60907207G>A	uc002agv.2	-						RORA_uc002agw.2_Silent_p.L53L|RORA_uc002agx.2_Intron	NM_134260	NP_599022			RAR-related orphan receptor A isoform b						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62238081	62238081	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62238081C>T	uc002agz.2	-	45	5055	c.4981G>A	c.(4981-4983)GCT>ACT	p.A1661T	VPS13C_uc002aha.2_Missense_Mutation_p.A1618T|VPS13C_uc002ahb.1_Missense_Mutation_p.A1661T|VPS13C_uc002ahc.1_Missense_Mutation_p.A1618T	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	1661					protein localization					ovary(2)	2																		---	---	---	---
ZNF609	23060	broad.mit.edu	37	15	64970450	64970450	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64970450A>G	uc002ann.2	+	5	3538	c.3538A>G	c.(3538-3540)AAG>GAG	p.K1180E		NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609	1180						nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
AAGAB	79719	broad.mit.edu	37	15	67528769	67528769	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67528769A>G	uc002aqk.3	-	3	443	c.338T>C	c.(337-339)GTC>GCC	p.V113A	AAGAB_uc002aql.2_Missense_Mutation_p.V4A|AAGAB_uc010uju.1_Missense_Mutation_p.V4A	NM_024666	NP_078942	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin-binding protein p34	113					protein transport	cytoplasm					0																		---	---	---	---
PAQR5	54852	broad.mit.edu	37	15	69682068	69682068	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69682068C>T	uc002arz.2	+	6	839	c.461C>T	c.(460-462)GCC>GTC	p.A154V	PAQR5_uc002asa.2_Missense_Mutation_p.A154V	NM_017705	NP_060175	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	154	Helical; Name=4; (Potential).				cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding			ovary(2)	2																		---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69728066	69728066	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69728066A>G	uc002asb.2	+	12	1345	c.1228A>G	c.(1228-1230)ATC>GTC	p.I410V	KIF23_uc002asc.2_Missense_Mutation_p.I410V|KIF23_uc010bii.2_Missense_Mutation_p.I300V|KIF23_uc010ukc.1_Missense_Mutation_p.I227V|KIF23_uc010bih.1_RNA	NM_138555	NP_612565	Q02241	KIF23_HUMAN	kinesin family member 23 isoform 1	410					blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71704166	71704166	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71704166A>C	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
PARP6	56965	broad.mit.edu	37	15	72541618	72541618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72541618C>T	uc002auc.2	-	19	1988	c.1529G>A	c.(1528-1530)AGC>AAC	p.S510N	PARP6_uc002aua.2_Missense_Mutation_p.S356N|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Missense_Mutation_p.S511N	NM_020214	NP_064599	Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	510	PARP catalytic.						NAD+ ADP-ribosyltransferase activity				0																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73418845	73418845	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73418845T>C	uc002avm.3	+	4	954	c.812T>C	c.(811-813)GTT>GCT	p.V271A	NEO1_uc010ukx.1_Missense_Mutation_p.V271A|NEO1_uc010uky.1_Missense_Mutation_p.V271A|NEO1_uc010ukz.1_5'UTR	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor	271	Extracellular (Potential).|Ig-like C2-type 3.				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1																		---	---	---	---
PTPN9	5780	broad.mit.edu	37	15	75798010	75798010	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75798010A>G	uc002bal.2	-							NM_002833	NP_002824			protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2																		---	---	---	---
FBXO22	26263	broad.mit.edu	37	15	76222249	76222249	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76222249G>A	uc002bbk.2	+	6	758	c.653G>A	c.(652-654)CGT>CAT	p.R218H	FBXO22_uc002bbj.1_Missense_Mutation_p.R218H|FBXO22_uc002bbl.2_Missense_Mutation_p.R114H	NM_147188	NP_671717	Q8NEZ5	FBX22_HUMAN	F-box only protein 22 isoform a	218					ubiquitin-dependent protein catabolic process		ubiquitin-protein ligase activity				0																		---	---	---	---
TBC1D2B	23102	broad.mit.edu	37	15	78317659	78317659	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78317659T>C	uc002bcy.3	-	5	1028	c.1028A>G	c.(1027-1029)CAG>CGG	p.Q343R	TBC1D2B_uc010bla.2_Missense_Mutation_p.Q343R	NM_144572	NP_653173	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B isoform a	343	Potential.					intracellular	protein binding|Rab GTPase activator activity			ovary(1)|large_intestine(1)|breast(1)	3																		---	---	---	---
MEX3B	84206	broad.mit.edu	37	15	82336434	82336434	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82336434G>A	uc002bgq.1	-	2	1092	c.777C>T	c.(775-777)TCC>TCT	p.S259S		NM_032246	NP_115622	Q6ZN04	MEX3B_HUMAN	mex-3 homolog B	259					protein autophosphorylation	cytoplasmic mRNA processing body|nucleus	calcium ion binding|RNA binding|zinc ion binding			breast(1)|kidney(1)	2																		---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85360124	85360124	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85360124C>T	uc002ble.2	+	1	214	c.47C>T	c.(46-48)GCG>GTG	p.A16V		NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	16					heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
ISG20	3669	broad.mit.edu	37	15	89195456	89195456	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89195456T>G	uc002bmv.1	+	3	637	c.344T>G	c.(343-345)CTG>CGG	p.L115R	ISG20_uc002bmu.1_RNA|ISG20_uc002bmw.1_RNA|ISG20_uc010upn.1_RNA	NM_002201	NP_002192	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease	115					cell proliferation|DNA catabolic process, exonucleolytic|response to virus|RNA catabolic process|type I interferon-mediated signaling pathway	PML body	3'-5'-exoribonuclease activity|exoribonuclease II activity|metal ion binding|RNA binding|single-stranded DNA specific 3'-5' exodeoxyribonuclease activity				0	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)															---	---	---	---
RHCG	51458	broad.mit.edu	37	15	90023542	90023542	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90023542C>A	uc002bnz.2	-	4	644	c.620G>T	c.(619-621)AGC>ATC	p.S207I	RHCG_uc002bny.2_5'Flank|RHCG_uc002boa.2_RNA|RHCG_uc010bnq.1_Missense_Mutation_p.S91I	NM_016321	NP_057405	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	207	Cytoplasmic (Potential).				amine transport|cellular ion homeostasis|epithelial cell differentiation|transepithelial ammonium transport	apical plasma membrane|basolateral plasma membrane|cytoplasmic vesicle|integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			kidney(1)	1	Lung NSC(78;0.0237)|all_lung(78;0.0478)																	---	---	---	---
AP3S2	10239	broad.mit.edu	37	15	90454008	90454008	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90454008G>A	uc002bos.3	-	2	291	c.136C>T	c.(136-138)CGG>TGG	p.R46W	C15orf38_uc002bot.1_RNA|C15orf38_uc002bou.2_Missense_Mutation_p.R46W	NM_182616	NP_872422	P59780	AP3S2_HUMAN	hypothetical protein LOC348110	Error:Variant_position_missing_in_P59780_after_alignment					intracellular protein transport|vesicle-mediated transport	cytoplasmic vesicle membrane|Golgi apparatus|membrane coat	protein transporter activity				0	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)															---	---	---	---
PRC1	9055	broad.mit.edu	37	15	91524789	91524789	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91524789G>A	uc002bqm.2	-	5	769	c.612C>T	c.(610-612)GAC>GAT	p.D204D	PRC1_uc002bqn.2_Silent_p.D204D|PRC1_uc002bqo.2_Silent_p.D204D|PRC1_uc010uqs.1_Silent_p.D163D|PRC1_uc010uqt.1_Silent_p.D152D	NM_003981	NP_003972	O43663	PRC1_HUMAN	protein regulator of cytokinesis 1 isoform 1	204	Dimerization.				cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding			ovary(1)|skin(1)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)																	---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99514341	99514341	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514341C>T	uc002bum.2	-	3	274	c.68G>A	c.(67-69)CGG>CAG	p.R23Q	PGPEP1L_uc010bop.2_5'UTR|PGPEP1L_uc002bun.2_RNA	NM_001102612	NP_001096082	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase 1-like protein	23					proteolysis		cysteine-type peptidase activity				0																		---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100636574	100636574	+	Silent	SNP	G	A	A	rs142335314		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100636574G>A	uc002bvv.1	-	15	2203	c.2124C>T	c.(2122-2124)CAC>CAT	p.H708H	ADAMTS17_uc002bvx.1_Silent_p.H465H	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	708	Spacer.				proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
PCSK6	5046	broad.mit.edu	37	15	101887963	101887963	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101887963C>T	uc002bwy.2	-						PCSK6_uc010bpd.2_Intron|PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Missense_Mutation_p.V642M|PCSK6_uc002bxd.1_3'UTR	NM_002570	NP_002561			paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
MSLN	10232	broad.mit.edu	37	16	816649	816649	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:816649T>C	uc002cjw.1	+	13	1287	c.1236T>C	c.(1234-1236)CCT>CCC	p.P412P	MSLN_uc002cjt.1_Intron|MSLN_uc002cju.1_Intron|MSLN_uc010brd.1_Intron|MSLN_uc002cjv.1_Intron|MSLN_uc002cjx.1_Intron|MSLN_uc002cjy.1_Intron	NM_013404	NP_037536	Q13421	MSLN_HUMAN	mesothelin isoform 2 preproprotein	412					cell adhesion	anchored to membrane|extracellular region|Golgi apparatus|plasma membrane				pancreas(1)	1		Hepatocellular(780;0.00335)																---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1257104	1257104	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1257104G>A	uc002cks.2	+	13	3141	c.2893G>A	c.(2893-2895)GTC>ATC	p.V965I	CACNA1H_uc002ckt.2_Missense_Mutation_p.V965I|CACNA1H_uc002cku.2_5'Flank|CACNA1H_uc010brj.2_5'Flank|CACNA1H_uc002ckv.2_5'Flank	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	965	II.|Extracellular (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
BAIAP3	8938	broad.mit.edu	37	16	1392275	1392275	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1392275A>G	uc002clk.1	+	11	1053	c.1053A>G	c.(1051-1053)ATA>ATG	p.I351M	BAIAP3_uc002clj.2_Missense_Mutation_p.I333M|BAIAP3_uc010uuz.1_Missense_Mutation_p.I316M|BAIAP3_uc010uva.1_Missense_Mutation_p.I288M|BAIAP3_uc010uvb.1_Missense_Mutation_p.I368M|BAIAP3_uc010uvc.1_Missense_Mutation_p.I316M	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3	351					G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
RPS2	6187	broad.mit.edu	37	16	2012459	2012459	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2012459T>C	uc002cnn.2	-						RPS2_uc010bsa.1_Intron|RPS2_uc002cnl.2_Intron|RPS2_uc002cnm.2_Intron|RPS2_uc002cno.2_Intron|SNORA10_uc002cnp.1_RNA|SNHG9_uc002cnr.2_5'Flank|SNORA78_uc002cns.1_5'Flank	NM_002952	NP_002943			ribosomal protein S2						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleoplasm	fibroblast growth factor 1 binding|fibroblast growth factor 3 binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
TBL3	10607	broad.mit.edu	37	16	2027295	2027295	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2027295G>A	uc002cnu.1	+						TBL3_uc002cnv.1_Intron|TBL3_uc010bsb.1_Intron|TBL3_uc010bsc.1_Intron|TBL3_uc010uvt.1_Intron|TBL3_uc002cnw.1_5'Flank	NM_006453	NP_006444			transducin beta-like 3						G-protein signaling, coupled to cGMP nucleotide second messenger|rRNA processing	nucleolus|small-subunit processome	receptor signaling protein activity				0																		---	---	---	---
TSC2	7249	broad.mit.edu	37	16	2106665	2106665	+	Silent	SNP	C	T	T	rs35501344		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2106665C>T	uc002con.2	+	8	775	c.669C>T	c.(667-669)GAC>GAT	p.D223D	TSC2_uc010bsd.2_Silent_p.D223D|TSC2_uc002coo.2_Silent_p.D223D|TSC2_uc010uvv.1_Silent_p.D186D|TSC2_uc010uvw.1_Silent_p.D174D|TSC2_uc002cop.2_Silent_p.D23D	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	223	Required for interaction with TSC1.				cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity	p.D223N(1)		central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)						D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
PKD1	5310	broad.mit.edu	37	16	2150211	2150211	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2150211G>A	uc002cos.1	-	28	9877	c.9668C>T	c.(9667-9669)ACG>ATG	p.T3223M	PKD1_uc002cot.1_Missense_Mutation_p.T3223M|PKD1_uc010bse.1_RNA	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	3223	PLAT.|Cytoplasmic (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
TRAF7	84231	broad.mit.edu	37	16	2223954	2223954	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2223954G>A	uc002cow.2	+	13	1267	c.1168G>A	c.(1168-1170)GGG>AGG	p.G390R		NM_032271	NP_115647	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7	390					activation of MAPKKK activity|apoptosis|regulation of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic membrane-bounded vesicle|ubiquitin ligase complex	identical protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
PGP	283871	broad.mit.edu	37	16	2263803	2263803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2263803C>T	uc002cpk.1	-	2	936	c.892G>A	c.(892-894)GTG>ATG	p.V298M	C16orf79_uc002cpi.1_5'Flank|C16orf79_uc010bsh.2_5'Flank|PGP_uc010uvz.1_RNA	NM_001042371	NP_001035830	A6NDG6	PGP_HUMAN	phosphoglycolate phosphatase	298					carbohydrate metabolic process		phosphoglycolate phosphatase activity			skin(1)	1																		---	---	---	---
PRSS27	83886	broad.mit.edu	37	16	2763683	2763683	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2763683C>T	uc002crf.2	-	5	916	c.525G>A	c.(523-525)CCG>CCA	p.P175P	PRSS27_uc002cre.2_Silent_p.P139P|PRSS27_uc002crg.2_Silent_p.P73P|PRSS27_uc010bst.1_Silent_p.P73P	NM_031948	NP_114154	Q9BQR3	PRS27_HUMAN	marapsin precursor	175	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
MEFV	4210	broad.mit.edu	37	16	3299587	3299587	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3299587G>A	uc002cun.1	-	3	1144	c.1104C>T	c.(1102-1104)AGC>AGT	p.S368S		NM_000243	NP_000234	O15553	MEFV_HUMAN	Mediterranean fever protein	368					inflammatory response	cytoplasm|microtubule|microtubule associated complex|nucleus	actin binding|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|lung(1)	6					Colchicine(DB01394)													---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3640962	3640962	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3640962C>A	uc002cvp.2	-	12	3304	c.2677G>T	c.(2677-2679)GGT>TGT	p.G893C		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	893	Interaction with PLK1 and TERF2-TERF2IP.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0													Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3781793	3781793	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3781793A>G	uc002cvv.2	-	29	5078	c.4874T>C	c.(4873-4875)ATG>ACG	p.M1625T	CREBBP_uc002cvw.2_Missense_Mutation_p.M1587T	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1625	Interaction with TRERF1.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding	p.M1625L(1)		haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
SRL	6345	broad.mit.edu	37	16	4247798	4247798	+	Splice_Site	SNP	A	G	G	rs112367857		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4247798A>G	uc002cvz.3	-	4	389	c.376_splice	c.e4+1	p.G126_splice	SRL_uc002cvy.3_Splice_Site	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
TFAP4	7023	broad.mit.edu	37	16	4312555	4312555	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4312555G>A	uc010uxg.1	-	2	491	c.237C>T	c.(235-237)GAC>GAT	p.D79D		NM_003223	NP_003214	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer	79	Helix-loop-helix motif.				DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle	transcriptional repressor complex	E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1																		---	---	---	---
TFAP4	7023	broad.mit.edu	37	16	4322659	4322659	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4322659C>A	uc010uxg.1	-	1	343	c.89G>T	c.(88-90)AGC>ATC	p.S30I		NM_003223	NP_003214	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer	30					DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle	transcriptional repressor complex	E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1																		---	---	---	---
ALG1	56052	broad.mit.edu	37	16	5129110	5129110	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5129110G>A	uc002cym.2	+						ALG1_uc002cyj.2_Intron|ALG1_uc002cyn.2_Intron|ALG1_uc010bue.2_Intron|ALG1_uc010uxy.1_Intron	NM_019109	NP_061982			beta-1,4-mannosyltransferase						dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(90;0.0164)																---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11219992	11219992	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11219992A>G	uc002dao.2	+	22	2860	c.2630A>G	c.(2629-2631)GAC>GGC	p.D877G	CLEC16A_uc002dan.3_Missense_Mutation_p.D859G|CLEC16A_uc002dap.2_5'UTR	NM_015226	NP_056041	Q2KHT3	CL16A_HUMAN	C-type lectin domain family 16, member A	877										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RUNDC2A	84127	broad.mit.edu	37	16	12142408	12142408	+	Missense_Mutation	SNP	G	A	A	rs143274296		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12142408G>A	uc002dbw.1	+	7	741	c.679G>A	c.(679-681)GTC>ATC	p.V227I		NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A	227										ovary(1)	1								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
PARN	5073	broad.mit.edu	37	16	14540793	14540793	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14540793T>C	uc010uzd.1	-	23	1958	c.1816A>G	c.(1816-1818)AAA>GAA	p.K606E	PARN_uc010uzc.1_Missense_Mutation_p.K545E|PARN_uc010uze.1_Missense_Mutation_p.K560E|PARN_uc010uzf.1_Missense_Mutation_p.K431E	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation	606					female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
NOMO1	23420	broad.mit.edu	37	16	14976505	14976505	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14976505C>T	uc002dcv.2	+	26	3148	c.3082C>T	c.(3082-3084)CGG>TGG	p.R1028W		NM_014287	NP_055102	Q15155	NOMO1_HUMAN	nodal modulator 1 precursor	1028	Extracellular (Potential).					integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			ovary(1)	1																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17232375	17232375	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17232375G>A	uc002dfa.2	-	8	1686	c.1601C>T	c.(1600-1602)ACG>ATG	p.T534M		NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	534	Lumenal (Potential).				glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
ACSM2A	123876	broad.mit.edu	37	16	20494494	20494494	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20494494A>G	uc010bwe.2	+	14	1863	c.1624A>G	c.(1624-1626)AGA>GGA	p.R542G	ACSM2A_uc002dhf.3_Missense_Mutation_p.R542G|ACSM2A_uc002dhg.3_Missense_Mutation_p.R542G|ACSM2A_uc010vay.1_Missense_Mutation_p.R463G|ACSM2A_uc002dhh.3_Missense_Mutation_p.R172G	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member	542	Coenzyme A binding.				fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			skin(2)|breast(1)	3																		---	---	---	---
LOC81691	81691	broad.mit.edu	37	16	20851786	20851786	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20851786G>A	uc002dhv.2	+	15	1885	c.1622G>A	c.(1621-1623)CGT>CAT	p.R541H	ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Missense_Mutation_p.R541H|LOC81691_uc002dhw.2_Missense_Mutation_p.R284H|LOC81691_uc002dhy.3_Missense_Mutation_p.R541H	NM_030941	NP_112203	Q96IC2	REXON_HUMAN	exonuclease NEF-sp isoform 1	541	RRM 1.					nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21042529	21042529	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21042529G>A	uc010vbe.1	-	37	5277	c.5277C>T	c.(5275-5277)TGC>TGT	p.C1759C		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1759	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21049222	21049222	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21049222C>T	uc010vbe.1	-	34	4811	c.4811G>A	c.(4810-4812)CGC>CAC	p.R1604H		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1604	AAA 1 (By similarity).			YGMR -> FGLH (in Ref. 5; CAB06059).	ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21109952	21109952	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21109952C>T	uc010vbe.1	-	17	2505	c.2505G>A	c.(2503-2505)GCG>GCA	p.A835A		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	835	Stem (By similarity).|Potential.				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
ZP2	7783	broad.mit.edu	37	16	21222833	21222833	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21222833G>T	uc002dii.2	-	1	36	c.36C>A	c.(34-36)CCC>CCA	p.P12P	ZP2_uc010bwn.1_Silent_p.P51P|ZP2_uc010bwo.2_Silent_p.P51P	NM_003460	NP_003451	Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 preproprotein	12					binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(48;0.0573)														---	---	---	---
ERN2	10595	broad.mit.edu	37	16	23706239	23706239	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23706239T>C	uc002dma.3	-	17	2223	c.2054A>G	c.(2053-2055)GAC>GGC	p.D685G	ERN2_uc010bxp.2_Missense_Mutation_p.D633G	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	637	Protein kinase.|Cytoplasmic (Potential).	Proton acceptor (By similarity).			apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)														---	---	---	---
CACNG3	10368	broad.mit.edu	37	16	24372978	24372978	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24372978T>C	uc002dmf.2	+	4	1942	c.742T>C	c.(742-744)TCC>CCC	p.S248P		NM_006539	NP_006530	O60359	CCG3_HUMAN	voltage-dependent calcium channel gamma-3	248					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)														---	---	---	---
TNRC6A	27327	broad.mit.edu	37	16	24803058	24803058	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24803058G>A	uc002dmm.2	+	6	3209	c.3095G>A	c.(3094-3096)CGT>CAT	p.R1032H	TNRC6A_uc010bxs.2_Missense_Mutation_p.R779H|TNRC6A_uc010vcc.1_Missense_Mutation_p.R779H|TNRC6A_uc002dmn.2_Missense_Mutation_p.R779H|TNRC6A_uc002dmo.2_Missense_Mutation_p.R779H	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1032	Sufficient for interaction with EIF2C1 and EIF2C4.				negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)														---	---	---	---
ZKSCAN2	342357	broad.mit.edu	37	16	25258442	25258442	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25258442G>A	uc002dod.3	-	5	1482	c.1075C>T	c.(1075-1077)CGC>TGC	p.R359C	ZKSCAN2_uc010vcl.1_Missense_Mutation_p.R155C|ZKSCAN2_uc002doe.2_Missense_Mutation_p.R359C	NM_001012981	NP_001012999	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	359					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|breast(1)	4				GBM - Glioblastoma multiforme(48;0.0378)														---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27523220	27523220	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27523220T>C	uc002dov.1	-	7	1016	c.976A>G	c.(976-978)ACC>GCC	p.T326A	GTF3C1_uc002dou.2_Missense_Mutation_p.T326A	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	326						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	27856393	27856393	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27856393G>T	uc002doz.2	-						GSG1L_uc010bya.1_Intron|GSG1L_uc010bxz.1_Intron|GSG1L_uc002doy.2_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
ATXN2L	11273	broad.mit.edu	37	16	28845512	28845512	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28845512C>A	uc002drc.2	+	16	2320	c.2152C>A	c.(2152-2154)CAC>AAC	p.H718N	uc010vct.1_Intron|ATXN2L_uc002drb.2_Missense_Mutation_p.H718N|ATXN2L_uc002dqy.2_Missense_Mutation_p.H718N|ATXN2L_uc002dra.2_Missense_Mutation_p.H718N|ATXN2L_uc002dqz.2_Missense_Mutation_p.H718N|ATXN2L_uc010vdb.1_Missense_Mutation_p.H724N|ATXN2L_uc002dre.2_Missense_Mutation_p.H718N|ATXN2L_uc002drf.2_Missense_Mutation_p.H127N|ATXN2L_uc002drg.2_5'UTR	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A	718						membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
TAOK2	9344	broad.mit.edu	37	16	29990346	29990346	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29990346C>T	uc002dva.1	+	6	1187	c.404C>T	c.(403-405)GCG>GTG	p.A135V	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TAOK2_uc002dvb.1_Missense_Mutation_p.A135V|TAOK2_uc002dvc.1_Missense_Mutation_p.A135V|TAOK2_uc010bzm.1_Missense_Mutation_p.A135V|TAOK2_uc002dvd.1_5'Flank	NM_016151	NP_057235	Q9UL54	TAOK2_HUMAN	TAO kinase 2 isoform 2	135	Protein kinase.				actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
CORO1A	11151	broad.mit.edu	37	16	30199690	30199690	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30199690G>A	uc002dww.2	+	10	1196	c.1074G>A	c.(1072-1074)CTG>CTA	p.L358L	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|CORO1A_uc010bzq.2_Silent_p.L358L|CORO1A_uc010bzr.2_Intron|CORO1A_uc002dwx.2_Silent_p.L252L|CORO1A_uc002dwy.1_3'UTR|LOC606724_uc002dwz.1_5'Flank	NM_007074	NP_009005	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	358					cell-substrate adhesion|innate immune response|leukocyte chemotaxis|negative regulation of actin nucleation|phagolysosome assembly|positive chemotaxis|regulation of cell shape|uropod organization	actin filament|cortical actin cytoskeleton|lamellipodium|phagocytic cup|phagocytic vesicle membrane	actin filament binding|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein homodimerization activity				0																		---	---	---	---
MYLPF	29895	broad.mit.edu	37	16	30387188	30387188	+	Silent	SNP	C	T	T	rs140103472		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30387188C>T	uc002dxv.1	+	2	107	c.51C>T	c.(49-51)AGC>AGT	p.S17S		NM_013292	NP_037424	Q96A32	MLRS_HUMAN	myosin light chain, phosphorylatable, fast	17					skeletal muscle tissue development	muscle myosin complex	calcium ion binding|structural constituent of muscle				0			Colorectal(24;0.193)															---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30734373	30734373	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30734373G>A	uc002dze.1	+	24	4367	c.3982G>A	c.(3982-3984)GCC>ACC	p.A1328T	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.A1123T|SRCAP_uc010bzz.1_Missense_Mutation_p.A898T	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1328	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30750440	30750440	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30750440C>T	uc002dze.1	+	34	9464	c.9079C>T	c.(9079-9081)CGT>TGT	p.R3027C	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.R2822C	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	3027					interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30970171	30970171	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30970171A>G	uc002ead.1	+	2	805	c.119A>G	c.(118-120)TAC>TGC	p.Y40C	SETD1A_uc002eae.1_Missense_Mutation_p.Y40C	NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	40					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
C16orf58	64755	broad.mit.edu	37	16	31502222	31502222	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31502222C>A	uc002eci.1	-	13	1353	c.1341G>T	c.(1339-1341)AAG>AAT	p.K447N	C16orf58_uc002ecg.2_5'Flank|C16orf58_uc002ech.1_Missense_Mutation_p.K185N	NM_022744	NP_073581	Q96GQ5	CP058_HUMAN	hypothetical protein LOC64755	447						integral to membrane				ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	33020752	33020752	+	IGR	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33020752A>T								SLC6A10P (124289 upstream) : MIR1826 (944756 downstream)																																			---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48158156	48158156	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48158156T>C	uc002efc.1	-	10	1901	c.1555A>G	c.(1555-1557)AAG>GAG	p.K519E	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA|ABCC12_uc002efe.1_Missense_Mutation_p.K519E	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	519	ABC transporter 1.|ATP 1 (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
ABCC11	85320	broad.mit.edu	37	16	48248902	48248902	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48248902C>T	uc002eff.1	-	8	1488	c.1138G>A	c.(1138-1140)GGG>AGG	p.G380R	ABCC11_uc002efg.1_Missense_Mutation_p.G380R|ABCC11_uc002efh.1_Missense_Mutation_p.G380R|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	380	ABC transmembrane type-1 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												Cerumen_Type				---	---	---	---
ABCC11	85320	broad.mit.edu	37	16	48249234	48249234	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48249234C>T	uc002eff.1	-	7	1323	c.973G>A	c.(973-975)GTG>ATG	p.V325M	ABCC11_uc002efg.1_Missense_Mutation_p.V325M|ABCC11_uc002efh.1_Missense_Mutation_p.V325M|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	325	ABC transmembrane type-1 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												Cerumen_Type				---	---	---	---
HEATR3	55027	broad.mit.edu	37	16	50102752	50102752	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50102752A>C	uc002efw.2	+	3	535	c.373A>C	c.(373-375)ACC>CCC	p.T125P	HEATR3_uc002efx.2_Missense_Mutation_p.T39P	NM_182922	NP_891552	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	125							binding			ovary(1)|skin(1)	2																		---	---	---	---
NKD1	85407	broad.mit.edu	37	16	50667513	50667513	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50667513G>T	uc002egg.1	+	10	1458	c.1234G>T	c.(1234-1236)GGC>TGC	p.G412C		NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1	412					Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)														---	---	---	---
SNX20	124460	broad.mit.edu	37	16	50707351	50707351	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50707351A>G	uc002egk.2	-	4	1090	c.917T>C	c.(916-918)CTG>CCG	p.L306P	SNX20_uc010vgp.1_Intron|SNX20_uc002egi.3_Intron	NM_182854	NP_878274	Q7Z614	SNX20_HUMAN	sorting nexin 20 isoform 1	306					cell communication|protein transport	endosome membrane|nucleus|plasma membrane	phosphatidylinositol binding|protein binding			ovary(1)	1																		---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53190809	53190809	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53190809T>A	uc002ehb.2	+	1	972	c.808T>A	c.(808-810)TTT>ATT	p.F270I	CHD9_uc002egy.2_Missense_Mutation_p.F270I|CHD9_uc002egz.1_Missense_Mutation_p.F270I|CHD9_uc002eha.1_Missense_Mutation_p.F270I|CHD9_uc002ehc.2_Missense_Mutation_p.F270I	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	270	Ser-rich.				cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
SLC6A2	6530	broad.mit.edu	37	16	55706069	55706069	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55706069C>T	uc002eif.2	+	4	737	c.626C>T	c.(625-627)CCG>CTG	p.P209L	SLC6A2_uc010ccd.2_Missense_Mutation_p.P209L|SLC6A2_uc002eig.2_Missense_Mutation_p.P209L|SLC6A2_uc002eih.2_Missense_Mutation_p.P209L|SLC6A2_uc002eii.2_Missense_Mutation_p.P104L	NM_001043	NP_001034	P23975	SC6A2_HUMAN	solute carrier family 6 member 2	209	Extracellular (Potential).				synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity	p.P209P(1)		lung(4)|ovary(2)|pancreas(2)	8				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)													---	---	---	---
CES1	1066	broad.mit.edu	37	16	55860176	55860176	+	Missense_Mutation	SNP	G	T	T	rs5023781		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55860176G>T	uc002eim.2	-	3	397	c.289C>A	c.(289-291)CTC>ATC	p.L97I	CES1_uc002eil.2_Missense_Mutation_p.L98I|CES1_uc002ein.2_Missense_Mutation_p.L97I	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor	97					response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)													---	---	---	---
CES1	1066	broad.mit.edu	37	16	55860205	55860205	+	Missense_Mutation	SNP	C	A	A	rs5023782		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55860205C>A	uc002eim.2	-	3	368	c.260G>T	c.(259-261)TGC>TTC	p.C87F	CES1_uc002eil.2_Missense_Mutation_p.C88F|CES1_uc002ein.2_Missense_Mutation_p.C87F	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor	87					response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)													---	---	---	---
CX3CL1	6376	broad.mit.edu	37	16	57416565	57416565	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57416565C>T	uc002eli.2	+	3	882	c.815C>T	c.(814-816)ACG>ATG	p.T272M		NM_002996	NP_002987	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1 precursor	272	Mucin-like stalk.|Extracellular (Potential).				cell adhesion|cytokine-mediated signaling pathway|defense response|immune response|leukocyte adhesive activation|positive regulation of calcium-independent cell-cell adhesion|positive regulation of inflammatory response	cell surface|extracellular space|integral to membrane|plasma membrane	chemokine activity				0																		---	---	---	---
CX3CL1	6376	broad.mit.edu	37	16	57416914	57416914	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57416914T>C	uc002eli.2	+	3	1231	c.1164T>C	c.(1162-1164)GGT>GGC	p.G388G		NM_002996	NP_002987	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1 precursor	388	Cytoplasmic (Potential).				cell adhesion|cytokine-mediated signaling pathway|defense response|immune response|leukocyte adhesive activation|positive regulation of calcium-independent cell-cell adhesion|positive regulation of inflammatory response	cell surface|extracellular space|integral to membrane|plasma membrane	chemokine activity				0																		---	---	---	---
GPR97	222487	broad.mit.edu	37	16	57702267	57702267	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57702267C>T	uc002emh.2	+	1	111	c.8C>T	c.(7-9)ACG>ATG	p.T3M	GPR97_uc010cdc.2_Missense_Mutation_p.T3M|GPR97_uc010vhv.1_Translation_Start_Site|GPR97_uc010cdd.2_RNA	NM_170776	NP_740746	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97 precursor	3					neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58593706	58593706	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58593706A>G	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron|SNORA50_uc002eoa.1_RNA	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
GOT2	2806	broad.mit.edu	37	16	58750636	58750636	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58750636G>A	uc002eof.1	-	7	898	c.784C>T	c.(784-786)CGC>TGC	p.R262C	GOT2_uc010vim.1_Missense_Mutation_p.R219C	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor	262					aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61689544	61689544	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61689544C>G	uc002eog.1	-	11	1988	c.1736G>C	c.(1735-1737)AGT>ACT	p.S579T		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	579	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
CDH11	1009	broad.mit.edu	37	16	65032470	65032470	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65032470T>G	uc002eoi.2	-	4	952	c.518A>C	c.(517-519)AAT>ACT	p.N173T	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Missense_Mutation_p.N173T|CDH11_uc010vin.1_Missense_Mutation_p.N47T|CDH11_uc010vio.1_Missense_Mutation_p.N173T	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	173	Cadherin 2.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)				T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			---	---	---	---
SLC9A5	6553	broad.mit.edu	37	16	67286608	67286608	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67286608G>A	uc002esm.2	+	2	414	c.351G>A	c.(349-351)TTG>TTA	p.L117L	SLC9A5_uc010cee.2_5'UTR|SLC9A5_uc010vji.1_5'UTR	NM_004594	NP_004585	Q14940	SL9A5_HUMAN	solute carrier family 9 (sodium/hydrogen	117	Helical; (Potential).				regulation of pH	integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			ovary(1)|pancreas(1)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)														---	---	---	---
AGRP	181	broad.mit.edu	37	16	67516936	67516936	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67516936A>G	uc002etg.1	-	3	508	c.208T>C	c.(208-210)TTG>CTG	p.L70L	ATP6V0D1_uc002ete.1_5'Flank|ATP6V0D1_uc010vjo.1_5'Flank	NM_001138	NP_001129	O00253	AGRP_HUMAN	agouti related protein homolog isoform 1	70					hormone-mediated signaling pathway|neuropeptide signaling pathway|regulation of feeding behavior	extracellular space|Golgi lumen	neuropeptide hormone activity				0		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)														---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67861807	67861807	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67861807G>A	uc002euj.2	+	16	2282	c.1888G>A	c.(1888-1890)GTG>ATG	p.V630M	TSNAXIP1_uc002euf.3_3'UTR|TSNAXIP1_uc010vka.1_Missense_Mutation_p.V684M|TSNAXIP1_uc010vkb.1_Missense_Mutation_p.V615M|TSNAXIP1_uc002eug.3_Missense_Mutation_p.V338M|TSNAXIP1_uc002euh.3_Missense_Mutation_p.V338M|TSNAXIP1_uc002eui.3_Missense_Mutation_p.V338M|TSNAXIP1_uc002euk.2_Missense_Mutation_p.V363M	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	630					cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)														---	---	---	---
NUTF2	10204	broad.mit.edu	37	16	67904812	67904812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67904812G>A	uc002eup.2	+	5	479	c.380G>A	c.(379-381)GGC>GAC	p.G127D	NUTF2_uc002euq.3_RNA|EDC4_uc002eur.2_5'Flank|EDC4_uc010cer.2_5'Flank|EDC4_uc010vkg.1_5'Flank	NM_005796	NP_005787	P61970	NTF2_HUMAN	nuclear transport factor 2	127					protein transport	cytosol|nuclear pore	protein binding|transporter activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00443)|Epithelial(162;0.0199)|all cancers(182;0.129)														---	---	---	---
EDC4	23644	broad.mit.edu	37	16	67916384	67916384	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67916384T>C	uc002eur.2	+	25	3495	c.3329T>C	c.(3328-3330)ATG>ACG	p.M1110T	EDC4_uc010cer.2_Missense_Mutation_p.M729T|EDC4_uc002eus.2_Missense_Mutation_p.M840T|EDC4_uc002eut.1_Missense_Mutation_p.M1T|NRN1L_uc002euu.2_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	1110					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)														---	---	---	---
LCAT	3931	broad.mit.edu	37	16	67976607	67976607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67976607G>A	uc002euy.1	-	4	501	c.490C>T	c.(490-492)CGC>TGC	p.R164C		NM_000229	NP_000220	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase precursor	164			R -> C (in LCATD).|R -> H (in LCATD; also in a compound heterozygote carrying R-95 with intermediate phenotype between LCATD and FED; loss of activity).		cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|high-density lipoprotein particle remodeling|phosphatidylcholine biosynthetic process|reverse cholesterol transport|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle	apolipoprotein A-I binding|phosphatidylcholine-sterol O-acyltransferase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)														---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69969758	69969758	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69969758G>A	uc002exu.1	+	19	1934	c.1845G>A	c.(1843-1845)GCG>GCA	p.A615A	WWP2_uc002exv.1_Silent_p.A615A|WWP2_uc010vlm.1_Silent_p.A499A|WWP2_uc010vln.1_Silent_p.A233A|WWP2_uc002exw.1_Silent_p.A176A	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase	615	HECT.				entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																		---	---	---	---
MTSS1L	92154	broad.mit.edu	37	16	70708260	70708260	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70708260G>A	uc002ezj.2	-	11	1262	c.1002C>T	c.(1000-1002)GAC>GAT	p.D334D		NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	334	Ser-rich.				filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1																		---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	71025201	71025201	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71025201C>A	uc002ezr.2	-	25	4012	c.3884G>T	c.(3883-3885)GGG>GTG	p.G1295V		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment										ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
FTSJD1	55783	broad.mit.edu	37	16	71317725	71317725	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71317725C>T	uc010cga.2	-	3	2505	c.2099G>A	c.(2098-2100)CGA>CAA	p.R700Q	FTSJD1_uc002ezy.3_Missense_Mutation_p.R700Q|FTSJD1_uc002ezz.3_Missense_Mutation_p.R700Q	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	700						integral to membrane	methyltransferase activity|nucleic acid binding			skin(1)	1																		---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71683763	71683763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71683763C>T	uc002fax.2	-	18	3008	c.3002G>A	c.(3001-3003)CGT>CAT	p.R1001H	PHLPP2_uc002fav.2_Intron|PHLPP2_uc010cgf.2_Missense_Mutation_p.R934H	NM_015020	NP_055835	Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein	1001	PP2C-like.					cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PMFBP1	83449	broad.mit.edu	37	16	72173266	72173266	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72173266T>C	uc002fcc.3	-	7	1012	c.840A>G	c.(838-840)CTA>CTG	p.L280L	PMFBP1_uc002fcd.2_Silent_p.L280L|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Silent_p.L135L	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	280										ovary(2)	2		Ovarian(137;0.179)																---	---	---	---
PMFBP1	83449	broad.mit.edu	37	16	72184569	72184569	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72184569T>C	uc002fcc.3	-	5	746	c.574A>G	c.(574-576)ATC>GTC	p.I192V	PMFBP1_uc002fcd.2_Missense_Mutation_p.I192V|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Missense_Mutation_p.I47V	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	192	Potential.									ovary(2)	2		Ovarian(137;0.179)																---	---	---	---
ZFP1	162239	broad.mit.edu	37	16	75203278	75203278	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75203278T>C	uc002fdo.2	+	4	434	c.270T>C	c.(268-270)CTT>CTC	p.L90L	ZFP1_uc002fdp.2_Silent_p.L35L|ZFP1_uc010cgt.2_Silent_p.L57L|ZFP1_uc010cgs.2_Silent_p.L35L|ZFP1_uc002fdq.2_Silent_p.L90L	NM_153688	NP_710155	Q6P2D0	ZFP1_HUMAN	zinc finger protein 1 homolog	90					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
DYNLRB2	83657	broad.mit.edu	37	16	80574970	80574970	+	5'UTR	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80574970C>T	uc002ffo.2	+	3					DYNLRB2_uc002ffp.2_RNA|DYNLRB2_uc002ffq.2_RNA	NM_130897	NP_570967			dynein, light chain, roadblock-type 2						microtubule-based movement|transport	cytoplasmic dynein complex|microtubule	microtubule motor activity				0																		---	---	---	---
PKD1L2	114780	broad.mit.edu	37	16	81249951	81249951	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81249951G>A	uc002fgh.1	-	2	362	c.362C>T	c.(361-363)GCC>GTC	p.A121V	PKD1L2_uc002fgj.2_Missense_Mutation_p.A121V	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	121	Extracellular (Potential).|C-type lectin.				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
MLYCD	23417	broad.mit.edu	37	16	83948956	83948956	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83948956C>T	uc002fgz.2	+	5	1364	c.1344C>T	c.(1342-1344)TGC>TGT	p.C448C		NM_012213	NP_036345	O95822	DCMC_HUMAN	malonyl-CoA decarboxylase precursor	448					acyl-CoA metabolic process|fatty acid biosynthetic process	mitochondrion|peroxisome	malonyl-CoA decarboxylase activity|methylmalonyl-CoA decarboxylase activity				0																		---	---	---	---
ATP2C2	9914	broad.mit.edu	37	16	84494378	84494378	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84494378A>G	uc002fhx.2	+	24	2541	c.2452A>G	c.(2452-2454)AGC>GGC	p.S818G	ATP2C2_uc010chj.2_Missense_Mutation_p.S847G|ATP2C2_uc002fhy.2_Missense_Mutation_p.S835G|ATP2C2_uc002fhz.2_Missense_Mutation_p.S667G|ATP2C2_uc002fia.2_Missense_Mutation_p.S129G	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	818	Helical; Name=7; (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
FOXF1	2294	broad.mit.edu	37	16	86544748	86544748	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86544748C>T	uc002fjl.2	+	1	616	c.573C>T	c.(571-573)GGC>GGT	p.G191G	uc002fjk.1_5'Flank	NM_001451	NP_001442	Q12946	FOXF1_HUMAN	forkhead box F1	191					branching involved in open tracheal system development|cardiac left ventricle morphogenesis|embryonic ectodermal digestive tract morphogenesis|endocardial cushion development|in utero embryonic development|lung vasculature development|midgut development|pancreas development|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|ureter development|venous blood vessel development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0																		---	---	---	---
MTHFSD	64779	broad.mit.edu	37	16	86565850	86565850	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86565850C>T	uc002fjn.2	-	8	970	c.919G>A	c.(919-921)GAT>AAT	p.D307N	MTHFSD_uc010voo.1_Missense_Mutation_p.D287N|MTHFSD_uc002fjo.2_Missense_Mutation_p.D144N|MTHFSD_uc002fjm.2_Missense_Mutation_p.D306N|MTHFSD_uc010vop.1_Missense_Mutation_p.D144N|MTHFSD_uc010voq.1_Missense_Mutation_p.D306N|MTHFSD_uc010vor.1_Missense_Mutation_p.D307N	NM_001159377	NP_001152849	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain	307	RRM.				folic acid-containing compound biosynthetic process		5-formyltetrahydrofolate cyclo-ligase activity|ATP binding|RNA binding				0																		---	---	---	---
JPH3	57338	broad.mit.edu	37	16	87677940	87677940	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87677940C>T	uc002fkd.2	+	2	713	c.459C>T	c.(457-459)GCC>GCT	p.A153A	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	153	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)														---	---	---	---
KLHDC4	54758	broad.mit.edu	37	16	87743249	87743249	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87743249G>A	uc002fki.2	-	10	1115	c.1069C>T	c.(1069-1071)CGC>TGC	p.R357C	KLHDC4_uc002fkh.1_RNA|KLHDC4_uc010cht.1_Intron|KLHDC4_uc002fkj.2_Missense_Mutation_p.R326C|KLHDC4_uc002fkk.2_Missense_Mutation_p.R176C|KLHDC4_uc002fkl.2_Missense_Mutation_p.R300C|KLHDC4_uc010chu.1_Missense_Mutation_p.R176C	NM_017566	NP_060036	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	357	Kelch 5.									pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0283)														---	---	---	---
KLHDC4	54758	broad.mit.edu	37	16	87760364	87760364	+	Intron	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87760364G>C	uc002fki.2	-						KLHDC4_uc010cht.1_Intron|KLHDC4_uc002fkj.2_Intron|KLHDC4_uc002fkk.2_Intron|KLHDC4_uc002fkl.2_Intron|KLHDC4_uc010chu.1_Intron	NM_017566	NP_060036			kelch domain containing 4											pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0283)														---	---	---	---
SPIRE2	84501	broad.mit.edu	37	16	89911783	89911783	+	Intron	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89911783A>T	uc002foz.1	+						SPIRE2_uc010civ.1_Intron|SPIRE2_uc010ciw.1_Intron	NM_032451	NP_115827			spire homolog 2						transport	cytoplasm|cytoskeleton	actin binding			central_nervous_system(1)	1		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)														---	---	---	---
GLOD4	51031	broad.mit.edu	37	17	674707	674707	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:674707G>T	uc002frv.2	-						GLOD4_uc002frt.2_Intron|GLOD4_uc002fru.2_Intron|GLOD4_uc010vqc.1_Intron	NM_016080	NP_057164			glyoxalase domain containing 4							mitochondrion					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)														---	---	---	---
SLC43A2	124935	broad.mit.edu	37	17	1489203	1489203	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1489203G>A	uc002fsv.2	-						SLC43A2_uc002fsu.2_Intron|SLC43A2_uc002fsw.2_Silent_p.C407C|SLC43A2_uc002fsx.2_Silent_p.C407C	NM_152346	NP_689559			solute carrier family 43, member 2						cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)														---	---	---	---
SRR	63826	broad.mit.edu	37	17	2227145	2227145	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2227145C>T	uc002fue.1	+	8	1069	c.1001C>T	c.(1000-1002)TCT>TTT	p.S334F	SRR_uc002fui.1_Missense_Mutation_p.S185F|TSR1_uc002fuj.2_3'UTR	NM_021947	NP_068766	Q9GZT4	SRR_HUMAN	serine racemase	334					D-serine biosynthetic process|L-serine metabolic process|protein homotetramerization|pyruvate biosynthetic process|response to lipopolysaccharide	cytoplasm|neuronal cell body|soluble fraction	ATP binding|calcium ion binding|D-serine ammonia-lyase activity|glycine binding|L-serine ammonia-lyase activity|magnesium ion binding|PDZ domain binding|protein homodimerization activity|pyridoxal phosphate binding|serine racemase activity|threonine racemase activity				0		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
SLC25A11	8402	broad.mit.edu	37	17	4842264	4842264	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4842264C>T	uc002fzo.1	-	3	368	c.255G>A	c.(253-255)TCG>TCA	p.S85S	SLC25A11_uc002fzp.1_Silent_p.S81S|RNF167_uc002fzq.2_5'Flank|RNF167_uc002fzr.2_5'Flank|RNF167_uc002fzs.2_5'Flank|RNF167_uc002fzt.2_5'Flank|RNF167_uc002fzu.2_5'Flank|RNF167_uc002fzv.2_5'Flank|RNF167_uc002fzw.1_5'Flank|RNF167_uc002fzx.2_5'Flank	NM_003562	NP_003553	Q02978	M2OM_HUMAN	solute carrier family 25 member 11 isoform 1	85	Helical; Name=2; (Potential).|Solcar 1.				gluconeogenesis	integral to plasma membrane|mitochondrial inner membrane	oxoglutarate:malate antiporter activity				0																		---	---	---	---
ZNF594	84622	broad.mit.edu	37	17	5086767	5086767	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5086767G>C	uc010cla.1	-	2	941	c.785C>G	c.(784-786)ACT>AGT	p.T262S		NM_032530	NP_115919	Q96JF6	ZN594_HUMAN	zinc finger protein 594	262					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
NUP88	4927	broad.mit.edu	37	17	5290760	5290760	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5290760C>T	uc002gbo.1	-	14	1888	c.1862G>A	c.(1861-1863)CGT>CAT	p.R621H	NUP88_uc002gbn.2_5'Flank|NUP88_uc010vsx.1_Missense_Mutation_p.R637H	NM_002532	NP_002523	Q99567	NUP88_HUMAN	nucleoporin 88kDa	621	Potential.				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1																		---	---	---	---
ALOX12	239	broad.mit.edu	37	17	6905060	6905060	+	Missense_Mutation	SNP	C	T	T	rs143493293	by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6905060C>T	uc002gdx.3	+	8	1144	c.1091C>T	c.(1090-1092)ACT>ATT	p.T364I	uc002gdy.1_RNA	NM_000697	NP_000688	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	364	Lipoxygenase.				anti-apoptosis|cellular component movement|fatty acid oxidation|leukotriene biosynthetic process|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of cell proliferation|superoxide anion generation	cytosol|sarcolemma	arachidonate 12-lipoxygenase activity|hepoxilin-epoxide hydrolase activity|iron ion binding|lipoxygenase activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
BCL6B	255877	broad.mit.edu	37	17	6927125	6927125	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6927125C>T	uc002geg.2	+	2	192	c.135C>T	c.(133-135)GGC>GGT	p.G45G	BCL6B_uc010clt.1_Silent_p.G45G	NM_181844	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B (zinc finger	45	BTB.					nucleus	zinc ion binding			skin(1)	1																		---	---	---	---
ACAP1	9744	broad.mit.edu	37	17	7253540	7253540	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7253540G>A	uc002ggd.2	+	20	2262	c.2056G>A	c.(2056-2058)GCT>ACT	p.A686T	KCTD11_uc002gge.3_5'Flank	NM_014716	NP_055531	Q15027	ACAP1_HUMAN	centaurin beta1	686	Required for interaction with GULP1.|ANK 3.				intracellular signal transduction|lipid metabolic process|protein transport|regulation of ARF GTPase activity		ARF GTPase activator activity|phospholipase C activity|protein binding|zinc ion binding			breast(2)|large_intestine(1)	3																		---	---	---	---
POLR2A	5430	broad.mit.edu	37	17	7404634	7404634	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7404634A>G	uc002ghf.3	+	13	2311	c.2077A>G	c.(2077-2079)ATT>GTT	p.I693V		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	693					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)																---	---	---	---
TNFSF12-TNFSF13	407977	broad.mit.edu	37	17	7460226	7460226	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7460226C>T	uc002ghi.1	+						TNFSF12_uc002ghg.2_Intron|TNFSF12_uc002ghh.2_Intron|TNFSF13_uc002ghj.2_5'Flank|TNFSF13_uc002ghk.2_5'Flank|TNFSF13_uc002ghl.2_5'Flank|TNFSF13_uc010cmk.2_5'Flank|TNFSF13_uc010vua.1_5'Flank	NM_172089	NP_742086			TNFSF12-TNFSF13 protein						immune response	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0		Prostate(122;0.157)																---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7756423	7756423	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7756423C>A	uc002giw.1	+	21	5092	c.4716C>A	c.(4714-4716)GCC>GCA	p.A1572A	KDM6B_uc002gix.2_Silent_p.A874A|TMEM88_uc002giy.2_5'Flank	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1572					inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
ALOXE3	59344	broad.mit.edu	37	17	8000064	8000064	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8000064C>T	uc010cnr.2	-	16	2387	c.2017G>A	c.(2017-2019)GCC>ACC	p.A673T	ALOXE3_uc002gka.2_Missense_Mutation_p.A829T|ALOXE3_uc010vuo.1_Missense_Mutation_p.A805T	NM_021628	NP_067641	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3 isoform 2	673	Lipoxygenase.				leukotriene biosynthetic process		iron ion binding|lipoxygenase activity			skin(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
TMEM107	84314	broad.mit.edu	37	17	8077872	8077872	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8077872A>G	uc002gkg.3	-	4	429	c.319T>C	c.(319-321)TGC>CGC	p.C107R	TMEM107_uc002gkh.3_Missense_Mutation_p.C113R|TMEM107_uc002gki.3_Missense_Mutation_p.C113R|TMEM107_uc002gkj.3_Intron|TMEM107_uc002gkk.2_3'UTR	NM_183065	NP_898888	Q6UX40	TM107_HUMAN	transmembrane protein 107 isoform 2	107						integral to membrane					0																		---	---	---	---
C17orf68	80169	broad.mit.edu	37	17	8140698	8140698	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8140698C>T	uc002gkq.3	-	5	846	c.787G>A	c.(787-789)GTG>ATG	p.V263M	C17orf68_uc010cnv.2_RNA	NM_025099	NP_079375	Q2NKJ3	CTC1_HUMAN	alpha accessory factor 132	263					positive regulation of DNA replication|telomere maintenance	Stn1-Ten1 complex	protein binding|single-stranded DNA binding				0																		---	---	---	---
NDEL1	81565	broad.mit.edu	37	17	8350200	8350200	+	Silent	SNP	C	T	T	rs146379947	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8350200C>T	uc002glj.2	+	4	566	c.369C>T	c.(367-369)GAC>GAT	p.D123D	NDEL1_uc002gli.2_Silent_p.D123D	NM_030808	NP_110435	Q9GZM8	NDEL1_HUMAN	nudE nuclear distribution gene E homolog (A.	123	Required for interaction with PAFAH1B1.|Interaction with KATNB1 (By similarity).|Potential.|Self-association (By similarity).				chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|microtubule|spindle					0																		---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10304992	10304992	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10304992T>G	uc002gmm.2	-	23	2894	c.2799A>C	c.(2797-2799)GAA>GAC	p.E933D	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	933	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11														Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10315783	10315783	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10315783C>T	uc002gmm.2	-	14	1415	c.1320G>A	c.(1318-1320)CTG>CTA	p.L440L	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	440	Myosin head-like.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11														Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11790294	11790294	+	Intron	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11790294C>A	uc002gne.2	+						DNAH9_uc010coo.2_Intron|DNAH9_uc002gnf.2_Intron|DNAH9_uc010vvh.1_Intron	NM_001372	NP_001363			dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11845810	11845810	+	Intron	SNP	C	T	T	rs62062000		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11845810C>T	uc002gne.2	+						DNAH9_uc010coo.2_Intron|DNAH9_uc002gnf.2_Intron	NM_001372	NP_001363			dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
MAP2K4	6416	broad.mit.edu	37	17	11984731	11984731	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11984731C>T	uc002gnj.2	+	3	346	c.277C>T	c.(277-279)CAA>TAA	p.Q93*	MAP2K4_uc002gnk.2_Nonsense_Mutation_p.Q104*|MAP2K4_uc010vvi.1_5'UTR|MAP2K4_uc010vvj.1_Intron|MIR744_hsa-mir-744|MI0005559_5'Flank	NM_003010	NP_003001	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	93					cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(1)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)				D|Mis|N		pancreatic|breast|colorectal								---	---	---	---
MAP2K4	6416	broad.mit.edu	37	17	12028611	12028611	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12028611C>T	uc002gnj.2	+	8	883	c.814C>T	c.(814-816)CCT>TCT	p.P272S	MAP2K4_uc002gnk.2_Missense_Mutation_p.P283S|MAP2K4_uc010vvi.1_Missense_Mutation_p.P154S|MAP2K4_uc010vvj.1_Missense_Mutation_p.P144S	NM_003010	NP_003001	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	272	Protein kinase.				cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	p.?(3)		large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)				D|Mis|N		pancreatic|breast|colorectal								---	---	---	---
MYOCD	93649	broad.mit.edu	37	17	12639588	12639588	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12639588G>T	uc002gnn.2	+	6	825	c.526G>T	c.(526-528)GCG>TCG	p.A176S	MYOCD_uc002gno.2_Missense_Mutation_p.A176S|MYOCD_uc002gnp.1_Missense_Mutation_p.A80S	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2	176	HDAC5-binding (By similarity).				cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)														---	---	---	---
CDRT4	284040	broad.mit.edu	37	17	15341231	15341231	+	Silent	SNP	C	T	T	rs149000474	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15341231C>T	uc002gop.1	-	4	596	c.315G>A	c.(313-315)TCG>TCA	p.S105S	CDRT4_uc010vvw.1_3'UTR	NM_173622	NP_775893	Q8N9R6	CDRT4_HUMAN	CMT1A duplicated region transcript 4	105											0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)														---	---	---	---
TRIM16	10626	broad.mit.edu	37	17	15516133	15516133	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15516133G>T	uc002gor.1	-	11	2271	c.1934C>A	c.(1933-1935)TCC>TAC	p.S645Y	CDRT1_uc002gov.3_Missense_Mutation_p.S335Y			O95361	TRI16_HUMAN	SubName: Full=Putative uncharacterized protein; Flags: Fragment;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)														---	---	---	---
RAI1	10743	broad.mit.edu	37	17	17700590	17700590	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17700590C>T	uc002grm.2	+	3	4797	c.4328C>T	c.(4327-4329)GCG>GTG	p.A1443V	RAI1_uc002grn.1_Missense_Mutation_p.A1443V	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1443						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)														---	---	---	---
SMCR8	140775	broad.mit.edu	37	17	18220589	18220589	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18220589C>T	uc002gsy.3	+	1	1996	c.1486C>T	c.(1486-1488)CCA>TCA	p.P496S		NM_144775	NP_658988	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region,	496										central_nervous_system(1)	1																		---	---	---	---
SLC47A2	146802	broad.mit.edu	37	17	19618075	19618075	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19618075C>A	uc002gwe.3	-	3	428	c.253G>T	c.(253-255)GGA>TGA	p.G85*	SLC47A2_uc002gwg.3_Nonsense_Mutation_p.G85*|SLC47A2_uc002gwf.3_Nonsense_Mutation_p.G85*|SLC47A2_uc002gwh.3_RNA|SLC47A2_uc002gwi.2_RNA|SLC47A2_uc010cqs.1_RNA|SLC47A2_uc010cqt.1_RNA	NM_152908	NP_690872	Q86VL8	S47A2_HUMAN	solute carrier family 47, member 2 isoform 1	85	Helical; (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)																	---	---	---	---
ALDH3A1	218	broad.mit.edu	37	17	19645383	19645383	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19645383G>A	uc010cqu.2	-	4	953	c.623C>T	c.(622-624)ACG>ATG	p.T208M	ALDH3A1_uc010vzd.1_Missense_Mutation_p.T208M|ALDH3A1_uc002gwj.2_Missense_Mutation_p.T208M|ALDH3A1_uc010cqv.2_Missense_Mutation_p.T208M|ALDH3A1_uc002gwk.2_Missense_Mutation_p.T325M|ALDH3A1_uc002gwl.1_Missense_Mutation_p.T135M	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1	208					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)													---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26108199	26108199	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26108199C>T	uc002gzu.2	-	8	991	c.727G>A	c.(727-729)GCC>ACC	p.A243T	NOS2_uc010crh.1_Missense_Mutation_p.A243T|NOS2_uc010wab.1_Missense_Mutation_p.A243T	NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A	243					arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)													---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26114723	26114723	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26114723A>G	uc002gzu.2	-	5	712	c.448T>C	c.(448-450)TAT>CAT	p.Y150H	NOS2_uc010crh.1_Missense_Mutation_p.Y150H|NOS2_uc010wab.1_Missense_Mutation_p.Y150H	NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A	150					arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)													---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26951336	26951336	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26951336A>G	uc002hbu.2	-	25	4766	c.4667T>C	c.(4666-4668)ATG>ACG	p.M1556T	KIAA0100_uc002hbt.2_5'Flank	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	1556						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
TP53I13	90313	broad.mit.edu	37	17	27899538	27899538	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27899538C>T	uc002hee.2	+	6	930	c.892C>T	c.(892-894)CGG>TGG	p.R298W		NM_138349	NP_612358	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	298	Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane					0				READ - Rectum adenocarcinoma(3;0.236)														---	---	---	---
SSH2	85464	broad.mit.edu	37	17	27958011	27958011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27958011C>T	uc002heo.1	-	15	4120	c.4120G>A	c.(4120-4122)GTG>ATG	p.V1374M	SSH2_uc010wbh.1_Missense_Mutation_p.V1401M	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	1374					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
EVI2A	2123	broad.mit.edu	37	17	29645818	29645818	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29645818C>A	uc002hgm.2	-	2	429	c.214G>T	c.(214-216)GGT>TGT	p.G72C	NF1_uc002hgg.2_Intron|NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron|EVI2A_uc002hgl.2_Missense_Mutation_p.G95C	NM_014210	NP_055025	P22794	EVI2A_HUMAN	ecotropic viral integration site 2A isoform 2	72	Extracellular (Potential).					integral to membrane	transmembrane receptor activity			ovary(1)|breast(1)	2		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;5.94e-13)|Epithelial(4;7.98e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.4e-12)|GBM - Glioblastoma multiforme(4;0.18)														---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31075962	31075962	+	Silent	SNP	G	A	A	rs117036818	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31075962G>A	uc002hho.1	-	12	1542	c.1530C>T	c.(1528-1530)GGC>GGT	p.G510G	MYO1D_uc002hhp.1_Silent_p.G510G	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	510	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)															---	---	---	---
SPACA3	124912	broad.mit.edu	37	17	31322545	31322545	+	Silent	SNP	C	T	T	rs139396445		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31322545C>T	uc002hhs.1	+	2	228	c.153C>T	c.(151-153)GCC>GCT	p.A51A	SPACA3_uc010cte.1_RNA	NM_173847	NP_776246	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	51	Cytoplasmic (Potential).				cell wall macromolecule catabolic process|defense response to Gram-positive bacterium|monocyte activation|peptidoglycan catabolic process|positive regulation of macrophage activation|positive regulation of phagocytosis|response to virus	acrosomal membrane|extracellular region|integral to membrane|lysosome	bacterial cell surface binding|lysozyme activity|protein binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.193)															---	---	---	---
SLFN13	146857	broad.mit.edu	37	17	33768287	33768287	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33768287C>T	uc002hjk.1	-	4	2351	c.2021G>A	c.(2020-2022)CGT>CAT	p.R674H	SLFN13_uc010wch.1_Missense_Mutation_p.R674H|SLFN13_uc002hjl.2_Missense_Mutation_p.R674H|SLFN13_uc010ctt.2_Missense_Mutation_p.R356H|SLFN13_uc002hjm.2_Missense_Mutation_p.R343H	NM_144682	NP_653283	Q68D06	SLN13_HUMAN	schlafen family member 13	674						intracellular	ATP binding			ovary(1)|breast(1)	2				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
HNF1B	6928	broad.mit.edu	37	17	36091778	36091778	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36091778C>T	uc002hok.3	-	4	1074	c.853G>A	c.(853-855)GGC>AGC	p.G285S	HNF1B_uc010wdi.1_Missense_Mutation_p.G259S|HNF1B_uc010cve.1_Missense_Mutation_p.G93S	NM_000458	NP_000449	P35680	HNF1B_HUMAN	hepatocyte nuclear factor 1-beta isoform 1	285	Homeobox; HNF1-type.		G -> D (in RCAD).		endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)											Hereditary_Prostate_Cancer				---	---	---	---
PNMT	5409	broad.mit.edu	37	17	37826335	37826335	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37826335C>T	uc002hsi.1	+	3	764	c.542C>T	c.(541-543)GCC>GTC	p.A181V		NM_002686	NP_002677	P11086	PNMT_HUMAN	phenylethanolamine N-methyltransferase	181		S-adenosyl-L-methionine; via carbonyl oxygen.			catecholamine biosynthetic process|hormone biosynthetic process	cytosol	phenylethanolamine N-methyltransferase activity			ovary(1)	1	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
GRB7	2886	broad.mit.edu	37	17	37900873	37900873	+	Missense_Mutation	SNP	G	A	A	rs138362707		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37900873G>A	uc002hsr.2	+	8	1119	c.869G>A	c.(868-870)CGC>CAC	p.R290H	GRB7_uc002hss.2_Missense_Mutation_p.R290H|GRB7_uc010cwc.2_Missense_Mutation_p.R290H|GRB7_uc002hst.2_Missense_Mutation_p.R290H	NM_005310	NP_005301	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	290	PH.				blood coagulation|epidermal growth factor receptor signaling pathway|leukocyte migration|negative regulation of translation|positive regulation of cell migration|stress granule assembly	cytosol|focal adhesion|stress granule	phosphatidylinositol binding|protein kinase binding|SH3/SH2 adaptor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
TNS4	84951	broad.mit.edu	37	17	38633914	38633914	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38633914A>G	uc010cxb.2	-	13	2238	c.2074T>C	c.(2074-2076)TAT>CAT	p.Y692H	TNS4_uc002huu.3_Missense_Mutation_p.Y105H	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor	692	Phosphatase tensin-type.				apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)															---	---	---	---
KRT26	353288	broad.mit.edu	37	17	38928171	38928171	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38928171A>G	uc002hvf.2	-	1	241	c.195T>C	c.(193-195)AGT>AGC	p.S65S		NM_181539	NP_853517	Q7Z3Y9	K1C26_HUMAN	keratin 26	65	Head.|Gly-rich.					intermediate filament	structural molecule activity				0		Breast(137;0.00526)																---	---	---	---
KRT10	3858	broad.mit.edu	37	17	38975866	38975866	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38975866C>T	uc002hvi.2	-	6	1302	c.1276G>A	c.(1276-1278)GAG>AAG	p.E426K	KRT10_uc010cxd.2_RNA|TMEM99_uc002hvj.1_Intron	NM_000421	NP_000412	P13645	K1C10_HUMAN	keratin 10	426	Rod.|Gly-rich.|Coil 2.				epidermis development		protein binding|structural constituent of epidermis				0		Breast(137;0.000301)																---	---	---	---
KRT13	3860	broad.mit.edu	37	17	39661808	39661808	+	5'UTR	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39661808G>T	uc002hwu.1	-	1					KRT13_uc002hwv.1_5'UTR|KRT13_uc002hww.2_5'UTR|KRT13_uc010wfr.1_5'UTR|KRT13_uc010cxo.2_5'UTR|KRT13_uc002hwx.1_5'UTR	NM_153490	NP_705694			keratin 13 isoform a						epidermis development	intermediate filament	structural molecule activity			ovary(2)|skin(2)|pancreas(1)	5		Breast(137;0.000286)																---	---	---	---
KLHL10	317719	broad.mit.edu	37	17	40001941	40001941	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40001941C>A	uc010cxr.2	+	3	1390	c.1248C>A	c.(1246-1248)ATC>ATA	p.I416I	KLHL10_uc010wfv.1_Silent_p.I410I|KLHL10_uc010wfw.1_Silent_p.I328I	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10	416	Kelch 3.					cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)																---	---	---	---
KCNH4	23415	broad.mit.edu	37	17	40330908	40330908	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40330908G>A	uc002hzb.2	-	2	546	c.213C>T	c.(211-213)TAC>TAT	p.Y71Y		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	71	Cytoplasmic (Potential).|PAS.				regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	two-component sensor activity|voltage-gated potassium channel activity			large_intestine(1)	1		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)														---	---	---	---
COASY	80347	broad.mit.edu	37	17	40717259	40717259	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40717259A>G	uc002hzz.2	+	7	1474	c.1317A>G	c.(1315-1317)ATA>ATG	p.I439M	COASY_uc010cyj.2_Missense_Mutation_p.I468M|COASY_uc002iab.2_Missense_Mutation_p.I144M|COASY_uc002iad.2_Missense_Mutation_p.I439M|COASY_uc002iac.2_Missense_Mutation_p.I439M|COASY_uc002iae.2_Missense_Mutation_p.I234M|MLX_uc002iaf.2_5'Flank|MLX_uc002iag.2_5'Flank|MLX_uc002iah.2_5'Flank	NM_001042529	NP_001035994	Q13057	COASY_HUMAN	coenzyme A synthase isoform a	439	DPCK.				coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial outer membrane	ATP binding|dephospho-CoA kinase activity|pantetheine-phosphate adenylyltransferase activity				0		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)														---	---	---	---
FAM134C	162427	broad.mit.edu	37	17	40744063	40744063	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40744063A>G	uc002ial.2	-						FAM134C_uc010wgq.1_Intron|FAM134C_uc002iam.1_Intron|FAM134C_uc010cyk.1_Intron	NM_178126	NP_835227			hypothetical protein LOC162427							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)														---	---	---	---
RUNDC1	146923	broad.mit.edu	37	17	41143362	41143362	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41143362T>C	uc002ici.1	+	5	1483	c.1471T>C	c.(1471-1473)TCC>CCC	p.S491P	RUNDC1_uc010whi.1_Missense_Mutation_p.S261P	NM_173079	NP_775102	Q96C34	RUND1_HUMAN	RUN domain containing 1	491	RUN.										0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)														---	---	---	---
BRCA1	672	broad.mit.edu	37	17	41244853	41244853	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41244853C>G	uc002icq.2	-	10	2927	c.2695G>C	c.(2695-2697)GTC>CTC	p.V899L	BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Missense_Mutation_p.V828L|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Missense_Mutation_p.V852L|BRCA1_uc002ict.2_Missense_Mutation_p.V899L|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc010whq.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron|BRCA1_uc002idd.2_Missense_Mutation_p.V899L|BRCA1_uc002ide.1_Missense_Mutation_p.V730L|BRCA1_uc010cyy.1_Missense_Mutation_p.V899L|BRCA1_uc010whs.1_Missense_Mutation_p.V899L|BRCA1_uc010cyz.2_Missense_Mutation_p.V852L|BRCA1_uc010cza.2_Missense_Mutation_p.V873L|BRCA1_uc010wht.1_Missense_Mutation_p.V603L	NM_007294	NP_009225	P38398	BRCA1_HUMAN	breast cancer 1, early onset isoform 1	899					androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)				D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			---	---	---	---
NBR1	4077	broad.mit.edu	37	17	41343459	41343459	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41343459C>T	uc010czd.2	+	10	1074	c.934C>T	c.(934-936)CGT>TGT	p.R312C	NBR1_uc010diz.2_Missense_Mutation_p.R312C|NBR1_uc010whu.1_Missense_Mutation_p.R312C|NBR1_uc010whv.1_Missense_Mutation_p.R312C|NBR1_uc010whw.1_Missense_Mutation_p.R291C|NBR1_uc010whx.1_Missense_Mutation_p.R121C	NM_031862	NP_114068	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	312					macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)														---	---	---	---
MPP2	4355	broad.mit.edu	37	17	41958098	41958098	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41958098T>C	uc010wip.1	-	10	1303	c.1246A>G	c.(1246-1248)ATC>GTC	p.I416V	MPP2_uc002ien.1_Missense_Mutation_p.I388V|MPP2_uc010wim.1_Missense_Mutation_p.I360V|MPP2_uc002ieo.1_Missense_Mutation_p.I371V|MPP2_uc010win.1_Missense_Mutation_p.I232V|MPP2_uc010wio.1_Missense_Mutation_p.I360V	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2	395	Guanylate kinase-like.				signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)												OREG0024443	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42824781	42824781	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42824781G>T	uc002ihf.2	+	12	1175	c.962G>T	c.(961-963)CGG>CTG	p.R321L	DBF4B_uc002ihe.2_Missense_Mutation_p.R135L|DBF4B_uc010wjc.1_Missense_Mutation_p.R305L	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1	321	DBF4-type.				cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44115975	44115975	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44115975G>A	uc002ikb.2	-	9	2555	c.2470C>T	c.(2470-2472)CGA>TGA	p.R824*	KIAA1267_uc002ikc.2_Nonsense_Mutation_p.R824*|KIAA1267_uc002ikd.2_Nonsense_Mutation_p.R824*|KIAA1267_uc010dav.2_Nonsense_Mutation_p.R824*|KIAA1267_uc010wkb.1_Nonsense_Mutation_p.R155*|KIAA1267_uc010wkc.1_Nonsense_Mutation_p.R92*	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	824						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
C17orf57	124989	broad.mit.edu	37	17	45473245	45473245	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45473245C>G	uc002iln.2	+	17	2258	c.1847C>G	c.(1846-1848)ACG>AGG	p.T616R	C17orf57_uc002ilm.2_Missense_Mutation_p.T520R	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	616							calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
NFE2L1	4779	broad.mit.edu	37	17	46136704	46136704	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46136704C>T	uc002imz.3	+	6	2671	c.2020C>T	c.(2020-2022)CGC>TGC	p.R674C	NFE2L1_uc002ina.3_Missense_Mutation_p.R644C|NFE2L1_uc002inb.3_Missense_Mutation_p.R644C|NFE2L1_uc010wle.1_Missense_Mutation_p.R486C|NFE2L1_uc010wlf.1_Missense_Mutation_p.R518C	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1	674	Basic motif.				anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1																		---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48649364	48649364	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48649364C>T	uc002irk.1	+	5	1084	c.712C>T	c.(712-714)CGG>TGG	p.R238W	CACNA1G_uc002iri.1_Missense_Mutation_p.R238W|CACNA1G_uc002irj.1_Missense_Mutation_p.R238W|CACNA1G_uc002irl.1_Missense_Mutation_p.R238W|CACNA1G_uc002irm.1_Missense_Mutation_p.R238W|CACNA1G_uc002irn.1_Missense_Mutation_p.R238W|CACNA1G_uc002iro.1_Missense_Mutation_p.R238W|CACNA1G_uc002irp.1_Missense_Mutation_p.R238W|CACNA1G_uc002irq.1_Missense_Mutation_p.R238W|CACNA1G_uc002irr.1_Missense_Mutation_p.R238W|CACNA1G_uc002irs.1_Missense_Mutation_p.R238W|CACNA1G_uc002irt.1_Missense_Mutation_p.R238W|CACNA1G_uc002irv.1_Missense_Mutation_p.R238W|CACNA1G_uc002irw.1_Missense_Mutation_p.R238W|CACNA1G_uc002iru.1_Missense_Mutation_p.R238W|CACNA1G_uc002irx.1_Missense_Mutation_p.R151W|CACNA1G_uc002iry.1_Missense_Mutation_p.R151W|CACNA1G_uc002irz.1_Missense_Mutation_p.R151W|CACNA1G_uc002isa.1_Missense_Mutation_p.R151W|CACNA1G_uc002isb.1_Missense_Mutation_p.R151W|CACNA1G_uc002isc.1_Missense_Mutation_p.R151W|CACNA1G_uc002isd.1_Missense_Mutation_p.R151W|CACNA1G_uc002ise.1_Missense_Mutation_p.R151W|CACNA1G_uc002isf.1_Missense_Mutation_p.R151W|CACNA1G_uc002isg.1_Missense_Mutation_p.R151W|CACNA1G_uc002ish.1_Missense_Mutation_p.R151W|CACNA1G_uc002isi.1_Missense_Mutation_p.R151W	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	238	Extracellular (Potential).|I.				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
ABCC3	8714	broad.mit.edu	37	17	48744971	48744971	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48744971C>T	uc002isl.2	+	12	1568	c.1488C>T	c.(1486-1488)AAC>AAT	p.N496N	ABCC3_uc002isk.3_Silent_p.N496N	NM_003786	NP_003777	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C, member 3	496	ABC transmembrane type-1 1.|Cytoplasmic (By similarity).				bile acid metabolic process	integral to plasma membrane|membrane fraction	ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity			skin(3)|central_nervous_system(1)	4			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Glibenclamide(DB01016)													---	---	---	---
ANKRD40	91369	broad.mit.edu	37	17	48777241	48777241	+	Missense_Mutation	SNP	A	T	T	rs145395652		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48777241A>T	uc002iso.2	-	3	552	c.297T>A	c.(295-297)GAT>GAA	p.D99E		NM_052855	NP_443087	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	99	Poly-Asp.										0			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49098616	49098616	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49098616G>A	uc002itc.2	-	7	1103	c.894C>T	c.(892-894)AAC>AAT	p.N298N	SPAG9_uc002itb.2_Silent_p.N284N|SPAG9_uc002itd.2_Silent_p.N284N|SPAG9_uc002itf.2_Silent_p.N119N|SPAG9_uc002ita.2_Silent_p.N141N|SPAG9_uc002ite.2_Silent_p.N128N	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1	298					positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54554883	54554883	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54554883G>A	uc002iun.1	+	15	1852	c.1817G>A	c.(1816-1818)CGT>CAT	p.R606H		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	606										large_intestine(1)|ovary(1)	2																		---	---	---	---
COIL	8161	broad.mit.edu	37	17	55027965	55027965	+	Missense_Mutation	SNP	T	C	C	rs143886618	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55027965T>C	uc002iuu.2	-	2	669	c.638A>G	c.(637-639)AAT>AGT	p.N213S		NM_004645	NP_004636	P38432	COIL_HUMAN	coilin	213						Cajal body|nucleolus	protein C-terminus binding			ovary(1)	1	Breast(9;6.15e-08)																	---	---	---	---
SEPT4	5414	broad.mit.edu	37	17	56599207	56599207	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56599207G>A	uc002iwm.1	-	7	933	c.805C>T	c.(805-807)CCA>TCA	p.P269S	SEPT4_uc002iwk.1_Missense_Mutation_p.P122S|SEPT4_uc010wnw.1_Missense_Mutation_p.P122S|SEPT4_uc002iwl.1_Missense_Mutation_p.P122S|SEPT4_uc002iwn.1_Missense_Mutation_p.P170S|SEPT4_uc002iwo.1_Missense_Mutation_p.P250S|SEPT4_uc002iwp.1_3'UTR|SEPT4_uc010wnx.1_Missense_Mutation_p.P284S|SEPT4_uc010wny.1_Missense_Mutation_p.P261S|SEPT4_uc010dcy.1_3'UTR	NM_004574	NP_004565	O43236	SEPT4_HUMAN	septin 4 isoform 1	269					apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56690811	56690811	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56690811C>T	uc010dcz.1	-	9	1112	c.994G>A	c.(994-996)GGC>AGC	p.G332S	TEX14_uc002iwr.1_Missense_Mutation_p.G326S|TEX14_uc002iws.1_Missense_Mutation_p.G326S|TEX14_uc010dda.1_Missense_Mutation_p.G106S	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	332	Protein kinase.					cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56738862	56738862	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56738862T>G	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron|TEX14_uc010wnz.1_Missense_Mutation_p.E33D	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
PPM1E	22843	broad.mit.edu	37	17	57057506	57057506	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57057506G>A	uc002iwx.2	+	7	1509	c.1382G>A	c.(1381-1383)AGC>AAC	p.S461N	PPM1E_uc010ddd.2_Missense_Mutation_p.S224N	NM_014906	NP_055721	Q8WY54	PPM1E_HUMAN	protein phosphatase 1E	470	PP2C-like.				protein dephosphorylation	cytoplasm|nucleolus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(3)|lung(1)|skin(1)	5	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)															---	---	---	---
C17orf71	55181	broad.mit.edu	37	17	57289173	57289173	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57289173T>C	uc002ixi.2	+	1	1801	c.1759_splice	c.e1+2	p.G587_splice		NM_018149	NP_060619			SMG8 protein						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of protein kinase activity		protein binding				0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)																	---	---	---	---
GDPD1	284161	broad.mit.edu	37	17	57326152	57326152	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57326152A>G	uc002ixk.1	+						GDPD1_uc002ixj.2_Intron	NM_182569	NP_872375			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process	cytoplasm|integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding				0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)																	---	---	---	---
DHX40	79665	broad.mit.edu	37	17	57679906	57679906	+	Silent	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57679906C>A	uc002ixn.1	+	15	1977	c.1830C>A	c.(1828-1830)ACC>ACA	p.T610T	DHX40_uc010woe.1_Silent_p.T533T|DHX40_uc010wof.1_Silent_p.T125T	NM_024612	NP_078888	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	610							ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)																	---	---	---	---
BRIP1	83990	broad.mit.edu	37	17	59853933	59853933	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59853933G>A	uc002izk.1	-						BRIP1_uc002izl.1_Intron	NM_032043	NP_114432			BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1								F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
STRADA	92335	broad.mit.edu	37	17	61780974	61780974	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61780974G>A	uc002jbm.2	-	13	1440	c.1281C>T	c.(1279-1281)GAC>GAT	p.D427D	LIMD2_uc002jbl.3_5'Flank|STRADA_uc002jbn.2_Silent_p.D369D|STRADA_uc002jbo.2_Silent_p.D390D|STRADA_uc002jbp.2_3'UTR|STRADA_uc002jbq.2_Silent_p.D369D|STRADA_uc010wpq.1_3'UTR|STRADA_uc010wpr.1_3'UTR|STRADA_uc010ddw.2_Silent_p.D398D|STRADA_uc002jbr.2_3'UTR	NM_001003787	NP_001003787	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha isoform 1	427					activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|kinase binding|protein kinase activity			ovary(1)	1																		---	---	---	---
SCN4A	6329	broad.mit.edu	37	17	62049563	62049563	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62049563T>C	uc002jds.1	-	3	492	c.415A>G	c.(415-417)ATC>GTC	p.I139V		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	139	Helical; Name=S1 of repeat I; (Potential).|I.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)													---	---	---	---
SMURF2	64750	broad.mit.edu	37	17	62587239	62587239	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62587239C>T	uc002jep.1	-	5	751	c.363G>A	c.(361-363)GGG>GGA	p.G121G	SMURF2_uc002jeq.1_5'UTR|SMURF2_uc002jer.1_5'UTR	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	121					BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)															---	---	---	---
KIF19	124602	broad.mit.edu	37	17	72346594	72346594	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72346594G>A	uc002jkm.3	+	11	1406	c.1268G>A	c.(1267-1269)CGG>CAG	p.R423Q	KIF19_uc002jkj.2_Missense_Mutation_p.R423Q|KIF19_uc002jkk.2_Missense_Mutation_p.R381Q|KIF19_uc002jkl.2_Missense_Mutation_p.R381Q	NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	423					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0																		---	---	---	---
CD300LB	124599	broad.mit.edu	37	17	72521917	72521917	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72521917C>A	uc002jkx.2	-	2	464	c.451G>T	c.(451-453)GGG>TGG	p.G151W	CD300LB_uc010wqz.1_Missense_Mutation_p.G151W	NM_174892	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	114	Ig-like V-type.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)	1																		---	---	---	---
NUP85	79902	broad.mit.edu	37	17	73227720	73227720	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73227720T>C	uc002jng.1	+	13	1491	c.1231T>C	c.(1231-1233)TTT>CTT	p.F411L	NUP85_uc010dgd.1_Missense_Mutation_p.F366L|NUP85_uc010wrv.1_Missense_Mutation_p.F365L|NUP85_uc002jnh.1_Missense_Mutation_p.F14L	NM_024844	NP_079120	Q9BW27	NUP85_HUMAN	nucleoporin 85	411					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|nuclear membrane|Nup107-160 complex|spindle	protein binding			ovary(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)															---	---	---	---
RECQL5	9400	broad.mit.edu	37	17	73654438	73654438	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73654438G>A	uc010dgl.2	-	7	1245	c.1089C>T	c.(1087-1089)TAC>TAT	p.Y363Y	RECQL5_uc010dgk.2_Silent_p.Y336Y|RECQL5_uc002jpb.1_Silent_p.Y363Y|RECQL5_uc002joz.3_Silent_p.Y363Y|RECQL5_uc002jpa.3_Silent_p.Y363Y	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1	363	Helicase C-terminal.				DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)										Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
RECQL5	9400	broad.mit.edu	37	17	73654499	73654499	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73654499T>C	uc010dgl.2	-	7	1184	c.1028A>G	c.(1027-1029)TAC>TGC	p.Y343C	RECQL5_uc010dgk.2_Missense_Mutation_p.Y316C|RECQL5_uc002jpb.1_Missense_Mutation_p.Y343C|RECQL5_uc002joz.3_Missense_Mutation_p.Y343C|RECQL5_uc002jpa.3_Missense_Mutation_p.Y343C	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1	343	Helicase C-terminal.				DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)										Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
UBE2O	63893	broad.mit.edu	37	17	74395938	74395938	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74395938G>C	uc002jrm.3	-	9	1285	c.1220C>G	c.(1219-1221)TCC>TGC	p.S407C	UBE2O_uc002jrn.3_Missense_Mutation_p.S407C|UBE2O_uc002jrl.3_Missense_Mutation_p.S10C	NM_022066	NP_071349	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	407							ATP binding|ubiquitin-protein ligase activity			breast(2)|skin(2)|lung(1)	5																		---	---	---	---
AANAT	15	broad.mit.edu	37	17	74465822	74465822	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74465822C>T	uc002jro.2	+	4	628	c.394C>T	c.(394-396)CAG>TAG	p.Q132*	AANAT_uc010wte.1_RNA	NM_001088	NP_001079	Q16613	SNAT_HUMAN	arylalkylamine N-acetyltransferase	132	N-acetyltransferase.|Acetyl-CoA binding (By similarity).				circadian rhythm|melatonin biosynthetic process	cytosol	aralkylamine N-acetyltransferase activity				0																		---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76099610	76099610	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76099610C>T	uc002jud.2	+	20	5288	c.4688C>T	c.(4687-4689)GCC>GTC	p.A1563V	TNRC6C_uc002juf.2_Missense_Mutation_p.A1599V	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2	1563	Sufficient for translational repression when tethered to a target mRNA.				gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)															---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76421579	76421579	+	Missense_Mutation	SNP	G	A	A	rs149945771		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76421579G>A	uc010dhp.1	-	25	4211	c.3989C>T	c.(3988-3990)TCG>TTG	p.S1330L	DNAH17_uc002jvq.2_Missense_Mutation_p.S615L|DNAH17_uc002jvs.2_RNA					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	76488855	76488855	+	IGR	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76488855A>T								DNAH17 (19999 upstream) : CYTH1 (181276 downstream)																																			---	---	---	---
AATK	9625	broad.mit.edu	37	17	79095107	79095107	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79095107C>T	uc010dia.2	-	11	2709	c.2629G>A	c.(2629-2631)GAC>AAC	p.D877N	AATK_uc010dhz.2_RNA	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	877						integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)															---	---	---	---
DUS1L	64118	broad.mit.edu	37	17	80021384	80021384	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80021384G>A	uc002kdq.2	-	3	776	c.357C>T	c.(355-357)GGC>GGT	p.G119G	DUS1L_uc002kdp.2_5'UTR|DUS1L_uc002kdr.2_Silent_p.G119G|DUS1L_uc002kds.2_RNA|DUS1L_uc002kdt.2_RNA|DUS1L_uc010wvi.1_Intron	NM_022156	NP_071439	Q6P1R4	DUS1L_HUMAN	PP3111 protein	119					tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity			skin(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)															---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	331668	331668	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:331668T>C	uc002kkm.2	-	8	2278	c.2063A>G	c.(2062-2064)AAA>AGA	p.K688R		NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	688	Extracellular (Potential).|C-type lectin.				carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	348092	348092	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:348092C>A	uc002kkm.2	-	4	468	c.253G>T	c.(253-255)GCA>TCA	p.A85S		NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	85	Potential.|Extracellular (Potential).				carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
YES1	7525	broad.mit.edu	37	18	732942	732942	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:732942T>C	uc002kky.2	-	11	1536	c.1315A>G	c.(1315-1317)ACA>GCA	p.T439A	YES1_uc002kkz.2_Missense_Mutation_p.T439A	NM_005433	NP_005424	P07947	YES_HUMAN	viral oncogene yes-1 homolog 1	439	Protein kinase.				blood coagulation|leukocyte migration|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)													---	---	---	---
LPIN2	9663	broad.mit.edu	37	18	2937883	2937883	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2937883C>T	uc002klo.2	-	7	1214	c.975G>A	c.(973-975)GTG>GTA	p.V325V		NM_014646	NP_055461	Q92539	LPIN2_HUMAN	lipin 2	325					fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)														---	---	---	---
LRRC30	339291	broad.mit.edu	37	18	7231916	7231916	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7231916C>T	uc010wzk.1	+	1	780	c.780C>T	c.(778-780)ATC>ATT	p.I260I		NM_001105581	NP_001099051	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	260										ovary(1)|liver(1)	2																		---	---	---	---
KIAA0802	23255	broad.mit.edu	37	18	8824926	8824926	+	Missense_Mutation	SNP	C	T	T	rs141975395	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8824926C>T	uc002knr.2	+	15	3560	c.3418C>T	c.(3418-3420)CGG>TGG	p.R1140W	KIAA0802_uc002knq.2_Missense_Mutation_p.R1099W|KIAA0802_uc002kns.2_Missense_Mutation_p.R480W	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	1450											0																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10696408	10696408	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10696408G>A	uc002kor.3	-	4	629	c.489C>T	c.(487-489)TTC>TTT	p.F163F	FAM38B_uc002koq.2_Silent_p.F61F	NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	family with sequence similarity 38, member B	2206	Helical; (Potential).					integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
CHMP1B	57132	broad.mit.edu	37	18	11851987	11851987	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11851987G>T	uc002kqe.2	+	1	599	c.477G>T	c.(475-477)GAG>GAT	p.E159D	GNAL_uc002kqc.2_Intron|GNAL_uc010dkz.2_Intron|GNAL_uc002kqd.2_Intron	NM_020412	NP_065145	Q7LBR1	CHM1B_HUMAN	chromatin modifying protein 1B	159				DE->AA: Diminishes interaction with VPS4B.	cell cycle|cell division|protein transport	cytosol|late endosome membrane	protein domain specific binding				0																		---	---	---	---
C18orf19	125228	broad.mit.edu	37	18	13681823	13681823	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13681823T>C	uc010dlh.2	-	3	686	c.254A>G	c.(253-255)CAA>CGA	p.Q85R	C18orf19_uc010dlg.2_Missense_Mutation_p.Q85R|C18orf19_uc010dli.2_Missense_Mutation_p.Q85R|C18orf19_uc002ksj.3_Missense_Mutation_p.Q85R|C18orf19_uc010dlj.2_Intron	NM_001098801	NP_001092271	Q96ND0	CR019_HUMAN	hypothetical protein LOC125228	85						integral to membrane				breast(2)	2																		---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19383856	19383856	+	Intron	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19383856T>A	uc002ktq.2	+						MIB1_uc002ktp.2_Intron	NM_020774	NP_065825			mindbomb homolog 1						Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)															---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21422380	21422380	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21422380C>T	uc002kuq.2	+	28	3444	c.3358C>T	c.(3358-3360)CGT>TGT	p.R1120C	LAMA3_uc002kur.2_Missense_Mutation_p.R1120C	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1120	Domain IV 1 (domain IV B).				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25589847	25589847	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25589847A>G	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
DSC2	1824	broad.mit.edu	37	18	28654830	28654830	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28654830G>A	uc002kwl.3	-	12	2161	c.1707C>T	c.(1705-1707)GAC>GAT	p.D569D	DSC2_uc002kwk.3_Silent_p.D569D	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein	569	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)															---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29867432	29867432	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29867432G>A	uc002kxl.2	-	4	1184	c.1128C>T	c.(1126-1128)CGC>CGT	p.R376R	FAM59A_uc002kxk.1_Silent_p.R376R	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	376										ovary(1)|skin(1)	2																		---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30260447	30260447	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30260447G>A	uc002kxm.1	-	6	1742	c.1354C>T	c.(1354-1356)CGC>TGC	p.R452C	KLHL14_uc010dmd.1_5'UTR	NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14	452	Kelch 3.					cytosol|endoplasmic reticulum membrane		p.R452C(1)		ovary(1)	1																		---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30275498	30275498	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30275498C>T	uc002kxm.1	-	4	1475	c.1087G>A	c.(1087-1089)GCC>ACC	p.A363T	KLHL14_uc010dmd.1_5'UTR	NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14	363	Kelch 1.					cytosol|endoplasmic reticulum membrane				ovary(1)	1																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32346001	32346001	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32346001C>T	uc010dmn.1	+	2	145	c.144C>T	c.(142-144)TGC>TGT	p.C48C	DTNA_uc002kxu.2_Silent_p.C48C|DTNA_uc010xbx.1_Silent_p.C48C|DTNA_uc002kxv.3_Silent_p.C48C|DTNA_uc002kxw.2_Silent_p.C48C|DTNA_uc002kxx.2_Silent_p.C48C|DTNA_uc010dmj.2_Silent_p.C48C|DTNA_uc002kxz.2_Silent_p.C48C|DTNA_uc002kxy.2_Silent_p.C48C|DTNA_uc010dmk.1_RNA|DTNA_uc010dml.2_Silent_p.C48C|DTNA_uc002kyb.3_Silent_p.C48C|DTNA_uc010dmm.2_Silent_p.C48C	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	48	Interaction with MAGEE1 (By similarity).				neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32391993	32391993	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32391993A>C	uc010dmn.1	+	5	520	c.519A>C	c.(517-519)GAA>GAC	p.E173D	DTNA_uc002kxu.2_Missense_Mutation_p.E173D|DTNA_uc010xbx.1_Missense_Mutation_p.E173D|DTNA_uc002kxv.3_Missense_Mutation_p.E173D|DTNA_uc002kxw.2_Missense_Mutation_p.E173D|DTNA_uc002kxx.2_Missense_Mutation_p.E173D|DTNA_uc010dmj.2_Missense_Mutation_p.E173D|DTNA_uc002kxz.2_Missense_Mutation_p.E173D|DTNA_uc002kxy.2_Missense_Mutation_p.E173D|DTNA_uc010dmk.1_RNA|DTNA_uc010dml.2_Missense_Mutation_p.E173D|DTNA_uc002kyb.3_Missense_Mutation_p.E173D|DTNA_uc010dmm.2_Missense_Mutation_p.E173D	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	173	Interaction with MAGEE1 (By similarity).				neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43205723	43205723	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43205723G>A	uc010dnj.2	+	4	547	c.226G>A	c.(226-228)GAC>AAC	p.D76N	SLC14A2_uc002lbb.2_Missense_Mutation_p.D76N|SLC14A2_uc002lbe.2_Missense_Mutation_p.D76N	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	76						apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43532417	43532417	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43532417G>A	uc002lbm.2	-	3	1301	c.1201C>T	c.(1201-1203)CTC>TTC	p.L401F	KIAA1632_uc002lbo.1_Missense_Mutation_p.L401F	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	401					autophagy						0																		---	---	---	---
RNF165	494470	broad.mit.edu	37	18	44036544	44036544	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44036544A>C	uc002lcb.1	+	8	1037	c.986A>C	c.(985-987)AAG>ACG	p.K329T	RNF165_uc002lby.1_Missense_Mutation_p.K262T|RNF165_uc010dnn.1_Missense_Mutation_p.K125T	NM_152470	NP_689683	Q6ZSG1	RN165_HUMAN	ring finger protein 165	329	RING-type; atypical.						zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)														---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47511134	47511134	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47511134G>A	uc002leb.2	-	8	1188	c.900C>T	c.(898-900)GAC>GAT	p.D300D	MYO5B_uc002lec.1_Silent_p.D299D	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	300	Myosin head-like.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50278453	50278453	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50278453C>T	uc002lfe.1	+	2	708	c.121C>T	c.(121-123)CGC>TGC	p.R41C	DCC_uc010xdr.1_5'UTR	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	41	Extracellular (Potential).|Ig-like C2-type 1.				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
ZNF532	55205	broad.mit.edu	37	18	56586354	56586354	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56586354G>A	uc002lho.2	+	4	1382	c.835G>A	c.(835-837)GCT>ACT	p.A279T	ZNF532_uc002lhp.2_Missense_Mutation_p.A277T|ZNF532_uc010xeg.1_Missense_Mutation_p.A277T|ZNF532_uc002lhr.2_Missense_Mutation_p.A277T|ZNF532_uc002lhs.2_Missense_Mutation_p.A277T	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	279					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
HMSD	284293	broad.mit.edu	37	18	61621687	61621687	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61621687C>T	uc010dqj.2	+	3	267	c.118C>T	c.(118-120)CGA>TGA	p.R40*		NM_001123366	NP_001116838	A8MTL9	HMSD_HUMAN	histocompatibility (minor) serpin domain	40						extracellular region	serine-type endopeptidase inhibitor activity				0																		---	---	---	---
DSEL	92126	broad.mit.edu	37	18	65180462	65180462	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65180462T>G	uc002lke.1	-	2	2638	c.1414A>C	c.(1414-1416)AGT>CGT	p.S472R		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	462						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)																---	---	---	---
SOCS6	9306	broad.mit.edu	37	18	67993058	67993058	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67993058A>G	uc002lkr.1	+	2	1470	c.1154A>G	c.(1153-1155)TAC>TGC	p.Y385C	SOCS6_uc010dqq.2_Missense_Mutation_p.Y385C	NM_004232	NP_004223	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	385	SH2.				defense response|JAK-STAT cascade|negative regulation of signal transduction|regulation of growth	cytoplasm				large_intestine(1)|lung(1)	2		Esophageal squamous(42;0.129)|Colorectal(73;0.152)																---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74649204	74649204	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74649204G>A	uc002lmi.2	+	26	4879	c.4681G>A	c.(4681-4683)GTG>ATG	p.V1561M	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1561					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)														---	---	---	---
KCNG2	26251	broad.mit.edu	37	18	77659062	77659062	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77659062G>A	uc010xfl.1	+	2	647	c.647G>A	c.(646-648)CGC>CAC	p.R216H		NM_012283	NP_036415	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G,	216					energy reserve metabolic process|regulation of heart contraction|regulation of insulin secretion	voltage-gated potassium channel complex	delayed rectifier potassium channel activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)														---	---	---	---
PQLC1	80148	broad.mit.edu	37	18	77679327	77679327	+	Silent	SNP	G	A	A	rs34425104	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77679327G>A	uc002lnl.2	-	5	637	c.465C>T	c.(463-465)GGC>GGT	p.G155G	PQLC1_uc010dre.2_Silent_p.G72G|PQLC1_uc002lnk.2_Silent_p.G137G|PQLC1_uc010xfm.1_Intron	NM_025078	NP_079354	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1 isoform 1	155	Helical; (Potential).					integral to membrane				large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)														---	---	---	---
PPAP2C	8612	broad.mit.edu	37	19	288132	288132	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:288132G>A	uc002loi.2	-	2	191	c.92C>T	c.(91-93)CCG>CTG	p.P31L	PPAP2C_uc002loh.2_Missense_Mutation_p.P52L|PPAP2C_uc002loj.2_5'UTR	NM_003712	NP_003703	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C isoform 1	31					sphingolipid metabolic process	integral to membrane|plasma membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)														---	---	---	---
MIER2	54531	broad.mit.edu	37	19	313553	313553	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:313553C>T	uc002lok.1	-	8	755	c.746G>A	c.(745-747)CGT>CAT	p.R249H		NM_017550	NP_060020	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family	249	ELM2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		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)														---	---	---	---
THEG	51298	broad.mit.edu	37	19	362241	362241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:362241C>T	uc002lol.2	-	8	1138	c.1099G>A	c.(1099-1101)GCA>ACA	p.A367T	THEG_uc002lom.2_Missense_Mutation_p.A343T	NM_016585	NP_057669	Q9P2T0	THEG_HUMAN	Theg homolog isoform 1	367					cell differentiation|chaperone-mediated protein complex assembly|multicellular organismal development|spermatogenesis	nucleus	protein binding			ovary(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)														---	---	---	---
BSG	682	broad.mit.edu	37	19	580705	580705	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:580705A>G	uc002loz.2	+	5	813	c.715A>G	c.(715-717)ATG>GTG	p.M239V	BSG_uc002loy.2_Missense_Mutation_p.M59V|BSG_uc002lpa.2_Missense_Mutation_p.M123V|BSG_uc002lpb.2_RNA|BSG_uc010drr.2_Missense_Mutation_p.M123V|BSG_uc002lpc.2_Missense_Mutation_p.M286V|BSG_uc002lpd.2_5'Flank	NM_001728	NP_001719	P35613	BASI_HUMAN	basigin isoform 1 precursor	239	Extracellular (Potential).|Ig-like V-type.				blood coagulation|cell surface receptor linked signaling pathway|leukocyte migration|pyruvate metabolic process	Golgi membrane|integral to membrane|melanosome	lactate transmembrane transporter activity|mannose binding|protein binding				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)														---	---	---	---
LPPR3	79948	broad.mit.edu	37	19	814902	814902	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:814902C>T	uc002lpx.1	-	5	647	c.583G>A	c.(583-585)GCC>ACC	p.A195T	LPPR3_uc010dru.1_Missense_Mutation_p.A107T|LPPR3_uc002lpw.1_Missense_Mutation_p.A195T|LPPR3_uc002lpy.1_5'UTR	NM_024888	NP_079164	Q6T4P5	LPPR3_HUMAN	plasticity-related protein 2	195						integral to membrane	phosphatidate phosphatase activity				0																		---	---	---	---
HMHA1	23526	broad.mit.edu	37	19	1074128	1074128	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1074128C>T	uc002lqz.1	+	7	1047	c.816C>T	c.(814-816)GAC>GAT	p.D272D	HMHA1_uc010xgd.1_Silent_p.D288D|HMHA1_uc010xge.1_Silent_p.D112D|HMHA1_uc002lra.1_Silent_p.D112D|HMHA1_uc002lrb.1_Silent_p.D155D	NM_012292	NP_036424	Q92619	HMHA1_HUMAN	minor histocompatibility antigen HA-1	272					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding			lung(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)														---	---	---	---
MUM1	84939	broad.mit.edu	37	19	1360408	1360408	+	Missense_Mutation	SNP	C	T	T	rs117812723	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1360408C>T	uc010xgm.1	+	4	557	c.488C>T	c.(487-489)TCG>TTG	p.S163L	MUM1_uc010dsi.2_Missense_Mutation_p.S95L|MUM1_uc002lrz.2_Missense_Mutation_p.S164L|MUM1_uc002lsb.2_Missense_Mutation_p.S95L|MUM1_uc002lsc.1_Missense_Mutation_p.S95L			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;	163					chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|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)												OREG0025088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ADAMTSL5	339366	broad.mit.edu	37	19	1510219	1510219	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1510219C>T	uc002ltd.2	-	5	735	c.291G>A	c.(289-291)CAG>CAA	p.Q97Q	ADAMTSL5_uc010dsl.2_Translation_Start_Site|ADAMTSL5_uc010xgq.1_Silent_p.Q107Q	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor	97						proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)														---	---	---	---
ATP8B3	148229	broad.mit.edu	37	19	1789638	1789638	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1789638G>T	uc002ltw.2	-	23	2801	c.2567C>A	c.(2566-2568)TCC>TAC	p.S856Y	ATP8B3_uc002ltv.2_Missense_Mutation_p.S819Y|ATP8B3_uc002ltx.2_Intron	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3	856	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ATP8B3	148229	broad.mit.edu	37	19	1796808	1796808	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1796808A>G	uc002ltw.2	-	16	1889	c.1655T>C	c.(1654-1656)CTC>CCC	p.L552P	ATP8B3_uc002ltv.2_Missense_Mutation_p.L505P|ATP8B3_uc002ltx.2_RNA	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3	552	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2129435	2129435	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2129435T>C	uc002luz.2	-	7	837	c.614A>G	c.(613-615)AAT>AGT	p.N205S	AP3D1_uc002luy.2_Intron|AP3D1_uc002lva.2_Missense_Mutation_p.N205S	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	205	HEAT 4.				eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF554	115196	broad.mit.edu	37	19	2823039	2823039	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2823039T>C	uc002lwm.2	+	2	253	c.55T>C	c.(55-57)TCT>CCT	p.S19P	ZNF554_uc002lwl.2_5'UTR	NM_001102651	NP_001096121	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	19					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		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)														---	---	---	---
PIAS4	51588	broad.mit.edu	37	19	4037403	4037403	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4037403G>T	uc002lzg.2	+	10	1184	c.1174G>T	c.(1174-1176)GAC>TAC	p.D392Y		NM_015897	NP_056981	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	392					positive regulation of protein sumoylation|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|PML body	DNA binding|SUMO ligase activity|ubiquitin protein ligase binding|zinc ion binding			pancreas(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TMIGD2	126259	broad.mit.edu	37	19	4292852	4292852	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4292852C>T	uc002lzx.1	-	5	639	c.593G>A	c.(592-594)CGG>CAG	p.R198Q	TMIGD2_uc010dtv.1_Missense_Mutation_p.R194Q	NM_144615	NP_653216	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain	198	Cytoplasmic (Potential).					integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
UBXN6	80700	broad.mit.edu	37	19	4453937	4453937	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4453937G>A	uc002man.1	-	2	333	c.237C>T	c.(235-237)ATC>ATT	p.I79I	UBXN6_uc010dty.1_Silent_p.I26I|UBXN6_uc002mam.1_Silent_p.I26I	NM_025241	NP_079517	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	79						microtubule organizing center|nucleus	protein binding				0																		---	---	---	---
UHRF1	29128	broad.mit.edu	37	19	4932942	4932942	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4932942G>A	uc002mbo.2	+	5	927	c.759G>A	c.(757-759)CGG>CGA	p.R253R	UHRF1_uc010xik.1_Intron|UHRF1_uc010duf.2_RNA|UHRF1_uc002mbp.2_Silent_p.R266R	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains	253					cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)														---	---	---	---
UHRF1	29128	broad.mit.edu	37	19	4950920	4950920	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4950920G>A	uc002mbo.2	+	13	1898	c.1730G>A	c.(1729-1731)CGC>CAC	p.R577H	UHRF1_uc010xik.1_RNA|UHRF1_uc010duf.2_RNA|UHRF1_uc002mbp.2_Missense_Mutation_p.R590H	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains	577	YDG.				cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)														---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5244164	5244164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5244164C>T	uc002mbv.2	-	11	1552	c.1318G>A	c.(1318-1320)GCG>ACG	p.A440T	PTPRS_uc002mbu.1_Missense_Mutation_p.A427T|PTPRS_uc010xin.1_Missense_Mutation_p.A427T|PTPRS_uc002mbw.2_Missense_Mutation_p.A427T|PTPRS_uc002mbx.2_Missense_Mutation_p.A431T|PTPRS_uc002mby.2_Missense_Mutation_p.A427T	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	440	Extracellular (Potential).|Fibronectin type-III 2.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
ZNRF4	148066	broad.mit.edu	37	19	5455507	5455507	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5455507C>T	uc002mca.3	+	1	82	c.5C>T	c.(4-6)CCG>CTG	p.P2L		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	2						integral to membrane	zinc ion binding			large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)														---	---	---	---
LONP1	9361	broad.mit.edu	37	19	5699204	5699204	+	Missense_Mutation	SNP	C	T	T	rs143983421		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5699204C>T	uc002mcx.2	-	10	1552	c.1519G>A	c.(1519-1521)GTT>ATT	p.V507I	LONP1_uc002mcy.2_Missense_Mutation_p.V443I|LONP1_uc010duh.2_Missense_Mutation_p.V248I|LONP1_uc010dui.2_Missense_Mutation_p.V491I|LONP1_uc002mcz.2_Missense_Mutation_p.V311I	NM_004793	NP_004784	P36776	LONM_HUMAN	mitochondrial lon peptidase 1 precursor	507					cellular chaperone-mediated protein complex assembly|cellular response to oxidative stress|misfolded or incompletely synthesized protein catabolic process|mitochondrial DNA metabolic process|oxidation-dependent protein catabolic process|protein homooligomerization|response to hypoxia	mitochondrial nucleoid	ADP binding|ATP binding|ATP-dependent peptidase activity|DNA polymerase binding|G-quadruplex DNA binding|mitochondrial heavy strand promoter anti-sense binding|mitochondrial light strand promoter anti-sense binding|sequence-specific DNA binding|serine-type endopeptidase activity|single-stranded DNA binding|single-stranded RNA binding				0																		---	---	---	---
MLLT1	4298	broad.mit.edu	37	19	6213094	6213094	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6213094C>T	uc002mek.2	-	12	1803	c.1639G>A	c.(1639-1641)GTG>ATG	p.V547M		NM_005934	NP_005925	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	547					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1								T	MLL	AL								---	---	---	---
FCER2	2208	broad.mit.edu	37	19	7754113	7754113	+	Missense_Mutation	SNP	C	T	T	rs149654388		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7754113C>T	uc002mhn.2	-	11	1116	c.932G>A	c.(931-933)CGC>CAC	p.R311H	FCER2_uc010xjs.1_Missense_Mutation_p.R233H|FCER2_uc010xjt.1_Missense_Mutation_p.R233H|FCER2_uc002mhm.2_Missense_Mutation_p.R311H	NM_002002	NP_001993	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor	311	Extracellular (Potential).				positive regulation of killing of cells of other organism|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of nitric-oxide synthase activity	extracellular region|integral to plasma membrane	IgE binding|integrin binding|receptor activity|sugar binding				0																		---	---	---	---
EVI5L	115704	broad.mit.edu	37	19	7914211	7914211	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7914211A>G	uc002min.2	+	5	776	c.622A>G	c.(622-624)ATG>GTG	p.M208V	EVI5L_uc010xjz.1_Missense_Mutation_p.M208V|EVI5L_uc002mio.1_5'Flank	NM_145245	NP_660288	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like isoform	208	Rab-GAP TBC.					intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
SNAPC2	6618	broad.mit.edu	37	19	7986931	7986931	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7986931C>T	uc002miw.1	+	4	407	c.384C>T	c.(382-384)ATC>ATT	p.I128I	SNAPC2_uc002mix.1_RNA	NM_003083	NP_003074	Q13487	SNPC2_HUMAN	small nuclear RNA activating complex,	128					snRNA transcription|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8190851	8190851	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8190851C>T	uc002mjf.2	-	21	2677	c.2656G>A	c.(2656-2658)GTC>ATC	p.V886I		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	886	EGF-like 11; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
LASS4	79603	broad.mit.edu	37	19	8321559	8321559	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8321559C>T	uc002mjg.2	+	8	897	c.577C>T	c.(577-579)CTG>TTG	p.L193L	LASS4_uc002mjh.2_Silent_p.L142L|LASS4_uc002mji.2_Silent_p.L29L|LASS4_uc010dvz.2_Silent_p.L193L	NM_024552	NP_078828	Q9HA82	CERS4_HUMAN	LAG1 homolog, ceramide synthase 4	193	TLC.|Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(1)	1																		---	---	---	---
ACTL9	284382	broad.mit.edu	37	19	8808899	8808899	+	Silent	SNP	C	T	T	rs138094625	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8808899C>T	uc002mkl.2	-	1	274	c.153G>A	c.(151-153)GTG>GTA	p.V51V		NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN	actin-like 9	51						cytoplasm|cytoskeleton				large_intestine(2)|pancreas(1)	3																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9018427	9018427	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9018427G>T	uc002mkp.2	-							NM_024690	NP_078966			mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9046249	9046249	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9046249T>G	uc002mkp.2	-	5	35586	c.35382A>C	c.(35380-35382)CAA>CAC	p.Q11794H		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11796	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9049228	9049228	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9049228C>T	uc002mkp.2	-	5	32607	c.32403G>A	c.(32401-32403)GCG>GCA	p.A10801A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10803	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
OR7D4	125958	broad.mit.edu	37	19	9324694	9324694	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9324694C>T	uc002mla.1	-	1	820	c.820G>A	c.(820-822)GCC>ACC	p.A274T		NM_001005191	NP_001005191	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D,	274	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
ZNF559	84527	broad.mit.edu	37	19	9453697	9453697	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9453697T>G	uc002mlg.2	+	7	2217	c.1570T>G	c.(1570-1572)TGT>GGT	p.C524G	ZNF559_uc002mlf.2_Missense_Mutation_p.C293G|ZNF559_uc010dwl.1_Missense_Mutation_p.C293G|ZNF559_uc010xkn.1_Missense_Mutation_p.C516G|ZNF559_uc010dwm.1_3'UTR|ZNF559_uc002mle.3_Missense_Mutation_p.C588G|ZNF559_uc010dwk.1_Missense_Mutation_p.C293G|ZNF559_uc002mld.2_3'UTR|ZNF559_uc010dwo.1_Intron|ZNF177_uc002mli.2_Intron|ZNF177_uc002mlj.2_Intron	NM_032497	NP_115886	Q9BR84	ZN559_HUMAN	zinc finger protein 559	524					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10251513	10251513	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10251513C>T	uc002mng.2	-	31	3599	c.3419G>A	c.(3418-3420)CGG>CAG	p.R1140Q	DNMT1_uc002mne.2_5'Flank|DNMT1_uc002mnf.2_Missense_Mutation_p.R64Q|DNMT1_uc010xlc.1_Missense_Mutation_p.R1156Q|DNMT1_uc002mnh.2_Missense_Mutation_p.R1035Q|DNMT1_uc010xld.1_Missense_Mutation_p.R1140Q	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	1140	Catalytic.|Interaction with the PRC2/EED-EZH2 complex (By similarity).				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10260184	10260184	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10260184A>G	uc002mng.2	-	25	2663	c.2483T>C	c.(2482-2484)ATC>ACC	p.I828T	DNMT1_uc010xlc.1_Missense_Mutation_p.I844T|DNMT1_uc002mnh.2_Missense_Mutation_p.I723T|DNMT1_uc010xld.1_Missense_Mutation_p.I828T	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	828	BAH 1.				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
CARM1	10498	broad.mit.edu	37	19	11032425	11032425	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11032425G>A	uc002mpz.2	+	16	1945	c.1819G>A	c.(1819-1821)GGG>AGG	p.G607R	CARM1_uc010dxn.2_RNA|CARM1_uc002mqa.2_Missense_Mutation_p.G367R	NM_199141	NP_954592	Q86X55	CARM1_HUMAN	coactivator-associated arginine	607	Transactivation domain (By similarity).				cellular lipid metabolic process|histone H3-R2 methylation|interspecies interaction between organisms|pathogenesis|positive regulation of fat cell differentiation|regulation of estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleoplasm	beta-catenin binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-R17 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein-arginine omega-N asymmetric methyltransferase activity|transcription regulatory region DNA binding				0																		---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11526717	11526717	+	Missense_Mutation	SNP	G	A	A	rs139040605		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11526717G>A	uc002mrp.2	-	5	597	c.533C>T	c.(532-534)GCG>GTG	p.A178V	RGL3_uc002mrn.2_5'UTR|RGL3_uc002mrm.2_5'UTR|RGL3_uc002mro.2_Missense_Mutation_p.A178V	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation	178	N-terminal Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
CCDC151	115948	broad.mit.edu	37	19	11534692	11534692	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11534692G>A	uc002mrs.2	-	8	1113	c.970C>T	c.(970-972)CGC>TGC	p.R324C	CCDC151_uc002mrr.2_Missense_Mutation_p.R259C|CCDC151_uc010dxz.2_Missense_Mutation_p.R264C	NM_145045	NP_659482	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	324	Potential.									ovary(1)	1																		---	---	---	---
PRKCSH	5589	broad.mit.edu	37	19	11558373	11558373	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11558373A>G	uc002mrt.2	+	11	1305	c.969A>G	c.(967-969)GAA>GAG	p.E323E	PRKCSH_uc002mru.2_Silent_p.E323E|PRKCSH_uc010xlz.1_Silent_p.E323E|PRKCSH_uc010dya.2_Intron|PRKCSH_uc002mrv.1_Silent_p.E323E|PRKCSH_uc010dyb.2_Silent_p.E323E	NM_002743	NP_002734	P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H isoform 1	323	Glu-rich (acidic).				innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding				0																		---	---	---	---
ZNF439	90594	broad.mit.edu	37	19	11979192	11979192	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11979192A>G	uc002mss.2	+	3	1436	c.1308A>G	c.(1306-1308)AAA>AAG	p.K436K	ZNF439_uc002msr.2_Silent_p.K300K	NM_152262	NP_689475	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	436					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
ZNF709	163051	broad.mit.edu	37	19	12575998	12575998	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12575998G>T	uc002mtv.3	-	4	899	c.738C>A	c.(736-738)CAC>CAA	p.H246Q	ZNF709_uc002mtw.3_Missense_Mutation_p.H214Q|ZNF709_uc002mtx.3_Missense_Mutation_p.H246Q	NM_152601	NP_689814	Q8N972	ZN709_HUMAN	zinc finger protein 709 isoform a	246	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ASNA1	439	broad.mit.edu	37	19	12848425	12848425	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12848425A>G	uc002muv.2	+	1	120	c.106A>G	c.(106-108)AGC>GGC	p.S36G	C19orf43_uc002muu.2_5'Flank|ASNA1_uc002muw.2_Missense_Mutation_p.S36G	NM_004317	NP_004308	O43681	ASNA_HUMAN	arsA arsenite transporter, ATP-binding, homolog	36					response to arsenic-containing substance	endoplasmic reticulum|nucleolus|soluble fraction	arsenite-transporting ATPase activity|ATP binding|metal ion binding			ovary(2)	2					Adenosine triphosphate(DB00171)													---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12962928	12962928	+	Splice_Site	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12962928G>T	uc002mvm.2	+	9	1005	c.877_splice	c.e9-1	p.E293_splice	MAST1_uc002mvk.2_Splice_Site_p.E289_splice	NM_014975	NP_055790			microtubule associated serine/threonine kinase						cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12977542	12977542	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12977542G>A	uc002mvm.2	+	18	2233	c.2105G>A	c.(2104-2106)CGC>CAC	p.R702H		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	702	AGC-kinase C-terminal.				cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12984600	12984600	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12984600C>T	uc002mvm.2	+	26	3757	c.3629C>T	c.(3628-3630)ACG>ATG	p.T1210M		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	1210					cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
GCDH	2639	broad.mit.edu	37	19	13006913	13006913	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13006913A>G	uc002mvq.2	+	7	690	c.613A>G	c.(613-615)ACC>GCC	p.T205A	GCDH_uc010xms.1_Missense_Mutation_p.T172A|GCDH_uc002mvp.2_Missense_Mutation_p.T205A|GCDH_uc010xmt.1_Silent_p.T50T|GCDH_uc010xmu.1_Missense_Mutation_p.T161A	NM_000159	NP_000150	Q92947	GCDH_HUMAN	glutaryl-Coenzyme A dehydrogenase isoform a	205					lysine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|glutaryl-CoA dehydrogenase activity|protein binding				0																		---	---	---	---
C19orf57	79173	broad.mit.edu	37	19	14000134	14000134	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14000134T>C	uc002mxl.1	-	6	1594	c.1535A>G	c.(1534-1536)CAG>CGG	p.Q512R	C19orf57_uc002mxk.1_Missense_Mutation_p.Q394R|C19orf57_uc002mxm.1_Intron	NM_024323	NP_077299	Q0VDD7	CS057_HUMAN	hypothetical protein LOC79173	512					multicellular organismal development		protein binding			ovary(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(19;2e-21)															---	---	---	---
IL27RA	9466	broad.mit.edu	37	19	14150483	14150483	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14150483G>A	uc002mxx.2	+							NM_004843	NP_004834			class I cytokine receptor precursor						cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0																		---	---	---	---
LPHN1	22859	broad.mit.edu	37	19	14269309	14269309	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14269309C>T	uc010xnn.1	-	13	2516	c.2220G>A	c.(2218-2220)ACG>ACA	p.T740T	LPHN1_uc010xno.1_Silent_p.T735T|uc002myf.2_Intron	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	740	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5																		---	---	---	---
LPHN1	22859	broad.mit.edu	37	19	14271040	14271040	+	Missense_Mutation	SNP	C	T	T	rs149895143	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14271040C>T	uc010xnn.1	-	9	1995	c.1699G>A	c.(1699-1701)GCG>ACG	p.A567T	LPHN1_uc010xno.1_Missense_Mutation_p.A562T|uc002myf.2_Intron	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	567	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5																		---	---	---	---
SYDE1	85360	broad.mit.edu	37	19	15223187	15223187	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15223187C>T	uc002nah.1	+	7	1640	c.1609C>T	c.(1609-1611)CGC>TGC	p.R537C	SYDE1_uc002nai.1_Missense_Mutation_p.R470C|SYDE1_uc002naj.1_Missense_Mutation_p.R194C	NM_033025	NP_149014	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1	537	Rho-GAP.				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15302455	15302455	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15302455C>T	uc002nan.2	-	6	892	c.816G>A	c.(814-816)ACG>ACA	p.T272T	NOTCH3_uc002nao.1_Silent_p.T272T	NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	272	Extracellular (Potential).|EGF-like 6; calcium-binding (Potential).				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
WIZ	58525	broad.mit.edu	37	19	15558926	15558926	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15558926C>A	uc002nbb.3	-	2	407	c.193G>T	c.(193-195)GGT>TGT	p.G65C	MIR1470_hsa-mir-1470|MI0007075_5'Flank	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						nucleus	zinc ion binding				0																		---	---	---	---
OR10H5	284433	broad.mit.edu	37	19	15904931	15904931	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15904931C>G	uc010xos.1	+	1	73	c.73C>G	c.(73-75)CTG>GTG	p.L25V		NM_001004466	NP_001004466	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H,	25	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17014528	17014528	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17014528A>G	uc002nfb.2	-	33	4564	c.4532T>C	c.(4531-4533)GTT>GCT	p.V1511A	CPAMD8_uc002nfd.1_5'Flank	NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	1464						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
MAP1S	55201	broad.mit.edu	37	19	17836734	17836734	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17836734G>A	uc002nhe.1	+	5	550	c.541G>A	c.(541-543)GCT>ACT	p.A181T	MAP1S_uc010eaz.1_RNA|MAP1S_uc010eba.1_Missense_Mutation_p.A181T|MAP1S_uc002nhf.1_Intron|MAP1S_uc010xpv.1_Missense_Mutation_p.A155T	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN	BPY2 interacting protein 1	181	Necessary for the microtubule-organizing center localization.				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding			central_nervous_system(1)	1																		---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17983369	17983369	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17983369T>C	uc002nhr.3	+	1	588	c.241T>C	c.(241-243)TAT>CAT	p.Y81H		NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide	81	Extracellular (Potential).				cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
COMP	1311	broad.mit.edu	37	19	18897335	18897335	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18897335C>T	uc002nke.2	-						COMP_uc002nkd.2_Intron|COMP_uc010xqj.1_Intron	NM_000095	NP_000086			cartilage oligomeric matrix protein precursor						anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding				0																		---	---	---	---
NCAN	1463	broad.mit.edu	37	19	19337487	19337487	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19337487A>C	uc002nlz.2	+	7	1364	c.1265A>C	c.(1264-1266)AAG>ACG	p.K422T	NCAN_uc010ecc.1_5'UTR	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	422					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)															---	---	---	---
ZNF431	170959	broad.mit.edu	37	19	21350433	21350433	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21350433A>G	uc002npp.2	+	4	430	c.283A>G	c.(283-285)AAT>GAT	p.N95D	ZNF431_uc010ecq.2_5'UTR|ZNF431_uc010ecr.2_Missense_Mutation_p.N96D	NM_133473	NP_597730	Q8TF32	ZN431_HUMAN	zinc finger protein 431	95	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
ZNF100	163227	broad.mit.edu	37	19	21927746	21927746	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21927746A>C	uc002nqi.2	-	3	419	c.220T>G	c.(220-222)TTG>GTG	p.L74V	ZNF100_uc002nqh.2_Missense_Mutation_p.L11V	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	74	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF43	7594	broad.mit.edu	37	19	21992387	21992387	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21992387C>T	uc002nqj.2	-	4	582	c.452G>A	c.(451-453)TGT>TAT	p.C151Y	ZNF43_uc010ecv.2_Missense_Mutation_p.C145Y|ZNF43_uc002nql.2_Missense_Mutation_p.C145Y|ZNF43_uc002nqm.2_Missense_Mutation_p.C145Y|ZNF43_uc002nqk.2_Missense_Mutation_p.C81Y	NM_003423	NP_003414	P17038	ZNF43_HUMAN	zinc finger protein 43	151					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)														---	---	---	---
TSHZ3	57616	broad.mit.edu	37	19	31769144	31769144	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31769144C>T	uc002nsy.3	-	2	1620	c.1555G>A	c.(1555-1557)GGG>AGG	p.G519R		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	519					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)																	---	---	---	---
ZNF507	22847	broad.mit.edu	37	19	32873756	32873756	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32873756A>G	uc002nte.2	+	7	2901	c.2629A>G	c.(2629-2631)ACC>GCC	p.T877A	ZNF507_uc002ntd.2_Missense_Mutation_p.T877A	NM_001136156	NP_001129628	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	877					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(110;0.162)																	---	---	---	---
ZNF302	55900	broad.mit.edu	37	19	35173767	35173767	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35173767T>C	uc002nvr.1	+	4	490	c.227T>C	c.(226-228)GTG>GCG	p.V76A	ZNF302_uc010xrz.1_Missense_Mutation_p.V32A|ZNF302_uc002nvp.1_Missense_Mutation_p.V32A|ZNF302_uc002nvq.1_Missense_Mutation_p.V32A|ZNF302_uc002nvs.1_Missense_Mutation_p.V32A	NM_018443	NP_060913	Q9NR11	ZN302_HUMAN	zinc finger protein 302	Error:Variant_position_missing_in_Q9NR11_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
GRAMD1A	57655	broad.mit.edu	37	19	35501006	35501006	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35501006C>T	uc010xse.1	+	5	473	c.336C>T	c.(334-336)TGC>TGT	p.C112C	GRAMD1A_uc002nxi.1_Silent_p.C199C|GRAMD1A_uc002nxk.2_Silent_p.C105C|GRAMD1A_uc002nxl.2_5'UTR|GRAMD1A_uc010xsf.1_Silent_p.C117C	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	112	GRAM.					integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
FFAR2	2867	broad.mit.edu	37	19	35940790	35940790	+	Silent	SNP	G	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35940790G>C	uc002nzg.2	+	2	254	c.174G>C	c.(172-174)CTG>CTC	p.L58L	FFAR2_uc010eea.2_Silent_p.L58L	NM_005306	NP_005297	O15552	FFAR2_HUMAN	free fatty acid receptor 2	58	Helical; Name=2; (Potential).					integral to plasma membrane	G-protein coupled receptor activity|lipid binding			central_nervous_system(1)	1	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)															---	---	---	---
ARHGAP33	115703	broad.mit.edu	37	19	36273690	36273690	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36273690T>C	uc002obr.1	+	15	1425	c.1340T>C	c.(1339-1341)CTG>CCG	p.L447P	ARHGAP33_uc002obs.1_Missense_Mutation_p.L447P|ARHGAP33_uc002obt.1_Missense_Mutation_p.L311P|ARHGAP33_uc010eel.2_Missense_Mutation_p.L35P|ARHGAP33_uc002obv.1_Missense_Mutation_p.L35P	NM_052948	NP_443180	O14559	RHG33_HUMAN	sorting nexin 26	447	Rho-GAP.				cell communication|protein transport|signal transduction	intracellular	GTPase activator activity|phosphatidylinositol binding|protein binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ALKBH6	84964	broad.mit.edu	37	19	36501501	36501501	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36501501G>A	uc002oct.2	-	6	521	c.421C>T	c.(421-423)CGG>TGG	p.R141W	C19orf46_uc002ocr.1_5'Flank|C19orf46_uc002ocs.1_5'Flank|C19orf46_uc002ocq.1_5'Flank|C19orf46_uc010een.1_5'Flank|ALKBH6_uc002ocv.1_Missense_Mutation_p.R169W|ALKBH6_uc002ocx.1_Missense_Mutation_p.R72W|ALKBH6_uc002ocw.1_Missense_Mutation_p.A156V|ALKBH6_uc010eeo.1_Missense_Mutation_p.R141W|ALKBH6_uc010eep.1_3'UTR	NM_032878	NP_116267	Q3KRA9	ALKB6_HUMAN	alkB, alkylation repair homolog 6 isoform 2	141	Fe2OG dioxygenase.					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)															---	---	---	---
ZNF567	163081	broad.mit.edu	37	19	37209843	37209843	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37209843T>C	uc010xtl.1	+						ZNF567_uc002oeo.1_Intron|ZNF567_uc010xtk.1_Intron|ZNF567_uc002oep.3_Intron|ZNF567_uc002oeq.1_Intron	NM_152603	NP_689816			zinc finger protein 567						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
ZNF790	388536	broad.mit.edu	37	19	37310989	37310989	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37310989T>A	uc002oew.2	-	5	376	c.257A>T	c.(256-258)AAG>ATG	p.K86M	uc002oev.1_Intron	NM_206894	NP_996777	Q6PG37	ZN790_HUMAN	zinc finger protein 790	86					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|skin(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
ZNF527	84503	broad.mit.edu	37	19	37879314	37879314	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37879314T>C	uc010efk.1	+	5	474	c.363T>C	c.(361-363)CTT>CTC	p.L121L	ZNF527_uc002ogf.3_Silent_p.L89L|ZNF527_uc010xtq.1_RNA	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527	121	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF540	163255	broad.mit.edu	37	19	38074869	38074869	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38074869T>C	uc002ogq.2	+						uc002ogm.2_Intron|uc002ogn.2_Intron|ZNF540_uc002ogo.2_Intron|ZNF540_uc002ogp.2_Intron|ZNF571_uc002ogr.1_Intron|ZNF571_uc002ogt.2_Intron|ZNF571_uc010efp.2_Intron	NM_152606	NP_689819			zinc finger protein 540						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39009883	39009883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39009883C>T	uc002oit.2	+	67	10178	c.10048C>T	c.(10048-10050)CGG>TGG	p.R3350W	RYR1_uc002oiu.2_Missense_Mutation_p.R3350W|RYR1_uc002oiv.1_Missense_Mutation_p.R270W|RYR1_uc010xuf.1_Missense_Mutation_p.R270W	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	3350					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39014577	39014577	+	Intron	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39014577C>A	uc002oit.2	+						RYR1_uc002oiu.2_Intron|RYR1_uc002oiv.1_Intron|RYR1_uc010xuf.1_Intron	NM_000540	NP_000531			skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39038900	39038900	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39038900G>A	uc002oit.2	+	89	12252	c.12122G>A	c.(12121-12123)CGG>CAG	p.R4041Q	RYR1_uc002oiu.2_Missense_Mutation_p.R4036Q|RYR1_uc002oiv.1_Missense_Mutation_p.R950Q	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4041					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
MAP4K1	11184	broad.mit.edu	37	19	39090799	39090799	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39090799G>T	uc002oix.1	-						MAP4K1_uc002oiw.1_Intron|MAP4K1_uc002oiy.1_Intron|MAP4K1_uc010xug.1_Intron	NM_007181	NP_009112			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
LGALS4	3960	broad.mit.edu	37	19	39292738	39292738	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39292738C>T	uc002ojg.2	-	9	933	c.719G>A	c.(718-720)CGC>CAC	p.R240H		NM_006149	NP_006140	P56470	LEG4_HUMAN	galectin-4	240	Galectin 2.				cell adhesion	cytosol|plasma membrane	sugar binding			ovary(1)|skin(1)	2	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)															---	---	---	---
PAPL	390928	broad.mit.edu	37	19	39600757	39600757	+	Nonstop_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39600757A>G	uc002oki.2	+	13	1590	c.1316A>G	c.(1315-1317)TAG>TGG	p.*439W	PAPL_uc010egl.2_3'UTR	NM_001004318	NP_001004318	Q6ZNF0	PAPL_HUMAN	iron/zinc purple acid phosphatase-like protein	439						extracellular region	acid phosphatase activity|metal ion binding				0																OREG0025457	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SAMD4B	55095	broad.mit.edu	37	19	39870619	39870619	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39870619C>T	uc002olb.2	+	12	2579	c.1544C>T	c.(1543-1545)ACG>ATG	p.T515M	SAMD4B_uc002ola.2_Missense_Mutation_p.T515M	NM_018028	NP_060498	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	515							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)															---	---	---	---
SUPT5H	6829	broad.mit.edu	37	19	39949665	39949665	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39949665T>C	uc002olo.3	+	7	589	c.410T>C	c.(409-411)CTG>CCG	p.L137P	SUPT5H_uc002olp.3_Missense_Mutation_p.L137P|SUPT5H_uc002olq.3_Missense_Mutation_p.L133P|SUPT5H_uc002oln.3_Missense_Mutation_p.L137P|SUPT5H_uc002olr.3_Missense_Mutation_p.L137P	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	137					cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
SHKBP1	92799	broad.mit.edu	37	19	41086254	41086254	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41086254G>A	uc002oob.2	+	7	474	c.425G>A	c.(424-426)CGG>CAG	p.R142Q	SHKBP1_uc002ooc.2_Missense_Mutation_p.R142Q|SHKBP1_uc002ood.2_Missense_Mutation_p.R142Q|SHKBP1_uc010xvl.1_Missense_Mutation_p.R65Q|SHKBP1_uc002ooe.2_5'UTR|SHKBP1_uc002oof.2_5'UTR|SHKBP1_uc010xvm.1_5'UTR|SHKBP1_uc010xvn.1_Missense_Mutation_p.R20Q	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	142						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
HNRNPUL1	11100	broad.mit.edu	37	19	41808741	41808741	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41808741G>A	uc002oqb.3	+	12	2148	c.1859G>A	c.(1858-1860)CGC>CAC	p.R620H	CYP2F1_uc010xvw.1_Intron|HNRNPUL1_uc002opz.3_Missense_Mutation_p.R520H|HNRNPUL1_uc002oqa.3_Missense_Mutation_p.R520H|HNRNPUL1_uc010ehm.2_Missense_Mutation_p.R620H|HNRNPUL1_uc002oqc.3_Missense_Mutation_p.R506H|HNRNPUL1_uc002oqe.3_Intron|HNRNPUL1_uc002oqd.3_Missense_Mutation_p.R520H|HNRNPUL1_uc010ehn.2_Missense_Mutation_p.R520H|HNRNPUL1_uc010eho.2_Missense_Mutation_p.R520H|HNRNPUL1_uc010xvy.1_Missense_Mutation_p.R520H|HNRNPUL1_uc010ehp.2_Missense_Mutation_p.R476H|HNRNPUL1_uc002oqf.3_Missense_Mutation_p.R144H	NM_007040	NP_008971	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	620	Necessary for transcription repression.|Necessary for interaction with TP53.|Gly-rich.|1-2.|5 X 3 AA repeats of R-G-G.				nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	enzyme binding|RNA binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
B9D2	80776	broad.mit.edu	37	19	41860649	41860649	+	Missense_Mutation	SNP	C	T	T	rs138230110		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41860649C>T	uc002oqj.2	-	4	704	c.484G>A	c.(484-486)GGC>AGC	p.G162S	CYP2F1_uc010xvw.1_Intron|TGFB1_uc002oqh.1_5'Flank|TMEM91_uc002oqi.2_Intron	NM_030578	NP_085055	Q9BPU9	B9D2_HUMAN	B9 protein domain 2	162					cilium assembly|mitotic prometaphase	centrosome|cilium axoneme|cytosol|microtubule basal body|nucleus	gamma-tubulin binding			ovary(1)	1																		---	---	---	---
GRIK5	2901	broad.mit.edu	37	19	42569549	42569549	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42569549C>T	uc002osj.1	-						GRIK5_uc010eib.1_Intron	NM_002088	NP_002079			glutamate receptor KA2 precursor							cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity				0		Prostate(69;0.059)			L-Glutamic Acid(DB00142)													---	---	---	---
CIC	23152	broad.mit.edu	37	19	42796628	42796628	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42796628G>A	uc002otf.1	+							NM_015125	NP_055940			capicua homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)						T	DUX4	soft tissue sarcoma								---	---	---	---
PSG4	5672	broad.mit.edu	37	19	43708390	43708390	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43708390G>A	uc002ovy.2	-	2	180	c.78C>T	c.(76-78)AAC>AAT	p.N26N	PSG4_uc002owa.2_RNA|PSG4_uc002owb.2_Silent_p.N26N|PSG4_uc002ovz.2_Silent_p.N26N	NM_002780	NP_002771	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4 isoform	26					defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
ZNF283	284349	broad.mit.edu	37	19	44352263	44352263	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44352263C>T	uc002oxr.3	+	7	1778	c.1510C>T	c.(1510-1512)CGA>TGA	p.R504*	ZNF283_uc002oxp.3_Nonsense_Mutation_p.R365*	NM_181845	NP_862828	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	504	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)																---	---	---	---
ZNF285	26974	broad.mit.edu	37	19	44891190	44891190	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44891190C>T	uc002ozd.3	-	4	1304	c.1217G>A	c.(1216-1218)GGC>GAC	p.G406D	ZFP112_uc010xwz.1_Intron|ZNF285_uc010xxa.1_Missense_Mutation_p.G413D	NM_152354	NP_689567	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	406	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(2)	4																		---	---	---	---
ZNF229	7772	broad.mit.edu	37	19	44936458	44936458	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44936458G>A	uc002oze.1	-	5	611	c.177C>T	c.(175-177)TAC>TAT	p.Y59Y	ZNF229_uc010ejk.1_5'UTR|ZNF229_uc010ejl.1_Silent_p.Y59Y	NM_014518	NP_055333	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	59	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4		Prostate(69;0.0352)																---	---	---	---
NKPD1	284353	broad.mit.edu	37	19	45655788	45655788	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45655788A>T	uc010xxi.1	-	4	1907	c.1907T>A	c.(1906-1908)CTG>CAG	p.L636Q		NM_198478	NP_940880			NTPase, KAP family P-loop domain containing 1												0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)														---	---	---	---
VASP	7408	broad.mit.edu	37	19	46020980	46020980	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46020980G>A	uc002pcg.2	+	2	407	c.65G>A	c.(64-66)CGA>CAA	p.R22Q	VASP_uc010eki.2_Missense_Mutation_p.D6N|VASP_uc002pci.2_Missense_Mutation_p.R9Q	NM_003370	NP_003361	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein	22	WH1.				axon guidance|cell junction assembly|T cell receptor signaling pathway	actin cytoskeleton|cytosol|filopodium membrane|focal adhesion|lamellipodium membrane	actin binding|profilin binding|SH3 domain binding				0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)														---	---	---	---
EML2	24139	broad.mit.edu	37	19	46117919	46117919	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46117919G>A	uc002pcn.2	-	17	1672	c.1637C>T	c.(1636-1638)GCT>GTT	p.A546V	EML2_uc002pco.2_RNA|EML2_uc002pcp.2_Missense_Mutation_p.A430V|EML2_uc010xxl.1_Missense_Mutation_p.A693V|EML2_uc010xxm.1_Missense_Mutation_p.A747V	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	546					sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)														---	---	---	---
EML2	24139	broad.mit.edu	37	19	46141865	46141865	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46141865C>T	uc002pcn.2	-	3	112	c.77G>A	c.(76-78)AGG>AAG	p.R26K	EML2_uc002pco.2_RNA|EML2_uc002pcp.2_Intron|EML2_uc010xxl.1_Missense_Mutation_p.R173K|EML2_uc010xxm.1_Missense_Mutation_p.R227K|EML2_uc010xxn.1_RNA|EML2_uc010xxo.1_Missense_Mutation_p.R26K|EML2_uc010ekj.2_Missense_Mutation_p.R26K	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	26					sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)														---	---	---	---
DMWD	1762	broad.mit.edu	37	19	46287977	46287977	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46287977C>T	uc002pdj.1	-						DMPK_uc002pdf.1_5'Flank|DMPK_uc002pdg.1_5'Flank|DMPK_uc002pdh.1_5'Flank|DMPK_uc002pdi.1_5'Flank|DMPK_uc010xxt.1_5'Flank|DMWD_uc002pdk.1_Intron|DMWD_uc010eko.1_Intron	NM_004943	NP_004934			dystrophia myotonica-containing WD repeat motif						meiosis						0		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)														---	---	---	---
PRKD2	25865	broad.mit.edu	37	19	47178330	47178330	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47178330C>T	uc002pfh.2	-	18	2726	c.2384G>A	c.(2383-2385)CGC>CAC	p.R795H	PRKD2_uc002pfd.2_Missense_Mutation_p.R169H|PRKD2_uc010eks.2_Missense_Mutation_p.R198H|PRKD2_uc010ekt.2_Missense_Mutation_p.R62H|PRKD2_uc002pfe.2_Missense_Mutation_p.R325H|PRKD2_uc002pff.2_Missense_Mutation_p.R315H|PRKD2_uc002pfg.2_Missense_Mutation_p.R638H|PRKD2_uc002pfi.2_Missense_Mutation_p.R795H|PRKD2_uc002pfj.2_Missense_Mutation_p.R795H|PRKD2_uc010xye.1_Missense_Mutation_p.R805H|PRKD2_uc002pfk.2_Missense_Mutation_p.R638H	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A	795	Protein kinase.				cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)														---	---	---	---
STRN4	29888	broad.mit.edu	37	19	47231155	47231155	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47231155A>G	uc002pfl.2	-	8	1182	c.1149T>C	c.(1147-1149)CAT>CAC	p.H383H	STRN4_uc002pfm.2_Silent_p.H383H|STRN4_uc010xyf.1_RNA|STRN4_uc010xyg.1_RNA	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1	383						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)														---	---	---	---
STRN4	29888	broad.mit.edu	37	19	47242087	47242087	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47242087A>G	uc002pfl.2	-	2	374	c.341T>C	c.(340-342)CTG>CCG	p.L114P	STRN4_uc002pfm.2_Missense_Mutation_p.L114P|STRN4_uc010xyf.1_RNA|STRN4_uc010xyg.1_RNA	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1	114	Potential.					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)														---	---	---	---
CYTH2	9266	broad.mit.edu	37	19	48977543	48977543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48977543C>T	uc002pjj.3	+	7	952	c.652C>T	c.(652-654)CGG>TGG	p.R218W	CYTH2_uc002pji.2_RNA	NM_017457	NP_059431	Q99418	CYH2_HUMAN	cytohesin 2 isoform 1	218					actin cytoskeleton organization|endocytosis|regulation of ARF protein signal transduction|regulation of cell adhesion	cytoplasm|membrane fraction|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1																		---	---	---	---
NUCB1	4924	broad.mit.edu	37	19	49409126	49409126	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49409126C>T	uc002plb.3	+	4	432	c.360C>T	c.(358-360)GAC>GAT	p.D120D	NUCB1_uc002pla.2_Silent_p.D120D|NUCB1_uc002plc.2_Silent_p.D120D	NM_006184	NP_006175	Q02818	NUCB1_HUMAN	nucleobindin 1 precursor	120						ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)														---	---	---	---
RPS11	6205	broad.mit.edu	37	19	50001234	50001234	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50001234A>G	uc002pob.1	+	4	364	c.284A>G	c.(283-285)TAC>TGC	p.Y95C		NM_001015	NP_001006	P62280	RS11_HUMAN	ribosomal protein S11	95					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|rRNA binding|structural constituent of ribosome				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00206)|GBM - Glioblastoma multiforme(486;0.0245)														---	---	---	---
TSKS	60385	broad.mit.edu	37	19	50266380	50266380	+	Missense_Mutation	SNP	C	T	T	rs146466500		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50266380C>T	uc002ppm.2	-	1	136	c.125G>A	c.(124-126)CGG>CAG	p.R42Q		NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate	42							protein binding			large_intestine(1)|skin(1)	2		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;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)														---	---	---	---
SIGLEC11	114132	broad.mit.edu	37	19	50455204	50455204	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50455204G>A	uc010ybh.1	-	10	1865	c.1774C>T	c.(1774-1776)CGC>TGC	p.R592C	SIGLEC11_uc010ybi.1_Missense_Mutation_p.R496C	NM_052884	NP_443116	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11 isoform 1	592	Cytoplasmic (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|central_nervous_system(2)|pancreas(1)	6		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)														---	---	---	---
C19orf41	126123	broad.mit.edu	37	19	50666247	50666247	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50666247C>T	uc002prp.1	-	1	292	c.205G>A	c.(205-207)GCG>ACG	p.A69T		NM_152358	NP_689571	Q6UXV1	IZUM2_HUMAN	hypothetical protein LOC126123 precursor	69	Extracellular (Potential).					integral to membrane					0		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00364)|OV - Ovarian serous cystadenocarcinoma(262;0.0052)														---	---	---	---
KLK11	11012	broad.mit.edu	37	19	51525925	51525925	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51525925T>C	uc002pvd.1	-	6	837	c.725A>G	c.(724-726)AAC>AGC	p.N242S	KLK10_uc002puy.2_5'Flank|KLK10_uc002puz.2_5'Flank|KLK10_uc002pva.2_5'Flank|KLK11_uc002pvb.1_Missense_Mutation_p.N235S|KLK11_uc002pve.1_Missense_Mutation_p.N99S|KLK11_uc002pvf.1_Missense_Mutation_p.N210S|KLK11_uc002pvc.3_Missense_Mutation_p.N210S	NM_144947	NP_659196	Q9UBX7	KLK11_HUMAN	kallikrein 11 isoform 2 precursor	242	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)														---	---	---	---
ETFB	2109	broad.mit.edu	37	19	51848577	51848577	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51848577G>A	uc002pwh.2	-	6	748	c.656C>T	c.(655-657)ACC>ATC	p.T219I	ETFB_uc002pwg.2_Missense_Mutation_p.T310I	NM_001985	NP_001976	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	219					respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)														---	---	---	---
SIGLEC10	89790	broad.mit.edu	37	19	51919552	51919552	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51919552G>A	uc002pwo.2	-						SIGLEC10_uc002pwp.2_Intron|SIGLEC10_uc002pwq.2_Intron|SIGLEC10_uc002pwr.2_Intron|SIGLEC10_uc010ycy.1_Intron|SIGLEC10_uc010ycz.1_Intron|SIGLEC10_uc010eow.2_Silent_p.A20A|SIGLEC10_uc002pws.1_Intron	NM_033130	NP_149121			sialic acid binding Ig-like lectin 10 precursor						cell adhesion	extracellular region|integral to membrane|plasma membrane	sugar binding			skin(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)														---	---	---	---
ZNF480	147657	broad.mit.edu	37	19	52825530	52825530	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52825530T>C	uc010ydl.1	+	5	1097	c.1027T>C	c.(1027-1029)TAC>CAC	p.Y343H	ZNF480_uc002pyv.2_Missense_Mutation_p.Y266H|ZNF480_uc010ydm.1_Missense_Mutation_p.Y300H|ZNF480_uc010epn.2_Missense_Mutation_p.Y174H|uc002pyw.1_Intron	NM_144684	NP_653285	Q8WV37	ZN480_HUMAN	zinc finger protein 480	343	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)														---	---	---	---
ZNF468	90333	broad.mit.edu	37	19	53344411	53344411	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53344411C>A	uc002qaf.2	-	4	1287	c.1136G>T	c.(1135-1137)GGA>GTA	p.G379V	ZNF468_uc002qae.2_Missense_Mutation_p.G326V	NM_001008801	NP_001008801	Q5VIY5	ZN468_HUMAN	zinc finger protein ZNF468 isoform 2	379					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0358)														---	---	---	---
ZNF347	84671	broad.mit.edu	37	19	53644898	53644898	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53644898G>T	uc002qbb.1	-	5	1252	c.1183C>A	c.(1183-1185)CAC>AAC	p.H395N	ZNF347_uc010eql.1_Missense_Mutation_p.H396N|ZNF347_uc002qbc.1_Missense_Mutation_p.H396N	NM_032584	NP_115973	Q96SE7	ZN347_HUMAN	zinc finger protein 347	395	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0179)														---	---	---	---
ZNF677	342926	broad.mit.edu	37	19	53740463	53740463	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53740463T>A	uc002qbf.1	-	5	1702	c.1517A>T	c.(1516-1518)AAG>ATG	p.K506M	ZNF677_uc002qbg.1_Missense_Mutation_p.K506M	NM_182609	NP_872415	Q86XU0	ZN677_HUMAN	zinc finger protein 677	506	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00352)														---	---	---	---
ZNF761	388561	broad.mit.edu	37	19	53958901	53958901	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53958901A>G	uc010eqp.2	+	7	1598	c.1140A>G	c.(1138-1140)AAA>AAG	p.K380K	ZNF761_uc010ydy.1_Silent_p.K326K|ZNF761_uc002qbt.1_Silent_p.K326K	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761	380					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)														---	---	---	---
ZNF813	126017	broad.mit.edu	37	19	53994944	53994944	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53994944G>A	uc002qbu.2	+	4	1586	c.1458G>A	c.(1456-1458)ACG>ACA	p.T486T	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	486	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)														---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54297342	54297342	+	Silent	SNP	C	T	T	rs148506660		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54297342C>T	uc002qch.3	-	10	3367	c.3147G>A	c.(3145-3147)GCG>GCA	p.A1049A	NLRP12_uc010eqw.2_Silent_p.A275A|NLRP12_uc002qci.3_Silent_p.A992A|NLRP12_uc002qcj.3_Silent_p.A1050A|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_3'UTR	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	1049	LRR 8.				negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
PRKCG	5582	broad.mit.edu	37	19	54406340	54406340	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54406340A>G	uc002qcq.1	+	15	1871	c.1589A>G	c.(1588-1590)CAG>CGG	p.Q530R	PRKCG_uc010yeg.1_Missense_Mutation_p.Q530R|PRKCG_uc010yeh.1_Missense_Mutation_p.Q417R	NM_002739	NP_002730	P05129	KPCG_HUMAN	protein kinase C, gamma	530	Protein kinase.				activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)														---	---	---	---
CACNG7	59284	broad.mit.edu	37	19	54416138	54416138	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54416138C>T	uc002qcr.1	+	1	68	c.53C>T	c.(52-54)GCG>GTG	p.A18V	CACNG7_uc010era.1_Missense_Mutation_p.A18V	NM_031896	NP_114102	P62955	CCG7_HUMAN	voltage-dependent calcium channel gamma-7	18	Helical; (Potential).				regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(1)	1	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)														---	---	---	---
PRPF31	26121	broad.mit.edu	37	19	54626916	54626916	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54626916C>T	uc002qdh.2	+	6	900	c.504C>T	c.(502-504)AGC>AGT	p.S168S	PRPF31_uc010yek.1_Silent_p.S168S	NM_015629	NP_056444	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31 homolog	168					assembly of spliceosomal tri-snRNP	Cajal body|MLL1 complex|nuclear speck|U4 snRNP|U4/U6 x U5 tri-snRNP complex|U4atac snRNP	RNA binding|snRNP binding			ovary(1)	1	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)																	---	---	---	---
CNOT3	4849	broad.mit.edu	37	19	54647433	54647433	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54647433A>G	uc002qdj.1	+	5	517	c.206A>G	c.(205-207)AAC>AGC	p.N69S	CNOT3_uc010yel.1_Missense_Mutation_p.N69S|CNOT3_uc002qdi.2_5'UTR|CNOT3_uc002qdk.1_Missense_Mutation_p.N69S|CNOT3_uc010ere.1_RNA	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	69					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)																	---	---	---	---
CNOT3	4849	broad.mit.edu	37	19	54649502	54649502	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54649502G>A	uc002qdj.1	+	8	963	c.652G>A	c.(652-654)GAC>AAC	p.D218N	CNOT3_uc010yel.1_Missense_Mutation_p.D218N|CNOT3_uc002qdi.2_Missense_Mutation_p.D131N|CNOT3_uc002qdk.1_Missense_Mutation_p.D218N|CNOT3_uc010ere.1_RNA	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	218					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)																	---	---	---	---
LAIR1	3903	broad.mit.edu	37	19	54875890	54875890	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54875890G>T	uc002qfk.1	-						LAIR1_uc002qfl.1_Intron|LAIR1_uc002qfm.1_Intron|LAIR1_uc002qfn.1_Intron|LAIR1_uc010yex.1_Intron|LAIR1_uc002qfo.2_Intron	NM_002287	NP_002278			leukocyte-associated immunoglobulin-like							integral to membrane|plasma membrane	protein binding|receptor activity			ovary(4)	4	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)														---	---	---	---
LENG8	114823	broad.mit.edu	37	19	54967522	54967522	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54967522C>T	uc002qfv.1	+	9	1356	c.1212C>T	c.(1210-1212)TCC>TCT	p.S404S	LENG8_uc002qfw.2_Silent_p.S441S			Q96PV6	LENG8_HUMAN	RecName: Full=Leukocyte receptor cluster member 8;	404	Ser-rich.						protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)														---	---	---	---
KIR2DL3	3804	broad.mit.edu	37	19	55263953	55263953	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55263953T>C	uc002qgv.2	+	8	1026	c.1008T>C	c.(1006-1008)CTT>CTC	p.L336L	KIR2DS4_uc010yfj.1_5'Flank|KIR2DL3_uc002qgx.2_Silent_p.L336L|KIR2DL3_uc002qgy.2_Silent_p.L238L|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR3DP1_uc010yfi.1_5'Flank	NM_015868	NP_056952	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two	336	Cytoplasmic (Potential).				immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
SYT5	6861	broad.mit.edu	37	19	55687082	55687082	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55687082A>G	uc002qjm.1	-	4	1595	c.535T>C	c.(535-537)TTC>CTC	p.F179L	SYT5_uc002qjp.2_Missense_Mutation_p.F176L|SYT5_uc002qjn.1_Missense_Mutation_p.F179L|SYT5_uc002qjo.1_Missense_Mutation_p.F179L	NM_003180	NP_003171	O00445	SYT5_HUMAN	synaptotagmin V	179	Cytoplasmic (Potential).|C2 1.				energy reserve metabolic process|regulation of insulin secretion|synaptic transmission	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane	metal ion binding|transporter activity				0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)														---	---	---	---
TMEM150B	284417	broad.mit.edu	37	19	55828178	55828178	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55828178C>T	uc010esw.1	-	7	654	c.481G>A	c.(481-483)GTC>ATC	p.V161I	TMEM150B_uc010yfu.1_Missense_Mutation_p.V161I|TMEM150B_uc010yfv.1_RNA|TMEM150B_uc010yfw.1_RNA	NM_001085488	NP_001078957	A6NC51	T150B_HUMAN	transmembrane protein 150B precursor	161	Helical; (Potential).					integral to membrane					0																		---	---	---	---
ZNF628	89887	broad.mit.edu	37	19	55994860	55994860	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55994860C>T	uc002qld.2	+	3	2853	c.2288C>T	c.(2287-2289)GCG>GTG	p.A763V	NAT14_uc002qle.1_5'Flank	NM_033113	NP_149104	Q5EBL2	ZN628_HUMAN	zinc finger protein 628	763	Gly-rich.					nucleus	DNA binding|zinc ion binding				0	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)														---	---	---	---
NLRP11	204801	broad.mit.edu	37	19	56321607	56321607	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56321607G>A	uc010ygf.1	-	5	1080	c.369C>T	c.(367-369)GAC>GAT	p.D123D	NLRP11_uc002qlz.2_Silent_p.D24D|NLRP11_uc002qmb.2_Silent_p.D24D|NLRP11_uc002qmc.2_RNA|NLRP11_uc010ete.1_RNA	NM_145007	NP_659444	P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	123							ATP binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)														---	---	---	---
NLRP4	147945	broad.mit.edu	37	19	56369846	56369846	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56369846C>A	uc002qmd.3	+	3	1509	c.1087C>A	c.(1087-1089)CTG>ATG	p.L363M	NLRP4_uc002qmf.2_Missense_Mutation_p.L288M|NLRP4_uc010etf.2_Missense_Mutation_p.L194M	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	363	NACHT.						ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)														---	---	---	---
NLRP5	126206	broad.mit.edu	37	19	56515446	56515446	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56515446C>T	uc002qmj.2	+	2	427	c.427C>T	c.(427-429)CGG>TGG	p.R143W	NLRP5_uc002qmi.2_Missense_Mutation_p.R143W	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	143	DAPIN.					mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)														---	---	---	---
ZNF471	57573	broad.mit.edu	37	19	57036593	57036593	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57036593T>C	uc002qnh.2	+	5	1290	c.1157T>C	c.(1156-1158)GTT>GCT	p.V386A		NM_020813	NP_065864	Q9BX82	ZN471_HUMAN	zinc finger protein 471	386	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)														---	---	---	---
ZNF71	58491	broad.mit.edu	37	19	57133348	57133348	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57133348G>A	uc002qnm.3	+	3	931	c.693G>A	c.(691-693)CAG>CAA	p.Q231Q		NM_021216	NP_067039	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	231	C2H2-type 4.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)														---	---	---	---
ZNF530	348327	broad.mit.edu	37	19	58117151	58117151	+	Silent	SNP	C	A	A	rs144915290		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58117151C>A	uc002qpk.2	+	3	478	c.258C>A	c.(256-258)TCC>TCA	p.S86S	ZNF547_uc002qpm.3_Intron|ZNF530_uc002qpl.2_RNA	NM_020880	NP_065931	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	86	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
ZNF551	90233	broad.mit.edu	37	19	58198191	58198191	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58198191G>A	uc002qpw.3	+	3	723	c.500G>A	c.(499-501)TGT>TAT	p.C167Y	ZNF551_uc002qpv.3_Missense_Mutation_p.C110Y|ZNF776_uc002qpx.2_Intron	NM_138347	NP_612356	Q7Z340	ZN551_HUMAN	zinc finger protein 551	183					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
ZNF671	79891	broad.mit.edu	37	19	58232420	58232420	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58232420T>C	uc002qpz.3	-	4	1133	c.1034A>G	c.(1033-1035)GAA>GGA	p.E345G	ZNF776_uc002qpx.2_Intron|ZNF671_uc010eug.2_Missense_Mutation_p.E268G|ZNF671_uc010yhf.1_Missense_Mutation_p.E247G	NM_024833	NP_079109	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	345	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)														---	---	---	---
ZNF606	80095	broad.mit.edu	37	19	58511172	58511172	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58511172T>C	uc002qqw.2	-						ZNF606_uc010yhp.1_Intron|ZNF606_uc002qqx.1_3'UTR|uc002qqy.1_5'Flank|uc002qqz.1_5'Flank	NM_025027	NP_079303			zinc finger protein 606						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)														---	---	---	---
ZNF132	7691	broad.mit.edu	37	19	58945384	58945384	+	Missense_Mutation	SNP	C	T	T	rs140714420		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58945384C>T	uc002qst.3	-	3	1828	c.1427G>A	c.(1426-1428)CGA>CAA	p.R476Q		NM_003433	NP_003424	P52740	ZN132_HUMAN	zinc finger protein 132	476	C2H2-type 10.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		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;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)														---	---	---	---
DEFB125	245938	broad.mit.edu	37	20	76676	76676	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:76676A>C	uc002wcw.2	+	2	89	c.89A>C	c.(88-90)AAT>ACT	p.N30T		NM_153325	NP_697020	Q8N687	DB125_HUMAN	defensin, beta 125 preproprotein	30					defense response to bacterium	extracellular region				ovary(1)|central_nervous_system(1)|skin(1)	3		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.156)															---	---	---	---
PDYN	5173	broad.mit.edu	37	20	1961052	1961052	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1961052C>T	uc010gaj.2	-	3	924	c.682G>A	c.(682-684)GGT>AGT	p.G228S	uc002wfu.1_Intron|PDYN_uc002wfv.2_Missense_Mutation_p.G228S|PDYN_uc010zpt.1_Missense_Mutation_p.G73S	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	228					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	3008359	3008359	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3008359C>T	uc010zqd.1	+	19	2142	c.1825C>T	c.(1825-1827)CGG>TGG	p.R609W	PTPRA_uc002whj.2_Missense_Mutation_p.R598W|PTPRA_uc002whk.2_Missense_Mutation_p.R589W|PTPRA_uc002whl.2_Missense_Mutation_p.R589W|PTPRA_uc002whm.2_Missense_Mutation_p.R365W|PTPRA_uc002whn.2_Missense_Mutation_p.R589W|PTPRA_uc002who.2_Missense_Mutation_p.R261W	NM_002836	NP_002827	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	598	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
HSPA12B	116835	broad.mit.edu	37	20	3729932	3729932	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3729932G>T	uc002wjd.2	+	9	1007	c.904G>T	c.(904-906)GGC>TGC	p.G302C	HSPA12B_uc010zqi.1_Missense_Mutation_p.G301C|HSPA12B_uc002wje.2_Missense_Mutation_p.G215C|HSPA12B_uc010zqj.1_Missense_Mutation_p.G136C	NM_052970	NP_443202	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	302							ATP binding				0																		---	---	---	---
CDC25B	994	broad.mit.edu	37	20	3781516	3781516	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3781516C>T	uc002wjn.2	+						CDC25B_uc010zqk.1_Intron|CDC25B_uc010zql.1_Intron|CDC25B_uc010zqm.1_Intron|CDC25B_uc002wjl.2_Intron|CDC25B_uc002wjm.2_Intron|CDC25B_uc002wjo.2_Intron|CDC25B_uc002wjp.2_Intron|CDC25B_uc002wjq.2_Intron|CDC25B_uc010gbc.2_5'Flank	NM_021873	NP_068659			cell division cycle 25B isoform 1						cell division|G2/M transition of mitotic cell cycle|mitosis|positive regulation of cell proliferation	cytosol|microtubule organizing center|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|ovary(2)	5																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8731496	8731496	+	Intron	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8731496C>G	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron|PLCB1_uc002wnd.1_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9319529	9319529	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9319529A>G	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13610646	13610646	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13610646G>T	uc002woi.2	-	2	197	c.80C>A	c.(79-81)GCC>GAC	p.A27D	TASP1_uc010zri.1_RNA|TASP1_uc002woh.2_Missense_Mutation_p.A27D|TASP1_uc010zrj.1_RNA|TASP1_uc010zrk.1_Missense_Mutation_p.A27D	NM_017714	NP_060184	Q9H6P5	TASP1_HUMAN	taspase 1 precursor	27					asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20177224	20177224	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20177224A>G	uc002wru.2	+	16	1677	c.1601A>G	c.(1600-1602)TAC>TGC	p.Y534C	C20orf26_uc010zse.1_Missense_Mutation_p.Y514C	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	534										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
CD93	22918	broad.mit.edu	37	20	23065849	23065849	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23065849C>T	uc002wsv.2	-	1	1129	c.981G>A	c.(979-981)ACG>ACA	p.T327T		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	327	EGF-like 2.|Extracellular (Potential).				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)																	---	---	---	---
CD93	22918	broad.mit.edu	37	20	23066467	23066467	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23066467C>A	uc002wsv.2	-	1	511	c.363G>T	c.(361-363)GAG>GAT	p.E121D		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	121	Extracellular (Potential).|C-type lectin.				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)																	---	---	---	---
CST11	140880	broad.mit.edu	37	20	23433327	23433327	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23433327T>C	uc002wtf.1	-	1	156	c.122A>G	c.(121-123)GAA>GGA	p.E41G	CST11_uc002wtg.1_Missense_Mutation_p.E41G	NM_130794	NP_570612	Q9H112	CST11_HUMAN	cystatin 11 isoform 1 precursor	41					defense response to bacterium	cytoplasm|nucleus	cysteine-type endopeptidase inhibitor activity				0	Colorectal(13;0.0431)|Lung NSC(19;0.235)																	---	---	---	---
ENTPD6	955	broad.mit.edu	37	20	25203547	25203547	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25203547A>G	uc002wuj.2	+	12	1299	c.1119A>G	c.(1117-1119)GAA>GAG	p.E373E	ENTPD6_uc010zsz.1_Silent_p.E155E|ENTPD6_uc002wum.2_Silent_p.E356E|ENTPD6_uc010zta.1_Silent_p.E373E|ENTPD6_uc002wun.2_Silent_p.E339E|ENTPD6_uc002wuk.2_Silent_p.E372E|ENTPD6_uc002wul.2_Silent_p.E372E|ENTPD6_uc010ztb.1_Silent_p.E345E|ENTPD6_uc010ztc.1_Silent_p.E345E|ENTPD6_uc002wuo.2_Silent_p.E125E|ENTPD6_uc010ztd.1_Silent_p.E121E|ENTPD6_uc010gdk.1_RNA|ENTPD6_uc010gdl.1_RNA	NM_001247	NP_001238	O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6	373	Lumenal (Potential).					Golgi membrane|integral to membrane	nucleoside-diphosphatase activity				0																		---	---	---	---
POFUT1	23509	broad.mit.edu	37	20	30818680	30818680	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30818680C>T	uc002wxp.2	+	6	843	c.794C>T	c.(793-795)CCG>CTG	p.P265L	POFUT1_uc010ztt.1_Missense_Mutation_p.P157L|POFUT1_uc010ztu.1_Missense_Mutation_p.P54L	NM_015352	NP_056167	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1 isoform 1	265					fucose metabolic process|Notch signaling pathway|O-glycan processing|regulation of transcription, DNA-dependent	endoplasmic reticulum|membrane	peptide-O-fucosyltransferase activity			breast(1)	1			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
C20orf185	359710	broad.mit.edu	37	20	31649647	31649647	+	Intron	SNP	C	T	T	rs75603797	byFrequency;by1000genomes	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31649647C>T	uc002wym.1	+							NM_182658	NP_872599			antimicrobial peptide RYA3 precursor						innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4																		---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32232389	32232389	+	Silent	SNP	G	A	A	rs148637844		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32232389G>A	uc002wzg.1	+	12	2289	c.1752G>A	c.(1750-1752)TCG>TCA	p.S584S	CBFA2T2_uc010zug.1_Silent_p.S358S|CBFA2T2_uc002wze.1_Silent_p.S575S|CBFA2T2_uc002wzf.1_RNA|CBFA2T2_uc002wzh.1_Silent_p.S555S|CBFA2T2_uc002wzi.1_RNA|CBFA2T2_uc002wzj.1_RNA|CBFA2T2_uc002wzk.1_Silent_p.S132S	NM_005093	NP_005084	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit	584						nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
EIF2S2	8894	broad.mit.edu	37	20	32684518	32684518	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32684518C>T	uc002xaf.2	-	6	797	c.628G>A	c.(628-630)GTC>ATC	p.V210I	EIF2S2_uc002xag.2_Missense_Mutation_p.V207I|EIF2S2_uc010ges.2_Missense_Mutation_p.V150I	NM_003908	NP_003899	P20042	IF2B_HUMAN	eukaryotic translation initiation factor 2 beta	210						cytosol|eukaryotic translation initiation factor 2 complex	metal ion binding|protein binding|translation initiation factor activity			large_intestine(1)	1																		---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34092703	34092703	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34092703G>A	uc002xcm.2	+	31	7177	c.6506G>A	c.(6505-6507)TGG>TAG	p.W2169*	CEP250_uc010zve.1_Nonsense_Mutation_p.W1537*	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	2169	Gln/Glu-rich.|Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36488350	36488350	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36488350T>A	uc010zvw.1	+	15	1533	c.1442T>A	c.(1441-1443)TTC>TAC	p.F481Y	CTNNBL1_uc002xhh.2_Missense_Mutation_p.F294Y|CTNNBL1_uc002xhi.2_RNA|CTNNBL1_uc002xhj.2_Missense_Mutation_p.F229Y	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1	481					apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PLCG1	5335	broad.mit.edu	37	20	39788762	39788762	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39788762T>C	uc002xjp.1	+	4	602	c.481T>C	c.(481-483)TTT>CTT	p.F161L	PLCG1_uc002xjo.1_Missense_Mutation_p.F161L	NM_182811	NP_877963	P19174	PLCG1_HUMAN	phospholipase C, gamma 1 isoform b	161	EF-hand.				activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PLCG1	5335	broad.mit.edu	37	20	39800838	39800838	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39800838T>C	uc002xjp.1	+	25	2935	c.2814T>C	c.(2812-2814)ACT>ACC	p.T938T	PLCG1_uc002xjo.1_Silent_p.T938T|PLCG1_uc010zwe.1_Silent_p.T564T	NM_182811	NP_877963	P19174	PLCG1_HUMAN	phospholipase C, gamma 1 isoform b	938					activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40049262	40049262	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40049262C>G	uc002xka.1	-	31	6191	c.6013G>C	c.(6013-6015)GAG>CAG	p.E2005Q		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2005					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40102043	40102043	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40102043C>T	uc002xka.1	-	17	2761	c.2583G>A	c.(2581-2583)GCG>GCA	p.A861A	CHD6_uc002xkd.2_Silent_p.A839A	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	861	Helicase C-terminal.				chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
R3HDML	140902	broad.mit.edu	37	20	42979427	42979427	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42979427T>C	uc002xls.1	+	5	929	c.757T>C	c.(757-759)TTC>CTC	p.F253L		NM_178491	NP_848586	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like precursor	253						extracellular region	peptidase inhibitor activity				0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
NCOA5	57727	broad.mit.edu	37	20	44695753	44695753	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44695753T>C	uc002xrd.2	-	4	1098	c.570A>G	c.(568-570)AGA>AGG	p.R190R	NCOA5_uc002xrc.2_Silent_p.R78R|NCOA5_uc002xre.2_Silent_p.R190R	NM_020967	NP_066018	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	190					regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding			central_nervous_system(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45875225	45875225	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45875225A>G	uc002xta.1	-	14	2005	c.1751T>C	c.(1750-1752)GTA>GCA	p.V584A	ZMYND8_uc010ghq.1_Missense_Mutation_p.V261A|ZMYND8_uc010ghr.1_Missense_Mutation_p.V559A|ZMYND8_uc002xst.1_Missense_Mutation_p.V512A|ZMYND8_uc002xsu.1_Missense_Mutation_p.V584A|ZMYND8_uc002xsv.1_Missense_Mutation_p.V512A|ZMYND8_uc002xsw.1_Missense_Mutation_p.V336A|ZMYND8_uc002xsx.1_Missense_Mutation_p.V336A|ZMYND8_uc002xsy.1_Missense_Mutation_p.V559A|ZMYND8_uc002xsz.1_Missense_Mutation_p.V521A|ZMYND8_uc010zxy.1_Missense_Mutation_p.V611A|ZMYND8_uc002xtb.1_Missense_Mutation_p.V604A|ZMYND8_uc002xss.2_Missense_Mutation_p.V584A|ZMYND8_uc010zxz.1_Missense_Mutation_p.V579A|ZMYND8_uc002xtc.1_Missense_Mutation_p.V604A|ZMYND8_uc002xtd.1_Missense_Mutation_p.V579A|ZMYND8_uc002xte.1_Missense_Mutation_p.V584A|ZMYND8_uc010zya.1_Missense_Mutation_p.V584A|ZMYND8_uc002xtf.1_Missense_Mutation_p.V604A|ZMYND8_uc002xtg.2_Missense_Mutation_p.V578A|ZMYND8_uc010ghs.1_Missense_Mutation_p.V578A	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b	584							protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)															---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46313165	46313165	+	Intron	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46313165G>A	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron	NM_018837	NP_061325			sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
STAU1	6780	broad.mit.edu	37	20	47734382	47734382	+	Missense_Mutation	SNP	C	T	T	rs146630196		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47734382C>T	uc002xud.2	-	11	1852	c.1441G>A	c.(1441-1443)GTA>ATA	p.V481I	STAU1_uc002xua.2_Missense_Mutation_p.V400I|STAU1_uc002xub.2_Missense_Mutation_p.V406I|STAU1_uc002xuc.2_Missense_Mutation_p.V400I|STAU1_uc002xue.2_Missense_Mutation_p.V400I|STAU1_uc002xuf.2_Missense_Mutation_p.V406I|STAU1_uc002xug.2_Missense_Mutation_p.V481I	NM_017453	NP_059347	O95793	STAU1_HUMAN	staufen isoform b	481						microtubule associated complex|rough endoplasmic reticulum|stress granule	double-stranded RNA binding			ovary(4)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)															---	---	---	---
B4GALT5	9334	broad.mit.edu	37	20	48256306	48256306	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48256306T>G	uc002xuu.3	-	7	1020	c.826A>C	c.(826-828)AGT>CGT	p.S276R		NM_004776	NP_004767	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	276	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)															---	---	---	---
TMEM189-UBE2V1	387522	broad.mit.edu	37	20	48747389	48747389	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48747389T>G	uc002xvf.2	-						TMEM189_uc010zyq.1_Intron|TMEM189_uc002xvg.2_Intron|TMEM189_uc010gif.2_Intron|TMEM189_uc010zyp.1_Intron	NM_199203	NP_954673			TMEM189-UBE2V1 readthrough transcript						cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein K63-linked ubiquitination|regulation of DNA repair|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-UEV1A complex|ubiquitin ligase complex	acid-amino acid ligase activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(9;8.29e-07)															---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50255941	50255941	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50255941T>C	uc002xwg.1	-	15	1609	c.1609A>G	c.(1609-1611)ACC>GCC	p.T537A	ATP9A_uc010gih.1_Missense_Mutation_p.T401A|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	537	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																OREG0026043	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51870150	51870150	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51870150C>T	uc002xwo.2	+	2	1109	c.153C>T	c.(151-153)GAC>GAT	p.D51D		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	51					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)															---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52193331	52193331	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52193331T>C	uc002xwq.3	-	3	2243	c.1972A>G	c.(1972-1974)AAC>GAC	p.N658D	ZNF217_uc010gij.1_Missense_Mutation_p.N650D	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	658					negative regulation of transcription, DNA-dependent	histone deacetylase complex	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1)	6	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)															---	---	---	---
ZNF217	7764	broad.mit.edu	37	20	52198795	52198795	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52198795C>A	uc002xwq.3	-	1	842	c.571G>T	c.(571-573)GGC>TGC	p.G191C	ZNF217_uc010gij.1_Missense_Mutation_p.G183C	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	191					negative regulation of transcription, DNA-dependent	histone deacetylase complex	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1)	6	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)															---	---	---	---
BCAS1	8537	broad.mit.edu	37	20	52645335	52645335	+	Missense_Mutation	SNP	T	C	C	rs143563841		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52645335T>C	uc002xws.2	-	4	657	c.319A>G	c.(319-321)ACC>GCC	p.T107A	BCAS1_uc010zzb.1_Missense_Mutation_p.T10A|BCAS1_uc010gim.2_Missense_Mutation_p.T10A|BCAS1_uc002xwt.2_Missense_Mutation_p.T107A|BCAS1_uc010gil.1_Missense_Mutation_p.T107A|BCAS1_uc010zzc.1_Missense_Mutation_p.T10A	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	107						cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)															---	---	---	---
ZBP1	81030	broad.mit.edu	37	20	56188310	56188310	+	Silent	SNP	T	C	C	rs141358064		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56188310T>C	uc002xyo.2	-	5	860	c.579A>G	c.(577-579)GGA>GGG	p.G193G	ZBP1_uc010gjm.2_Silent_p.G192G|ZBP1_uc002xyp.2_Silent_p.G118G|ZBP1_uc010zzn.1_Silent_p.G193G	NM_030776	NP_110403	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1 isoform a	193						cytoplasm|nucleus	double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding			ovary(2)	2	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)															---	---	---	---
ZNF831	128611	broad.mit.edu	37	20	57766920	57766920	+	Silent	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57766920T>A	uc002yan.2	+	1	846	c.846T>A	c.(844-846)TCT>TCA	p.S282S		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	282						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)																	---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58349364	58349364	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58349364C>T	uc002yau.2	+	7	1460	c.993C>T	c.(991-993)TCC>TCT	p.S331S	PHACTR3_uc002yat.2_Silent_p.S328S|PHACTR3_uc010zzw.1_Silent_p.S290S|PHACTR3_uc002yav.2_Silent_p.S290S|PHACTR3_uc002yaw.2_Silent_p.S290S|PHACTR3_uc002yax.2_Silent_p.S220S	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	331						nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
CABLES2	81928	broad.mit.edu	37	20	60971390	60971390	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60971390A>G	uc002ycv.2	-	3	515	c.508T>C	c.(508-510)TAC>CAC	p.Y170H		NM_031215	NP_112492	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	170					cell cycle|cell division|regulation of cell cycle|regulation of cell division		cyclin-dependent protein kinase regulator activity			pancreas(1)	1	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)															---	---	---	---
SLCO4A1	28231	broad.mit.edu	37	20	61297757	61297757	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61297757T>C	uc002ydb.1	+	7	1507	c.1302T>C	c.(1300-1302)GGT>GGC	p.G434G	SLCO4A1_uc002ydc.1_RNA|LOC100127888_uc002ydd.2_RNA|SLCO4A1_uc002yde.1_5'Flank	NM_016354	NP_057438	Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family	434	Helical; Name=8; (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)															---	---	---	---
TCFL5	10732	broad.mit.edu	37	20	61488984	61488984	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61488984G>A	uc002ydp.2	-	4	1094	c.1001C>T	c.(1000-1002)GCG>GTG	p.A334V	TCFL5_uc002ydo.2_Missense_Mutation_p.A107V|TCFL5_uc002ydq.2_Missense_Mutation_p.A333V	NM_006602	NP_006593	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 protein	334					cell differentiation|multicellular organismal development|regulation of cell differentiation|regulation of cell proliferation|spermatogenesis|transcription from RNA polymerase II promoter		DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)	1	Breast(26;5.68e-08)																	---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62070977	62070977	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62070977C>T	uc002yey.1	-	6	1078	c.901G>A	c.(901-903)GGT>AGT	p.G301S	KCNQ2_uc002yez.1_Missense_Mutation_p.G301S|KCNQ2_uc002yfa.1_Missense_Mutation_p.G301S|KCNQ2_uc002yfb.1_Missense_Mutation_p.G301S|KCNQ2_uc011aax.1_Missense_Mutation_p.G301S|KCNQ2_uc002yfc.1_Missense_Mutation_p.G301S	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein	301	Helical; Name=Segment S6; (Potential).				axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)													---	---	---	---
PRIC285	85441	broad.mit.edu	37	20	62196230	62196230	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62196230G>T	uc002yfm.2	-	9	4837	c.3945C>A	c.(3943-3945)ACC>ACA	p.T1315T	PRIC285_uc002yfl.1_Silent_p.T746T	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	1315					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)															---	---	---	---
ARFRP1	10139	broad.mit.edu	37	20	62333552	62333552	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62333552G>A	uc002yga.2	-	4	849	c.282C>T	c.(280-282)CAC>CAT	p.H94H	ARFRP1_uc002ygc.2_Silent_p.H94H|ARFRP1_uc002ygh.3_Silent_p.H94H|ARFRP1_uc011abf.1_Silent_p.H94H|ARFRP1_uc011abg.1_Silent_p.H94H|ARFRP1_uc002yge.2_RNA|ARFRP1_uc002ygd.2_RNA|ARFRP1_uc002ygf.2_Silent_p.H94H|ARFRP1_uc002ygg.2_RNA|ARFRP1_uc011abh.1_RNA	NM_003224	NP_003215	Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	94					small GTPase mediated signal transduction	Golgi apparatus|membrane fraction	GTP binding|GTPase activity			breast(1)|skin(1)	2	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)															---	---	---	---
C21orf34	388815	broad.mit.edu	37	21	17566875	17566875	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17566875A>G	uc002ykb.2	+						C21orf34_uc010glc.2_Intron|C21orf34_uc002ykc.2_RNA	NR_027790				Homo sapiens C21ORF34 (C21orf34) mRNA, partial cds, alternatively spliced.												0		Breast(209;0.152)		Epithelial(23;8.3e-05)|all cancers(11;0.000383)|Colorectal(24;0.00387)|COAD - Colon adenocarcinoma(22;0.0113)|OV - Ovarian serous cystadenocarcinoma(11;0.0127)|LUSC - Lung squamous cell carcinoma(23;0.153)														---	---	---	---
APP	351	broad.mit.edu	37	21	27425630	27425630	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27425630A>C	uc002ylz.2	-	4	590	c.390T>G	c.(388-390)CCT>CCG	p.P130P	APP_uc010glk.2_Silent_p.P125P|APP_uc002yma.2_Silent_p.P130P|APP_uc011ach.1_Silent_p.P74P|APP_uc002ymb.2_Silent_p.P130P|APP_uc010glj.2_Silent_p.P74P|APP_uc011aci.1_Silent_p.P95P|APP_uc011acj.1_Silent_p.P130P	NM_000484	NP_000475	P05067	A4_HUMAN	amyloid beta A4 protein isoform a precursor	130	Extracellular (Potential).				adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)																---	---	---	---
CYYR1	116159	broad.mit.edu	37	21	27938629	27938629	+	Silent	SNP	C	T	T	rs146759335	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27938629C>T	uc002ymd.2	-	2	454	c.132G>A	c.(130-132)ACG>ACA	p.T44T	CYYR1_uc011ack.1_RNA|CYYR1_uc002yme.2_Silent_p.T44T	NM_052954	NP_443186	Q96J86	CYYR1_HUMAN	cysteine and tyrosine-rich 1 protein precursor	44	Extracellular (Potential).					integral to membrane					0																		---	---	---	---
ADAMTS5	11096	broad.mit.edu	37	21	28296636	28296636	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28296636T>A	uc002ymg.2	-	8	3258	c.2529A>T	c.(2527-2529)TTA>TTT	p.L843F		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	843	Spacer.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31023434	31023434	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31023434T>G	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821			glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)													---	---	---	---
KRTAP19-6	337973	broad.mit.edu	37	21	31913970	31913970	+	3'UTR	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31913970A>G	uc002yok.1	-	1						NM_181612	NP_853643			keratin associated protein 19-6							intermediate filament					0																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32639181	32639181	+	Silent	SNP	C	T	T	rs144300474		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32639181C>T	uc002yow.1	-	5	580	c.108G>A	c.(106-108)ACG>ACA	p.T36T	TIAM1_uc011adk.1_Silent_p.T36T|TIAM1_uc011adl.1_Silent_p.T36T|TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	36					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34113929	34113929	+	Intron	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34113929A>G	uc002yqn.2	-						uc002yqk.2_Intron|GCFC1_uc002yql.2_Intron|GCFC1_uc002yqm.2_Intron|GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Missense_Mutation_p.I780T	NM_016631	NP_057715			GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
SON	6651	broad.mit.edu	37	21	34924556	34924556	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34924556C>T	uc002yse.1	+	3	3068	c.3019C>T	c.(3019-3021)CGT>TGT	p.R1007C	SON_uc002ysb.1_Missense_Mutation_p.R1007C|SON_uc002ysc.2_Missense_Mutation_p.R1007C|SON_uc002ysd.2_Translation_Start_Site|SON_uc002ysf.1_Intron|SON_uc002ysg.2_Translation_Start_Site	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	1007	1-1.|14 X 6 AA repeats of [ED]-R-S-M-M-S.				anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6																		---	---	---	---
DSCR6	53820	broad.mit.edu	37	21	38380463	38380463	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38380463G>A	uc002yvv.2	+	2	321	c.111G>A	c.(109-111)GCG>GCA	p.A37A	DSCR6_uc011aec.1_5'UTR|DSCR6_uc010gnd.2_5'UTR	NM_018962	NP_061835	P57055	DSCR6_HUMAN	Down syndrome critical region protein 6	37						nucleus				breast(1)	1		Myeloproliferative disorder(46;0.0632)																---	---	---	---
ZNF295	49854	broad.mit.edu	37	21	43412127	43412127	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43412127G>A	uc002zab.3	-	3	2292	c.2078C>T	c.(2077-2079)CCA>CTA	p.P693L	ZNF295_uc002yzz.3_Intron|ZNF295_uc002yzy.3_Missense_Mutation_p.P693L|ZNF295_uc002zaa.3_Missense_Mutation_p.P693L	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	693					negative regulation of transcription, DNA-dependent|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|nucleus	methyl-CpG binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
RSPH1	89765	broad.mit.edu	37	21	43902742	43902742	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43902742C>T	uc002zbg.2	-							NM_080860	NP_543136			testis-specific gene A2						meiosis	cytosol|nucleus				ovary(1)	1																		---	---	---	---
RRP1B	23076	broad.mit.edu	37	21	45107681	45107681	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45107681C>T	uc002zdk.2	+	13	1540	c.1426C>T	c.(1426-1428)CGG>TGG	p.R476W	RRP1B_uc002zdl.2_Missense_Mutation_p.R9W	NM_015056	NP_055871	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1 homolog B	476					rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.178)														---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46907379	46907379	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46907379G>A	uc011afs.1	+	16	3118	c.3097G>A	c.(3097-3099)GGG>AGG	p.G1033R	COL18A1_uc002zhg.2_Missense_Mutation_p.G618R|COL18A1_uc002zhi.2_Missense_Mutation_p.G798R	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	1033	Nonhelical region 4 (NC4).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
COL6A1	1291	broad.mit.edu	37	21	47422515	47422515	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47422515A>G	uc002zhu.1	+	33	2427	c.2325A>G	c.(2323-2325)CAA>CAG	p.Q775Q	COL6A1_uc010gqd.1_Silent_p.Q106Q|COL6A1_uc002zhv.1_Silent_p.Q106Q|COL6A1_uc002zhw.1_5'UTR	NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor	775	VWFA 2.|C-terminal globular domain.				axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)													---	---	---	---
COL6A2	1292	broad.mit.edu	37	21	47545909	47545909	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47545909C>T	uc002zia.1	+	26	2262	c.2180C>T	c.(2179-2181)GCG>GTG	p.A727V	COL6A2_uc002zhy.1_Missense_Mutation_p.A727V|COL6A2_uc002zhz.1_Missense_Mutation_p.A727V|COL6A2_uc002zib.1_Missense_Mutation_p.A133V|COL6A2_uc002zic.1_5'Flank	NM_001849	NP_001840	P12110	CO6A2_HUMAN	alpha 2 type VI collagen isoform 2C2 precursor	727	VWFA 2.|Nonhelical region.				axon guidance|cell-cell adhesion|extracellular matrix organization|protein heterotrimerization	collagen|extracellular space|protein complex	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(7)|ovary(1)	8	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
LSS	4047	broad.mit.edu	37	21	47633708	47633708	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47633708G>A	uc002zij.2	-	10	1132	c.1053C>T	c.(1051-1053)GAC>GAT	p.D351D	LSS_uc011afv.1_Silent_p.D340D|LSS_uc002zil.2_Silent_p.D351D|LSS_uc002zik.2_Silent_p.D271D	NM_001001438	NP_001001438	P48449	ERG7_HUMAN	lanosterol synthase isoform 1	351					cholesterol biosynthetic process	endoplasmic reticulum membrane	lanosterol synthase activity				0	Breast(49;0.214)																	---	---	---	---
DIP2A	23181	broad.mit.edu	37	21	47986480	47986480	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47986480C>T	uc002zjo.2	+	37	4530	c.4347C>T	c.(4345-4347)CAC>CAT	p.H1449H	DIP2A_uc011afz.1_Silent_p.H1445H|DIP2A_uc002zjs.2_Silent_p.H129H|DIP2A_uc002zjt.2_RNA	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	1449					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)														---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19241652	19241652	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19241652T>C	uc002zpb.2	-	3	424	c.349A>G	c.(349-351)AAC>GAC	p.N117D	CLTCL1_uc011agv.1_Missense_Mutation_p.N117D|CLTCL1_uc011agw.1_Missense_Mutation_p.N117D	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1	117	Globular terminal domain.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
TXNRD2	10587	broad.mit.edu	37	22	19905729	19905729	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19905729G>A	uc011ahc.1	-	5	419	c.386C>T	c.(385-387)GCA>GTA	p.A129V	TXNRD2_uc002zql.1_5'UTR|TXNRD2_uc002zqm.1_RNA|TXNRD2_uc002zqn.1_RNA|TXNRD2_uc002zqo.1_RNA|TXNRD2_uc002zqp.1_RNA|TXNRD2_uc002zqr.1_Missense_Mutation_p.A128V|TXNRD2_uc010grv.1_Missense_Mutation_p.A129V|TXNRD2_uc002zqj.1_RNA|TXNRD2_uc002zqs.2_Missense_Mutation_p.A97V	NM_006440	NP_006431	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2 precursor	129					cell redox homeostasis|response to oxygen radical	mitochondrion	flavin adenine dinucleotide binding|NADP binding|thioredoxin-disulfide reductase activity			ovary(2)	2	Colorectal(54;0.0993)																	---	---	---	---
RTN4R	65078	broad.mit.edu	37	22	20230039	20230039	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20230039C>T	uc002zrv.2	-	2	818	c.617G>A	c.(616-618)CGT>CAT	p.R206H	RTN4R_uc002zru.2_5'UTR	NM_023004	NP_075380	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor precursor	206	LRR 7.				axonogenesis|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	anchored to membrane|cell surface|endoplasmic reticulum|plasma membrane	protein binding|receptor activity				0	Colorectal(54;0.0993)																	---	---	---	---
ZNF74	7625	broad.mit.edu	37	22	20760268	20760268	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20760268C>T	uc010gsm.2	+	6	1157	c.945C>T	c.(943-945)TGC>TGT	p.C315C	ZNF74_uc002zsg.2_Silent_p.C244C|ZNF74_uc002zsh.2_Silent_p.C315C|ZNF74_uc002zsi.2_Silent_p.C244C|ZNF74_uc010gsn.2_Silent_p.C244C	NM_003426	NP_003417	Q16587	ZNF74_HUMAN	zinc finger protein 74	315	C2H2-type 3.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|nucleus	DNA binding|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
LZTR1	8216	broad.mit.edu	37	22	21340177	21340177	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21340177C>G	uc002zto.2	+	3	414	c.311C>G	c.(310-312)TCC>TGC	p.S104C	LZTR1_uc002ztn.2_Missense_Mutation_p.S63C|LZTR1_uc011ahy.1_Intron|LZTR1_uc010gsr.1_5'Flank	NM_006767	NP_006758	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	104	Kelch 1.				anatomical structure morphogenesis		sequence-specific DNA binding transcription factor activity			ovary(2)|lung(2)	4	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)															---	---	---	---
SLC7A4	6545	broad.mit.edu	37	22	21385698	21385698	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21385698C>T	uc002zud.2	-	2	472	c.404G>A	c.(403-405)CGT>CAT	p.R135H	SLC7A4_uc002zue.2_Missense_Mutation_p.R135H	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid	135					cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
ZNF280A	129025	broad.mit.edu	37	22	22869883	22869883	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22869883C>A	uc002zwe.2	-	2	325	c.72G>T	c.(70-72)GAG>GAT	p.E24D	LOC96610_uc011aim.1_Intron	NM_080740	NP_542778	P59817	Z280A_HUMAN	zinc finger protein 280A	24					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23264816	23264816	+	RNA	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23264816G>T	uc011aim.1	+	379		c.16637G>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23264817	23264817	+	RNA	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23264817A>T	uc011aim.1	+	379		c.16638A>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
BCR	613	broad.mit.edu	37	22	23615967	23615967	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23615967T>C	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.1_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
SUSD2	56241	broad.mit.edu	37	22	24581755	24581755	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24581755G>A	uc002zzn.1	+	8	1241	c.1197G>A	c.(1195-1197)ACG>ACA	p.T399T		NM_019601	NP_062547	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2 precursor	399	AMOP.|Extracellular (Potential).				immune response	integral to membrane	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
GGT1	2678	broad.mit.edu	37	22	25019835	25019835	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25019835C>T	uc003aan.1	+	11	1459	c.972C>T	c.(970-972)TAC>TAT	p.Y324Y	GGT1_uc003aas.1_Silent_p.Y324Y|GGT1_uc003aat.1_Silent_p.Y324Y|GGT1_uc003aau.1_Silent_p.Y324Y|GGT1_uc003aav.1_Silent_p.Y324Y|GGT1_uc003aaw.1_Silent_p.Y324Y|GGT1_uc003aax.1_Silent_p.Y324Y	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor	324	Extracellular (Potential).				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)													---	---	---	---
SGSM1	129049	broad.mit.edu	37	22	25251295	25251295	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25251295T>A	uc003abg.2	+	7	724	c.567T>A	c.(565-567)GAT>GAA	p.D189E	SGSM1_uc003abh.2_Missense_Mutation_p.D189E|SGSM1_uc010guu.1_Missense_Mutation_p.D189E|SGSM1_uc003abj.2_Missense_Mutation_p.D189E|SGSM1_uc003abi.1_Missense_Mutation_p.D164E|SGSM1_uc003abf.2_Missense_Mutation_p.D189E	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	189	RUN.					Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26736590	26736590	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26736590A>G	uc003acb.2	+	10	2360	c.2204A>G	c.(2203-2205)AAC>AGC	p.N735S	SEZ6L_uc003acc.2_Missense_Mutation_p.N735S|SEZ6L_uc011akc.1_Missense_Mutation_p.N735S|SEZ6L_uc003acd.2_Missense_Mutation_p.N735S|SEZ6L_uc011akd.1_Missense_Mutation_p.N735S|SEZ6L_uc003ace.2_Missense_Mutation_p.N735S|SEZ6L_uc003acf.1_Missense_Mutation_p.N508S|SEZ6L_uc010gvc.1_Missense_Mutation_p.N508S	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	735	CUB 3.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
CHEK2	11200	broad.mit.edu	37	22	29090021	29090021	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29090021T>C	uc003adu.1	-	13	1532	c.1460A>G	c.(1459-1461)CAG>CGG	p.Q487R	CHEK2_uc003ads.1_Missense_Mutation_p.Q266R|CHEK2_uc010gvh.1_Missense_Mutation_p.Q396R|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Missense_Mutation_p.Q530R|CHEK2_uc003adv.1_Missense_Mutation_p.Q458R|CHEK2_uc003adw.1_Missense_Mutation_p.Q487R|CHEK2_uc003adx.1_Missense_Mutation_p.Q266R|CHEK2_uc003ady.1_Missense_Mutation_p.Q476R|CHEK2_uc003adz.1_Missense_Mutation_p.Q291R	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	487					cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20								F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29440867	29440867	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29440867C>T	uc003aeg.2	+	5	598	c.433C>T	c.(433-435)CGA>TGA	p.R145*	ZNRF3_uc003aeh.1_Nonsense_Mutation_p.R145*	NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	245	Cytoplasmic (Potential).					integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
AP1B1	162	broad.mit.edu	37	22	29745219	29745219	+	Silent	SNP	G	A	A	rs144812422		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29745219G>A	uc003afj.2	-	11	1609	c.1425C>T	c.(1423-1425)GAC>GAT	p.D475D	AP1B1_uc003afi.2_Silent_p.D475D|AP1B1_uc003afk.2_Silent_p.D475D|AP1B1_uc003afl.2_Silent_p.D475D|AP1B1_uc011ako.1_Silent_p.D28D	NM_001127	NP_001118	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1 beta 1 subunit	475					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
AP1B1	162	broad.mit.edu	37	22	29754898	29754898	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29754898G>A	uc003afj.2	-	5	526	c.342C>T	c.(340-342)CGC>CGT	p.R114R	AP1B1_uc003afi.2_Silent_p.R114R|AP1B1_uc003afk.2_Silent_p.R114R|AP1B1_uc003afl.2_Silent_p.R114R	NM_001127	NP_001118	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1 beta 1 subunit	114					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
MTMR3	8897	broad.mit.edu	37	22	30408454	30408454	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30408454C>T	uc003agv.3	+	13	1547	c.1219C>T	c.(1219-1221)CGG>TGG	p.R407W	MTMR3_uc003agu.3_Missense_Mutation_p.R407W|MTMR3_uc003agw.3_Missense_Mutation_p.R407W	NM_021090	NP_066576	Q13615	MTMR3_HUMAN	myotubularin-related protein 3 isoform c	407	Myotubularin phosphatase.				phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			breast(3)|ovary(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)															---	---	---	---
MORC2	22880	broad.mit.edu	37	22	31331151	31331151	+	Intron	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31331151A>T	uc003aje.1	-							NM_014941	NP_055756			MORC family CW-type zinc finger 2								ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
MORC2	22880	broad.mit.edu	37	22	31332627	31332627	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31332627A>G	uc003aje.1	-	18	2786	c.1422T>C	c.(1420-1422)TGT>TGC	p.C474C		NM_014941	NP_055756	Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	536	CW-type.						ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
PLA2G3	50487	broad.mit.edu	37	22	31536019	31536019	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31536019G>A	uc003aka.2	-	1	451	c.322C>T	c.(322-324)CTG>TTG	p.L108L		NM_015715	NP_056530	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III precursor	108					cilium morphogenesis|lipid catabolic process|phospholipid metabolic process	centriole|extracellular space|plasma membrane	calcium ion binding|calcium-dependent phospholipase A2 activity				0																		---	---	---	---
PATZ1	23598	broad.mit.edu	37	22	31741479	31741479	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31741479C>T	uc003akq.2	-	1	771	c.110G>A	c.(109-111)GGC>GAC	p.G37D	PATZ1_uc003akp.2_Missense_Mutation_p.G37D|PATZ1_uc003akr.2_Missense_Mutation_p.G37D|PATZ1_uc003aks.2_Missense_Mutation_p.G37D|uc003akt.2_5'Flank	NM_014323	NP_055138	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	37					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/PATZ1(2)	soft_tissue(2)	2																		---	---	---	---
EIF4ENIF1	56478	broad.mit.edu	37	22	31840668	31840668	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31840668C>T	uc003akz.1	-	15	2161	c.1997G>A	c.(1996-1998)CGA>CAA	p.R666Q	EIF4ENIF1_uc003akx.1_Missense_Mutation_p.R321Q|EIF4ENIF1_uc003aky.1_Missense_Mutation_p.R346Q|EIF4ENIF1_uc003ala.1_Missense_Mutation_p.R666Q|EIF4ENIF1_uc003alb.1_Missense_Mutation_p.R492Q|EIF4ENIF1_uc003akw.1_Missense_Mutation_p.R156Q	NM_019843	NP_062817	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E	666						nucleus	protein binding|protein transporter activity			ovary(1)	1																OREG0003516	type=REGULATORY REGION|Gene=EIF4ENIF1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31924781	31924781	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31924781T>C	uc003ale.2	+	3	591	c.198T>C	c.(196-198)AGT>AGC	p.S66S	SFI1_uc003ald.1_Silent_p.S66S|SFI1_uc003alf.2_Silent_p.S66S|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Silent_p.S66S|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	66					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
SFI1	9814	broad.mit.edu	37	22	32009377	32009377	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32009377G>T	uc003ale.2	+	26	2996	c.2603G>T	c.(2602-2604)AGG>ATG	p.R868M	SFI1_uc003alf.2_Missense_Mutation_p.R837M|SFI1_uc003alg.2_Missense_Mutation_p.R786M|SFI1_uc011alp.1_Missense_Mutation_p.R774M|SFI1_uc011alq.1_Missense_Mutation_p.R813M|SFI1_uc003alh.2_RNA|SFI1_uc010gwi.2_RNA|SFI1_uc003ali.2_5'Flank|SFI1_uc003alj.2_5'Flank	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	868					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32179916	32179916	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32179916T>C	uc003als.2	+	9	649	c.507T>C	c.(505-507)GCT>GCC	p.A169A	DEPDC5_uc011als.1_Silent_p.A169A|DEPDC5_uc011alu.1_Silent_p.A169A|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_Silent_p.A169A|DEPDC5_uc003alr.1_Silent_p.A169A|DEPDC5_uc011alt.1_Silent_p.A141A	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	169					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
C22orf24	25775	broad.mit.edu	37	22	32334034	32334034	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32334034T>C	uc003aly.2	-	2	186	c.19A>G	c.(19-21)ACA>GCA	p.T7A	C22orf24_uc003alx.2_RNA	NM_015372	NP_056187	Q9Y442	CV024_HUMAN	hypothetical protein LOC25775	7						integral to membrane				central_nervous_system(1)	1																		---	---	---	---
HMOX1	3162	broad.mit.edu	37	22	35785929	35785929	+	Missense_Mutation	SNP	C	T	T	rs145427664	byFrequency	TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35785929C>T	uc003ant.1	+	4	789	c.709C>T	c.(709-711)CGC>TGC	p.R237C		NM_002133	NP_002124	P09601	HMOX1_HUMAN	heme oxygenase (decyclizing) 1	237					angiogenesis|anti-apoptosis|cell death|cellular iron ion homeostasis|endothelial cell proliferation|erythrocyte homeostasis|heme catabolic process|heme oxidation|intracellular protein kinase cascade|low-density lipoprotein particle clearance|negative regulation of leukocyte migration|negative regulation of smooth muscle cell proliferation|positive regulation of chemokine biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of smooth muscle cell proliferation|protein homooligomerization|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hydrogen peroxide|response to nicotine|smooth muscle hyperplasia|transmembrane transport|wound healing involved in inflammatory response	endoplasmic reticulum membrane|extracellular space|microsome	enzyme binding|heme binding|heme oxygenase (decyclizing) activity|protein homodimerization activity|signal transducer activity			ovary(1)	1					NADH(DB00157)													---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36140245	36140245	+	3'UTR	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36140245C>T	uc003aon.3	-	14					RBM9_uc003aog.3_3'UTR|RBM9_uc003aol.3_3'UTR|RBM9_uc003aoj.3_3'UTR|RBM9_uc003aok.3_Silent_p.T367T|RBM9_uc003aoh.3_Silent_p.T370T|RBM9_uc003aom.3_3'UTR|RBM9_uc010gwu.2_Silent_p.T370T|RBM9_uc003aoo.3_3'UTR	NM_001082578	NP_001076047			RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36689461	36689461	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36689461C>T	uc003apg.2	-	30	4240	c.4009G>A	c.(4009-4011)GAG>AAG	p.E1337K		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1337	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36695071	36695071	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36695071T>C	uc003apg.2	-	24	3225	c.2994A>G	c.(2992-2994)GAA>GAG	p.E998E		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	998	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36714301	36714301	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36714301C>T	uc003apg.2	-	11	1409	c.1178G>A	c.(1177-1179)CGC>CAC	p.R393H	MYH9_uc003aph.1_Missense_Mutation_p.R257H	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	393	Myosin head-like.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36714302	36714302	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36714302G>A	uc003apg.2	-	11	1408	c.1177C>T	c.(1177-1179)CGC>TGC	p.R393C	MYH9_uc003aph.1_Missense_Mutation_p.R257C	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	393	Myosin head-like.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37769252	37769252	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37769252G>A	uc003asq.3	-	3	3109	c.2323C>T	c.(2323-2325)CCC>TCC	p.P775S		NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	775	Cytoplasmic (Potential).					cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
ANKRD54	129138	broad.mit.edu	37	22	38228694	38228694	+	Missense_Mutation	SNP	G	A	A	rs144561541		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38228694G>A	uc003auc.2	-	7	836	c.778C>T	c.(778-780)CGC>TGC	p.R260C	ANKRD54_uc003aud.2_Missense_Mutation_p.R137C	NM_138797	NP_620152	Q6NXT1	ANR54_HUMAN	ankyrin repeat domain 54	260											0	Melanoma(58;0.045)																	---	---	---	---
MGAT3	4248	broad.mit.edu	37	22	39884545	39884545	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39884545G>A	uc003axv.3	+	2	1432	c.1193G>A	c.(1192-1194)CGC>CAC	p.R398H	MGAT3_uc010gxy.2_Missense_Mutation_p.R398H	NM_002409	NP_002400	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein	398	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity				0	Melanoma(58;0.04)																	---	---	---	---
SMCR7L	54471	broad.mit.edu	37	22	39909860	39909860	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39909860C>T	uc003axx.2	+	6	1422	c.924C>T	c.(922-924)CTC>CTT	p.L308L	SMCR7L_uc003axw.2_Silent_p.L308L|SMCR7L_uc010gxz.1_Silent_p.L130L|SMCR7L_uc003axy.2_Silent_p.L130L	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	308						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)															OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SGSM3	27352	broad.mit.edu	37	22	40804113	40804113	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40804113C>T	uc003ayu.1	+	15	1827	c.1618C>T	c.(1618-1620)CGC>TGC	p.R540C	SGSM3_uc011aos.1_Missense_Mutation_p.R473C|SGSM3_uc011aot.1_Missense_Mutation_p.R477C|SGSM3_uc010gyd.1_Missense_Mutation_p.R611C	NM_015705	NP_056520	Q96HU1	SGSM3_HUMAN	small G protein signaling modulator 3	540					cell cycle arrest|Rap protein signal transduction	cytoplasm	Rab GTPase activator activity|Rab GTPase binding			ovary(2)	2																		---	---	---	---
EP300	2033	broad.mit.edu	37	22	41513179	41513179	+	Intron	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41513179C>A	uc003azl.3	+							NM_001429	NP_001420			E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
SEPT3	55964	broad.mit.edu	37	22	42390663	42390663	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42390663T>C	uc003bbr.3	+	10	1094	c.956T>C	c.(955-957)ATC>ACC	p.I319T	WBP2NL_uc011ape.1_Intron|SEPT3_uc003bbs.3_Missense_Mutation_p.I319T|SEPT3_uc010gyr.2_Missense_Mutation_p.I255T|SEPT3_uc011apj.1_Missense_Mutation_p.I255T|SEPT3_uc010gys.2_Missense_Mutation_p.I99T	NM_145733	NP_663786	Q9UH03	SEPT3_HUMAN	septin 3 isoform A	319					cell cycle|cytokinesis	cell junction|septin complex	GTP binding				0																		---	---	---	---
ATXN10	25814	broad.mit.edu	37	22	46136420	46136420	+	Splice_Site	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46136420T>C	uc003bgm.1	+	9	1430	c.1173_splice	c.e9+2	p.K391_splice	ATXN10_uc011aqt.1_Splice_Site_p.K327_splice|ATXN10_uc003bgn.1_Splice_Site_p.K202_splice	NM_013236	NP_037368			ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)														---	---	---	---
PPARA	5465	broad.mit.edu	37	22	46611192	46611192	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46611192G>T	uc003bgw.1	+	5	597	c.331G>T	c.(331-333)GGC>TGC	p.G111C	PPARA_uc003bgx.1_Missense_Mutation_p.G111C|PPARA_uc010hab.1_Missense_Mutation_p.G111C|PPARA_uc003bha.2_Missense_Mutation_p.G111C|PPARA_uc003bhb.1_Missense_Mutation_p.G111C|PPARA_uc010hac.1_Translation_Start_Site	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,	111	Nuclear receptor.|NR C4-type.				fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)													---	---	---	---
PKDREJ	10343	broad.mit.edu	37	22	46655432	46655432	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46655432A>T	uc003bhh.2	-	1	3788	c.3788T>A	c.(3787-3789)GTG>GAG	p.V1263E		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1263	Cytoplasmic (Potential).|PLAT.				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46793716	46793716	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46793716G>A	uc003bhw.1	-	12	5556	c.5556C>T	c.(5554-5556)AAC>AAT	p.N1852N	CELSR1_uc011arc.1_Silent_p.N173N	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	1852	Extracellular (Potential).|Laminin G-like 2.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47033868	47033868	+	Intron	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47033868G>T	uc003bhx.2	+						GRAMD4_uc010had.2_Intron	NM_015124	NP_055939			death-inducing-protein						apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)														---	---	---	---
TBC1D22A	25771	broad.mit.edu	37	22	47308004	47308004	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47308004G>A	uc003bib.2	+	8	1070	c.935G>A	c.(934-936)CGC>CAC	p.R312H	TBC1D22A_uc010haf.2_Missense_Mutation_p.R282H|TBC1D22A_uc003bic.2_Missense_Mutation_p.R253H|TBC1D22A_uc003bie.2_Missense_Mutation_p.R234H|TBC1D22A_uc003bid.2_RNA|TBC1D22A_uc010hag.2_RNA|TBC1D22A_uc003bif.2_Missense_Mutation_p.R265H	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	312	Rab-GAP TBC.					intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)														---	---	---	---
BRD1	23774	broad.mit.edu	37	22	50169717	50169717	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50169717T>C	uc003biv.2	-	10	3306	c.2819A>G	c.(2818-2820)TAC>TGC	p.Y940C	BRD1_uc011arf.1_Missense_Mutation_p.Y666C|BRD1_uc011arg.1_Missense_Mutation_p.Y989C|BRD1_uc011arh.1_Missense_Mutation_p.Y940C|BRD1_uc003biu.3_Missense_Mutation_p.Y1071C	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	940	PWWP.				histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
BRD1	23774	broad.mit.edu	37	22	50197979	50197979	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50197979A>G	uc003biv.2	-	2	1884	c.1397T>C	c.(1396-1398)ATT>ACT	p.I466T	BRD1_uc011arf.1_Missense_Mutation_p.I61T|BRD1_uc011arg.1_Missense_Mutation_p.I520T|BRD1_uc011arh.1_Missense_Mutation_p.I466T|BRD1_uc003biu.3_Missense_Mutation_p.I466T	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	466					histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
ZBED4	9889	broad.mit.edu	37	22	50277790	50277790	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50277790C>T	uc003bix.2	+	2	950	c.480C>T	c.(478-480)CAC>CAT	p.H160H		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	160	BED-type 1.					cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
TTLL8	164714	broad.mit.edu	37	22	50470360	50470360	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50470360C>T	uc011ark.1	-	11	1462	c.1462G>A	c.(1462-1464)GCC>ACC	p.A488T		NM_001080447	NP_001073916			tubulin tyrosine ligase-like family, member 8											ovary(2)	2		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)														---	---	---	---
SELO	83642	broad.mit.edu	37	22	50655450	50655450	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50655450C>T	uc011arr.1	+	8	1796	c.1738C>T	c.(1738-1740)CAG>TAG	p.Q580*	SELO_uc010hap.2_Nonsense_Mutation_p.Q391*|SELO_uc003bjy.2_Nonsense_Mutation_p.Q260*|SELO_uc003bjz.2_Nonsense_Mutation_p.Q331*	NM_031454	NP_113642	Q9BVL4	SELO_HUMAN	selenoprotein O	580											0		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)														---	---	---	---
PLXNB2	23654	broad.mit.edu	37	22	50714358	50714358	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50714358A>G	uc003bkv.3	-	36	5478	c.5372T>C	c.(5371-5373)CTC>CCC	p.L1791P	PLXNB2_uc003bkt.1_Missense_Mutation_p.L583P|PLXNB2_uc003bku.1_Missense_Mutation_p.L776P	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	1791	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)												OREG0026679	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PLXNB2	23654	broad.mit.edu	37	22	50717305	50717305	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50717305T>A	uc003bkv.3	-	28	4631	c.4525A>T	c.(4525-4527)AGG>TGG	p.R1509W	PLXNB2_uc003bkt.1_Missense_Mutation_p.R301W|PLXNB2_uc003bku.1_Missense_Mutation_p.R494W	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	1509	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
MXRA5	25878	broad.mit.edu	37	X	3235646	3235646	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3235646C>T	uc004crg.3	-	6	6233	c.6076G>A	c.(6076-6078)GTG>ATG	p.V2026M		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2026	Ig-like C2-type 4.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)																---	---	---	---
CLCN4	1183	broad.mit.edu	37	X	10176320	10176320	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10176320G>A	uc004csy.3	+	9	1509	c.1079G>A	c.(1078-1080)CGC>CAC	p.R360H	CLCN4_uc011mid.1_Missense_Mutation_p.R266H	NM_001830	NP_001821	P51793	CLCN4_HUMAN	chloride channel 4	360						early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
FANCB	2187	broad.mit.edu	37	X	14883542	14883542	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14883542T>G	uc004cwg.1	-	3	359	c.91A>C	c.(91-93)AAT>CAT	p.N31H	FANCB_uc004cwh.1_Missense_Mutation_p.N31H	NM_001018113	NP_001018123	Q8NB91	FANCB_HUMAN	Fanconi anemia complementation group B	31					DNA repair	nucleoplasm				lung(1)	1	Hepatocellular(33;0.183)												Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
BMX	660	broad.mit.edu	37	X	15544230	15544230	+	Intron	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15544230A>T	uc004cww.2	+						BMX_uc004cwx.3_Intron|BMX_uc004cwy.3_Intron	NM_203281	NP_975010			BMX non-receptor tyrosine kinase						cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)																	---	---	---	---
NHS	4810	broad.mit.edu	37	X	17744772	17744772	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17744772C>T	uc004cxx.2	+	6	2821	c.2483C>T	c.(2482-2484)CCG>CTG	p.P828L	NHS_uc011mix.1_Missense_Mutation_p.P849L|NHS_uc004cxy.2_Missense_Mutation_p.P672L|NHS_uc004cxz.2_Missense_Mutation_p.P651L|NHS_uc004cya.2_Missense_Mutation_p.P551L	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	828						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
NHS	4810	broad.mit.edu	37	X	17745811	17745811	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17745811T>C	uc004cxx.2	+	6	3860	c.3522T>C	c.(3520-3522)ACT>ACC	p.T1174T	NHS_uc011mix.1_Silent_p.T1195T|NHS_uc004cxy.2_Silent_p.T1018T|NHS_uc004cxz.2_Silent_p.T997T|NHS_uc004cya.2_Silent_p.T897T	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	1174						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)																	---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19587236	19587236	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19587236G>A	uc004czm.2	-	13	1685	c.1369C>T	c.(1369-1371)CGC>TGC	p.R457C	SH3KBP1_uc011mje.1_Missense_Mutation_p.R196C|SH3KBP1_uc011mjf.1_Missense_Mutation_p.R219C|SH3KBP1_uc004czl.2_Missense_Mutation_p.R420C|SH3KBP1_uc010nfm.2_5'UTR	NM_031892	NP_114098	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1 isoform a	457					apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0																		---	---	---	---
SH3KBP1	30011	broad.mit.edu	37	X	19606847	19606847	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19606847C>T	uc004czm.2	-	12	1528	c.1212G>A	c.(1210-1212)CGG>CGA	p.R404R	SH3KBP1_uc011mje.1_Silent_p.R143R|SH3KBP1_uc011mjf.1_Silent_p.R166R|SH3KBP1_uc004czl.2_Silent_p.R367R	NM_031892	NP_114098	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1 isoform a	404	Pro-rich.				apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0																		---	---	---	---
MAP7D2	256714	broad.mit.edu	37	X	20082870	20082870	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20082870G>A	uc004czr.1	-	2	203	c.184C>T	c.(184-186)CGA>TGA	p.R62*	MAP7D2_uc011mji.1_Nonsense_Mutation_p.R18*|MAP7D2_uc010nfo.1_Nonsense_Mutation_p.R62*|MAP7D2_uc011mjj.1_Nonsense_Mutation_p.R62*|MAP7D2_uc004czs.1_Nonsense_Mutation_p.R18*	NM_152780	NP_689993	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	62	Potential.									ovary(2)|breast(1)	3																		---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21670629	21670629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21670629C>T	uc004czx.1	+	22	3131	c.3095C>T	c.(3094-3096)ACG>ATG	p.T1032M	CNKSR2_uc011mjo.1_Missense_Mutation_p.T1002M	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	1032					regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
ZNF645	158506	broad.mit.edu	37	X	22291373	22291373	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22291373G>A	uc004dai.1	+	1	314	c.265G>A	c.(265-267)GGA>AGA	p.G89R		NM_152577	NP_689790	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	89	RING-type.					intracellular	zinc ion binding			lung(1)|pancreas(1)	2																		---	---	---	---
ACOT9	23597	broad.mit.edu	37	X	23748967	23748967	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23748967G>A	uc004dap.2	-	4	447	c.301C>T	c.(301-303)CGA>TGA	p.R101*	ACOT9_uc004dao.2_Nonsense_Mutation_p.R110*|ACOT9_uc004daq.2_Nonsense_Mutation_p.R59*|ACOT9_uc004dar.2_Nonsense_Mutation_p.R41*|ACOT9_uc011mjt.1_RNA|ACOT9_uc004das.2_Nonsense_Mutation_p.R41*|ACOT9_uc004dat.1_Nonsense_Mutation_p.R101*	NM_001033583	NP_001028755	Q9Y305	ACOT9_HUMAN	acyl-Coenzyme A thioesterase 2, mitochondrial	101					acyl-CoA metabolic process	mitochondrion	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	24334982	24334982	+	IGR	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24334982C>A								FAM48B2 (3550 upstream) : FAM48B1 (45896 downstream)																																			---	---	---	---
TAB3	257397	broad.mit.edu	37	X	30870905	30870905	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30870905G>A	uc004dcj.2	-	7	2363	c.1700C>T	c.(1699-1701)GCG>GTG	p.A567V	TAB3_uc004dck.2_Missense_Mutation_p.A567V|TAB3_uc010ngl.2_Missense_Mutation_p.A567V	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	567					activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	31496309	31496309	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31496309G>A	uc004dda.1	-	59	9095	c.8851C>T	c.(8851-8853)CGC>TGC	p.R2951C	DMD_uc004dcq.1_Missense_Mutation_p.R222C|DMD_uc004dcr.1_Missense_Mutation_p.R491C|DMD_uc004dcs.1_Missense_Mutation_p.R491C|DMD_uc004dct.1_Missense_Mutation_p.R491C|DMD_uc004dcu.1_Missense_Mutation_p.R491C|DMD_uc004dcv.1_Missense_Mutation_p.R491C|DMD_uc004dcw.2_Missense_Mutation_p.R1607C|DMD_uc004dcx.2_Missense_Mutation_p.R1610C|DMD_uc004dcz.2_Missense_Mutation_p.R2828C|DMD_uc004dcy.1_Missense_Mutation_p.R2947C|DMD_uc004ddb.1_Missense_Mutation_p.R2943C	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2951	Spectrin 22.				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)																---	---	---	---
FAM47B	170062	broad.mit.edu	37	X	34961163	34961163	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34961163G>A	uc004ddi.1	+	1	233	c.215G>A	c.(214-216)CGC>CAC	p.R72H		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	72										ovary(3)|breast(1)	4																		---	---	---	---
FAM47B	170062	broad.mit.edu	37	X	34961839	34961839	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34961839G>A	uc004ddi.1	+	1	909	c.891G>A	c.(889-891)CCG>CCA	p.P297P		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	297	Pro-rich.									ovary(3)|breast(1)	4																		---	---	---	---
LANCL3	347404	broad.mit.edu	37	X	37526606	37526606	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37526606T>C	uc011mkd.1	+	4	1269	c.967T>C	c.(967-969)TGT>CGT	p.C323R	LANCL3_uc004ddp.1_Missense_Mutation_p.C323R	NM_198511	NP_940913	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3	323							catalytic activity				0																		---	---	---	---
TSPAN7	7102	broad.mit.edu	37	X	38535094	38535094	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38535094G>A	uc004deg.3	+	5	646	c.577G>A	c.(577-579)GCC>ACC	p.A193T	TSPAN7_uc011mkj.1_Missense_Mutation_p.A219T|TSPAN7_uc011mkk.1_Missense_Mutation_p.A210T|TSPAN7_uc004deh.2_Missense_Mutation_p.A101T	NM_004615	NP_004606	P41732	TSN7_HUMAN	tetraspanin 7	193	Extracellular (Potential).				interspecies interaction between organisms	integral to plasma membrane				ovary(1)	1																		---	---	---	---
NYX	60506	broad.mit.edu	37	X	41307141	41307141	+	5'UTR	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41307141G>T	uc004dfh.2	+	1					NYX_uc011mku.1_5'UTR	NM_022567	NP_072089			nyctalopin precursor						response to stimulus|visual perception	intracellular|proteinaceous extracellular matrix				lung(2)	2																		---	---	---	---
CASK	8573	broad.mit.edu	37	X	41481866	41481866	+	Intron	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41481866C>A	uc004dfl.3	-						CASK_uc004dfk.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron	NM_003688	NP_003679			calcium/calmodulin-dependent serine protein						cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6																		---	---	---	---
RBM10	8241	broad.mit.edu	37	X	47045755	47045755	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47045755G>A	uc004dhf.2	+	23	3015	c.2636G>A	c.(2635-2637)CGC>CAC	p.R879H	RBM10_uc004dhg.2_Missense_Mutation_p.R801H|RBM10_uc004dhh.2_Missense_Mutation_p.R878H|RBM10_uc010nhq.2_Missense_Mutation_p.R802H|RBM10_uc004dhi.2_Missense_Mutation_p.R944H	NM_005676	NP_005667	P98175	RBM10_HUMAN	RNA binding motif protein 10 isoform 1	879	G-patch.				mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			ovary(1)|large_intestine(1)|prostate(1)|breast(1)|pancreas(1)	5																		---	---	---	---
ARAF	369	broad.mit.edu	37	X	47430411	47430411	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47430411G>T	uc011mlq.1	+	15	1819	c.1686G>T	c.(1684-1686)CAG>CAT	p.Q562H		NM_001654	NP_001645	P10398	ARAF_HUMAN	v-raf murine sarcoma 3611 viral oncogene	562	Protein kinase.				intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity			large_intestine(3)|lung(2)|ovary(1)|skin(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	47663337	47663337	+	IGR	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47663337T>G								LOC100133957 (143561 upstream) : ZNF81 (32964 downstream)																																			---	---	---	---
ZNF81	347344	broad.mit.edu	37	X	47774350	47774350	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47774350A>G	uc010nhy.1	+	6	673	c.305A>G	c.(304-306)CAG>CGG	p.Q102R		NM_007137	NP_009068	P51508	ZNF81_HUMAN	zinc finger protein 81	102						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(315;0.0973)																---	---	---	---
ZNF81	347344	broad.mit.edu	37	X	47774500	47774500	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47774500G>A	uc010nhy.1	+	6	823	c.455G>A	c.(454-456)CGC>CAC	p.R152H		NM_007137	NP_009068	P51508	ZNF81_HUMAN	zinc finger protein 81	152						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(315;0.0973)																---	---	---	---
ZNF630	57232	broad.mit.edu	37	X	47917969	47917969	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47917969T>C	uc004div.3	-	5	2114	c.1862A>G	c.(1861-1863)CAC>CGC	p.H621R	ZNF630_uc010nhz.1_Intron|ZNF630_uc004diw.2_Missense_Mutation_p.H497R	NM_001037735	NP_001032824	Q2M218	ZN630_HUMAN	zinc finger protein 630	621	C2H2-type 13; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
MAGIX	79917	broad.mit.edu	37	X	49019249	49019249	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49019249G>A	uc010nin.1	+	1	69	c.22G>A	c.(22-24)GCC>ACC	p.A8T	MAGIX_uc010nio.1_Missense_Mutation_p.A8T|MAGIX_uc004dmt.2_Missense_Mutation_p.A8T|MAGIX_uc004dmu.2_5'Flank|MAGIX_uc004dmw.2_5'Flank	NM_024859	NP_079135	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked isoform a	8											0																		---	---	---	---
CLCN5	1184	broad.mit.edu	37	X	49837186	49837186	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49837186A>G	uc004dos.1	+	3	396	c.148A>G	c.(148-150)AGT>GGT	p.S50G	CLCN5_uc004dor.1_Missense_Mutation_p.S120G|CLCN5_uc004doq.1_Missense_Mutation_p.S120G|CLCN5_uc004dot.1_Missense_Mutation_p.S50G	NM_000084	NP_000075	P51795	CLCN5_HUMAN	chloride channel 5 isoform b	50	Cytoplasmic (By similarity).				excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)																	---	---	---	---
MAGED1	9500	broad.mit.edu	37	X	51637833	51637833	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51637833C>T	uc004dpm.2	+						MAGED1_uc004dpn.2_Silent_p.R52R|MAGED1_uc004dpo.2_Intron|MAGED1_uc011mnx.1_Intron	NM_001005332	NP_001005332			melanoma antigen family D, 1 isoform b						apoptosis|induction of apoptosis by extracellular signals|negative regulation of epithelial cell proliferation|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|plasma membrane|protein complex	protein binding			ovary(3)	3	Ovarian(276;0.236)														Multiple Myeloma(10;0.10)			---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53674333	53674333	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53674333C>T	uc004dsp.2	-	6	731	c.329G>A	c.(328-330)CGG>CAG	p.R110Q		NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	110					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17																		---	---	---	---
TSR2	90121	broad.mit.edu	37	X	54470968	54470968	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54470968C>T	uc004dte.2	+	5	563	c.561C>T	c.(559-561)GTC>GTT	p.V187V	TSR2_uc004dtf.2_Silent_p.V92V	NM_058163	NP_477511	Q969E8	TSR2_HUMAN	TSR2, 20S rRNA accumulation, homolog	187					rRNA processing		protein binding				0																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54577458	54577458	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54577458G>A	uc004dth.1	+	10	977	c.838G>A	c.(838-840)GTG>ATG	p.V280M	GNL3L_uc004dti.2_RNA	NM_019067	NP_061940	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3	280	G.				ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
MAGED2	10916	broad.mit.edu	37	X	54838668	54838668	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54838668G>A	uc004dtk.1	+	7	1163	c.1069G>A	c.(1069-1071)GCA>ACA	p.A357T	MAGED2_uc004dtl.1_Missense_Mutation_p.A357T|MAGED2_uc004dtm.1_Missense_Mutation_p.A272T|MAGED2_uc010nkc.1_Missense_Mutation_p.A357T|MAGED2_uc004dtn.1_Missense_Mutation_p.A357T|MAGED2_uc004dto.1_Missense_Mutation_p.A331T|SNORA11_uc004dtp.1_5'Flank	NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	357	MAGE.									ovary(2)|breast(1)	3																		---	---	---	---
ALAS2	212	broad.mit.edu	37	X	55051231	55051231	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55051231G>A	uc004dua.3	-	3	362	c.224C>T	c.(223-225)TCG>TTG	p.S75L	ALAS2_uc004dub.3_Missense_Mutation_p.S99L|ALAS2_uc004dud.3_Missense_Mutation_p.S75L	NM_000032	NP_000023	P22557	HEM0_HUMAN	5-aminolevulinate synthase 2 isoform a	75					cellular iron ion homeostasis|erythrocyte differentiation|heme biosynthetic process|hemoglobin biosynthetic process|oxygen homeostasis|response to hypoxia	mitochondrial inner membrane|mitochondrial matrix	5-aminolevulinate synthase activity|coenzyme binding|glycine binding|protein binding|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(1)	1					Glycine(DB00145)													---	---	---	---
RRAGB	10325	broad.mit.edu	37	X	55757835	55757835	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55757835G>A	uc004dup.2	+	6	1067	c.416G>A	c.(415-417)CGG>CAG	p.R139Q	RRAGB_uc004duq.2_Missense_Mutation_p.R111Q	NM_016656	NP_057740	Q5VZM2	RRAGB_HUMAN	Ras-related GTP binding B long isoform	139					cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|signal transduction	Golgi apparatus|lysosome|nucleus	GTP binding|protein binding				0																		---	---	---	---
KLF8	11279	broad.mit.edu	37	X	56259786	56259786	+	Intron	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56259786T>G	uc004dur.2	+						KLF8_uc010nkg.2_Intron|KLF8_uc011mop.1_Intron|KLF8_uc010nkh.2_Intron	NM_007250	NP_009181			Kruppel-like factor 8 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
FAAH2	158584	broad.mit.edu	37	X	57474979	57474979	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57474979G>T	uc004dvc.2	+	10	1400	c.1251G>T	c.(1249-1251)AAG>AAT	p.K417N		NM_174912	NP_777572	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	417						integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3															HNSCC(52;0.14)			---	---	---	---
FAM123B	139285	broad.mit.edu	37	X	63410310	63410310	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63410310G>T	uc004dvo.2	-	2	3130	c.2857C>A	c.(2857-2859)CCA>ACA	p.P953T		NM_152424	NP_689637	Q5JTC6	F123B_HUMAN	family with sequence similarity 123B	953	Pro-rich.				Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane		p.0?(40)		kidney(99)|large_intestine(6)|ovary(3)|lung(2)|breast(1)|liver(1)	112																		---	---	---	---
ZC4H2	55906	broad.mit.edu	37	X	64140060	64140060	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64140060T>C	uc004dvu.2	-	3	387	c.299A>G	c.(298-300)GAG>GGG	p.E100G	ZC4H2_uc004dvv.2_Missense_Mutation_p.E77G|ZC4H2_uc011mov.1_Missense_Mutation_p.E77G|ZC4H2_uc011mow.1_Missense_Mutation_p.E100G|ZC4H2_uc004dvw.1_Missense_Mutation_p.E100G	NM_018684	NP_061154	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	100	Potential.			E -> K (in Ref. 3; BAB14308).			metal ion binding|protein binding			ovary(1)	1																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69561789	69561789	+	Intron	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69561789C>A	uc004dyg.2	+						KIF4A_uc010nkw.2_Intron|KIF4A_uc004dyf.1_Intron	NM_012310	NP_036442			kinesin family member 4						anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4																		---	---	---	---
ITGB1BP2	26548	broad.mit.edu	37	X	70523138	70523138	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70523138C>T	uc004dzr.1	+	5	373	c.344C>T	c.(343-345)CCG>CTG	p.P115L	BCYRN1_uc011mpt.1_Intron|ITGB1BP2_uc004dzs.1_Missense_Mutation_p.P97L	NM_012278	NP_036410	Q9UKP3	ITBP2_HUMAN	integrin beta 1 binding protein 2	115					muscle organ development|signal transduction		SH3 domain binding			ovary(1)	1	Renal(35;0.156)																	---	---	---	---
ACRC	93953	broad.mit.edu	37	X	70823496	70823496	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70823496T>C	uc004eae.2	+	8	870	c.369T>C	c.(367-369)ATT>ATC	p.I123I	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	123						nucleus				ovary(3)	3	Renal(35;0.156)																	---	---	---	---
KIAA2022	340533	broad.mit.edu	37	X	73961039	73961039	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73961039G>A	uc004eby.2	-	3	3970	c.3353C>T	c.(3352-3354)ACC>ATC	p.T1118I		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	1118					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15																		---	---	---	---
MAGT1	84061	broad.mit.edu	37	X	77112905	77112905	+	Silent	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77112905A>C	uc004fof.2	-	4	638	c.576T>G	c.(574-576)GGT>GGG	p.G192G	MAGT1_uc004fog.3_Intron	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	160					protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				upper_aerodigestive_tract(1)	1																		---	---	---	---
ATP7A	538	broad.mit.edu	37	X	77244200	77244200	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77244200A>T	uc004ecx.3	+	3	743	c.583A>T	c.(583-585)AAA>TAA	p.K195*	ATP7A_uc004ecw.2_Nonsense_Mutation_p.K195*	NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	195	HMA 2.|Cytoplasmic (Potential).				ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0																		---	---	---	---
BRWD3	254065	broad.mit.edu	37	X	79932589	79932589	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79932589C>T	uc004edt.2	-	41	5191	c.4928G>A	c.(4927-4929)AGC>AAC	p.S1643N	BRWD3_uc010nmi.1_RNA|BRWD3_uc004edo.2_Missense_Mutation_p.S1239N|BRWD3_uc004edp.2_Missense_Mutation_p.S1472N|BRWD3_uc004edq.2_Missense_Mutation_p.S1239N|BRWD3_uc010nmj.1_Missense_Mutation_p.S1239N|BRWD3_uc004edr.2_Missense_Mutation_p.S1313N|BRWD3_uc004eds.2_Missense_Mutation_p.S1239N|BRWD3_uc004edu.2_Missense_Mutation_p.S1313N|BRWD3_uc004edv.2_Missense_Mutation_p.S1239N|BRWD3_uc004edw.2_Missense_Mutation_p.S1239N|BRWD3_uc004edx.2_Missense_Mutation_p.S1239N|BRWD3_uc004edy.2_Missense_Mutation_p.S1239N|BRWD3_uc004edz.2_Missense_Mutation_p.S1313N|BRWD3_uc004eea.2_Missense_Mutation_p.S1313N|BRWD3_uc004eeb.2_Missense_Mutation_p.S1239N|uc004edn.1_5'Flank	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1643										ovary(4)	4																		---	---	---	---
SATL1	340562	broad.mit.edu	37	X	84349197	84349197	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84349197A>G	uc011mqx.1	-	4	1813	c.1813T>C	c.(1813-1815)TAC>CAC	p.Y605H	SATL1_uc004een.2_Missense_Mutation_p.Y605H	NM_001163541	NP_001157013	Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	418	N-acetyltransferase.						N-acetyltransferase activity			breast(2)	2																		---	---	---	---
SATL1	340562	broad.mit.edu	37	X	84363029	84363029	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84363029T>A	uc011mqx.1	-	1	946	c.946A>T	c.(946-948)ATG>TTG	p.M316L	SATL1_uc004een.2_Missense_Mutation_p.M316L	NM_001163541	NP_001157013	Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	129	Gln-rich.						N-acetyltransferase activity			breast(2)	2																		---	---	---	---
ZNF711	7552	broad.mit.edu	37	X	84510747	84510747	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84510747A>G	uc004eeo.2	+	4	909	c.562A>G	c.(562-564)ACC>GCC	p.T188A	ZNF711_uc004eep.2_Missense_Mutation_p.T188A|ZNF711_uc004eeq.2_Missense_Mutation_p.T188A	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	188					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100505457	100505457	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100505457G>A	uc004egz.2	+	15	1955	c.1586G>A	c.(1585-1587)CGC>CAC	p.R529H	DRP2_uc011mrh.1_Missense_Mutation_p.R451H	NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	529					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
GLA	2717	broad.mit.edu	37	X	100653764	100653764	+	Intron	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100653764A>C	uc004ehl.1	-							NM_000169	NP_000160			alpha-galactosidase A precursor						glycoside catabolic process|glycosphingolipid catabolic process|glycosylceramide catabolic process|negative regulation of nitric oxide biosynthetic process|negative regulation of nitric-oxide synthase activity|oligosaccharide metabolic process	extracellular region|Golgi apparatus|lysosome	cation binding|protein homodimerization activity|raffinose alpha-galactosidase activity|receptor binding				0					Agalsidase beta(DB00103)													---	---	---	---
ESX1	80712	broad.mit.edu	37	X	103499192	103499192	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103499192T>C	uc004ely.2	-	2	207	c.149A>G	c.(148-150)AAA>AGA	p.K50R		NM_153448	NP_703149	Q8N693	ESX1_HUMAN	extraembryonic, spermatogenesis, homeobox	50					negative regulation of transcription, DNA-dependent|regulation of cell cycle	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
NRK	203447	broad.mit.edu	37	X	105142690	105142690	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105142690C>T	uc004emd.2	+	8	997	c.694C>T	c.(694-696)CGC>TGC	p.R232C	NRK_uc010npc.1_Translation_Start_Site	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	232	Protein kinase.						ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14															HNSCC(51;0.14)			---	---	---	---
MORC4	79710	broad.mit.edu	37	X	106224253	106224253	+	Intron	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106224253C>T	uc004emu.3	-						MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Intron|MORC4_uc004emw.3_Intron	NM_024657	NP_078933			zinc finger, CW type with coiled-coil domain 2								ATP binding|zinc ion binding			ovary(1)	1																		---	---	---	---
IRS4	8471	broad.mit.edu	37	X	107976465	107976465	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107976465C>T	uc004eoc.2	-	1	3143	c.3110G>A	c.(3109-3111)CGC>CAC	p.R1037H		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	1037						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	10																		---	---	---	---
IRS4	8471	broad.mit.edu	37	X	107977589	107977589	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107977589T>C	uc004eoc.2	-	1	2019	c.1986A>G	c.(1984-1986)GGA>GGG	p.G662G		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	662						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	10																		---	---	---	---
CAPN6	827	broad.mit.edu	37	X	110490593	110490593	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110490593T>C	uc004epc.1	-						CAPN6_uc011msu.1_Intron	NM_014289	NP_055104			calpain 6						microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
HTR2C	3358	broad.mit.edu	37	X	114141351	114141351	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114141351C>T	uc004epu.1	+	6	1478	c.750C>T	c.(748-750)CAC>CAT	p.H250H	HTR2C_uc010nqc.1_Silent_p.H250H|HTR2C_uc004epv.1_Missense_Mutation_p.R219W	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	250	Cytoplasmic (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)													---	---	---	---
WDR44	54521	broad.mit.edu	37	X	117480540	117480540	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117480540T>G	uc004eqn.2	+	1	499	c.74T>G	c.(73-75)GTG>GGG	p.V25G	WDR44_uc004eqo.2_Missense_Mutation_p.V25G|WDR44_uc011mtr.1_Missense_Mutation_p.V25G	NM_019045	NP_061918	Q5JSH3	WDR44_HUMAN	WD repeat domain 44 protein	25	Binding activity.					cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117712549	117712549	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117712549T>C	uc004eqp.2	+	13	1514	c.1451T>C	c.(1450-1452)GTA>GCA	p.V484A	DOCK11_uc004eqq.2_Missense_Mutation_p.V250A	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	484					blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
IL13RA1	3597	broad.mit.edu	37	X	117895240	117895240	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117895240T>C	uc004eqs.2	+	6	859	c.816T>C	c.(814-816)CAT>CAC	p.H272H	IL13RA1_uc004eqr.1_Silent_p.H272H|IL13RA1_uc004eqt.1_Silent_p.H272H	NM_001560	NP_001551	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1 precursor	272	Extracellular (Potential).					interleukin-13 receptor complex	cytokine receptor activity				0																		---	---	---	---
CXorf56	63932	broad.mit.edu	37	X	118676477	118676477	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118676477C>A	uc004erk.1	-	5	550	c.504G>T	c.(502-504)GAG>GAT	p.E168D	CXorf56_uc004erj.1_Missense_Mutation_p.E119D|CXorf56_uc011mtu.1_Missense_Mutation_p.E154D	NM_022101	NP_071384	Q9H5V9	CX056_HUMAN	hypothetical protein LOC63932	168							protein binding				0																		---	---	---	---
UBE2A	7319	broad.mit.edu	37	X	118717213	118717213	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118717213T>C	uc004erl.2	+	6	630	c.454T>C	c.(454-456)TGT>CGT	p.C152R	UBE2A_uc004erm.2_Missense_Mutation_p.C122R|UBE2A_uc004ern.2_RNA|UBE2A_uc004ero.2_RNA|UBE2A_uc004erp.2_Missense_Mutation_p.C77R	NM_003336	NP_003327	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A isoform 1	152					histone H2A ubiquitination|positive regulation of cell proliferation|postreplication repair|protein autoubiquitination|protein K11-linked ubiquitination|protein K48-linked ubiquitination|response to UV|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity				0													Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
MCTS1	28985	broad.mit.edu	37	X	119742168	119742168	+	Silent	SNP	T	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119742168T>G	uc004esx.2	+	4	699	c.351T>G	c.(349-351)ACT>ACG	p.T117T	MCTS1_uc011mub.1_Silent_p.T118T	NM_014060	NP_054779	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1 isoform 1	117	PUA.				cell cycle|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm	RNA binding				0																		---	---	---	---
STAG2	10735	broad.mit.edu	37	X	123229219	123229219	+	Intron	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123229219T>C	uc004etz.3	+						STAG2_uc004eua.2_Intron|STAG2_uc004eub.2_Intron|STAG2_uc004euc.2_Intron|STAG2_uc004eud.2_Intron|STAG2_uc004eue.2_Intron	NM_006603	NP_006594			stromal antigen 2 isoform b						cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123517968	123517968	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123517968C>T	uc004euj.2	-	29	6856	c.6792G>A	c.(6790-6792)GGG>GGA	p.G2264G	ODZ1_uc011muj.1_Silent_p.G2270G|ODZ1_uc010nqy.2_Silent_p.G2271G	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	2264	YD 21.|Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
SMARCA1	6594	broad.mit.edu	37	X	128599865	128599865	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128599865T>C	uc004eun.3	-	22	2886	c.2773A>G	c.(2773-2775)AGA>GGA	p.R925G	SMARCA1_uc004eup.3_Missense_Mutation_p.R913G|SMARCA1_uc011muk.1_Missense_Mutation_p.R925G|SMARCA1_uc011mul.1_Missense_Mutation_p.R913G	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	925					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4																		---	---	---	---
SMARCA1	6594	broad.mit.edu	37	X	128621096	128621096	+	Missense_Mutation	SNP	G	A	A	rs140388140		TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128621096G>A	uc004eun.3	-	17	2229	c.2116C>T	c.(2116-2118)CGC>TGC	p.R706C	SMARCA1_uc004eup.3_Missense_Mutation_p.R694C|SMARCA1_uc011muk.1_Missense_Mutation_p.R706C|SMARCA1_uc011mul.1_Missense_Mutation_p.R694C	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	706					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4																		---	---	---	---
ZDHHC9	51114	broad.mit.edu	37	X	128948693	128948693	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128948693A>G	uc004euv.2	-	5	935	c.566T>C	c.(565-567)CTT>CCT	p.L189P	ZDHHC9_uc004euw.2_Missense_Mutation_p.L189P|ZDHHC9_uc004eux.1_Missense_Mutation_p.L189P|ZDHHC9_uc004euy.1_Missense_Mutation_p.L116P	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9	189	Helical; (Potential).|DHHC-type.					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ZDHHC9	51114	broad.mit.edu	37	X	128957767	128957767	+	Silent	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128957767A>G	uc004euv.2	-	4	744	c.375T>C	c.(373-375)CGT>CGC	p.R125R	ZDHHC9_uc004euw.2_Silent_p.R125R|ZDHHC9_uc004eux.1_Silent_p.R125R|ZDHHC9_uc004euy.1_Silent_p.R52R	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9	125	Cytoplasmic (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
BCORL1	63035	broad.mit.edu	37	X	129149510	129149510	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129149510C>A	uc004evb.1	+	4	2876	c.2762C>A	c.(2761-2763)CCT>CAT	p.P921H	BCORL1_uc010nrd.1_Missense_Mutation_p.P823H	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	921					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7																		---	---	---	---
BCORL1	63035	broad.mit.edu	37	X	129162713	129162713	+	Silent	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129162713T>C	uc004evb.1	+	8	4296	c.4182T>C	c.(4180-4182)GAT>GAC	p.D1394D	BCORL1_uc010nrd.1_Silent_p.D1166D|BCORL1_uc004evc.1_Silent_p.D156D	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	1394					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7																OREG0019921	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
IGSF1	3547	broad.mit.edu	37	X	130410036	130410036	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130410036A>T	uc004ewd.2	-	15	3033	c.2795T>A	c.(2794-2796)GTT>GAT	p.V932D	IGSF1_uc004ewe.3_Missense_Mutation_p.V926D|IGSF1_uc004ewf.2_Missense_Mutation_p.V912D	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	932	Extracellular (Potential).|Ig-like C2-type 9.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
FAM122C	159091	broad.mit.edu	37	X	133941656	133941656	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133941656T>C	uc004exz.1	+	1	433	c.28T>C	c.(28-30)TTC>CTC	p.F10L	FAM122C_uc010nru.1_Missense_Mutation_p.F46L|FAM122C_uc004exw.2_Missense_Mutation_p.F10L|FAM122C_uc004exx.2_RNA|FAM122C_uc011mvq.1_RNA|FAM122C_uc004exy.1_Missense_Mutation_p.F10L	NM_138819	NP_620174	Q6P4D5	F222C_HUMAN	hypothetical protein LOC159091	10											0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
CXorf48	54967	broad.mit.edu	37	X	134303672	134303672	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134303672A>G	uc004eyk.1	-	2	781	c.125T>C	c.(124-126)GTT>GCT	p.V42A	CXorf48_uc004eyl.1_Missense_Mutation_p.V42A	NM_001031705	NP_001026875	Q8WUE5	CX048_HUMAN	hypothetical protein LOC54967 isoform 1	42											0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ZNF449	203523	broad.mit.edu	37	X	134494771	134494771	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134494771A>C	uc004eys.2	+	5	1492	c.1327A>C	c.(1327-1329)AGT>CGT	p.S443R	ZNF449_uc004eyt.2_Missense_Mutation_p.S323R|ZNF449_uc004eyu.2_Missense_Mutation_p.S249R	NM_152695	NP_689908	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	443	C2H2-type 5.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
DDX26B	203522	broad.mit.edu	37	X	134685909	134685909	+	Intron	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134685909T>A	uc004eyw.3	+							NM_182540	NP_872346			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide												0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
FHL1	2273	broad.mit.edu	37	X	135290680	135290680	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135290680A>G	uc004ezo.2	+	5	668	c.568A>G	c.(568-570)ACC>GCC	p.T190A	FHL1_uc010nrz.2_Missense_Mutation_p.T190A|FHL1_uc004ezm.2_RNA|FHL1_uc004ezl.2_Missense_Mutation_p.T190A|FHL1_uc004ezq.2_Intron|FHL1_uc011mvy.1_Missense_Mutation_p.T190A|FHL1_uc011mvz.1_Missense_Mutation_p.T190A|FHL1_uc004ezn.2_Missense_Mutation_p.T190A|FHL1_uc011mwa.1_Missense_Mutation_p.T219A|FHL1_uc011mwb.1_RNA|FHL1_uc004ezp.2_Missense_Mutation_p.T206A|FHL1_uc004ezr.2_Silent_p.L8L	NM_001159702	NP_001153174	Q13642	FHL1_HUMAN	four and a half LIM domains 1 isoform 1	190	LIM zinc-binding 3.				cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135313712	135313712	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135313712G>A	uc004ezt.2	-	8	1495	c.1404C>T	c.(1402-1404)GAC>GAT	p.D468D	MAP7D3_uc004ezs.2_Silent_p.D432D|MAP7D3_uc011mwc.1_Silent_p.D450D|MAP7D3_uc010nsa.1_Silent_p.D426D	NM_024597	NP_078873	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	468						cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
VGLL1	51442	broad.mit.edu	37	X	135630774	135630774	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135630774C>T	uc004ezy.2	+	3	411	c.241C>T	c.(241-243)CGT>TGT	p.R81C	MIR934_hsa-mir-934|MI0005756_5'Flank	NM_016267	NP_057351	Q99990	VGLL1_HUMAN	vestigial like 1	81					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription coactivator activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MCF2	4168	broad.mit.edu	37	X	138698521	138698521	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138698521C>T	uc004fau.2	-	9	1405	c.1111G>A	c.(1111-1113)GAA>AAA	p.E371K	MCF2_uc004fav.2_Missense_Mutation_p.E371K|MCF2_uc011mwl.1_Missense_Mutation_p.E332K|MCF2_uc010nsh.1_Missense_Mutation_p.E371K|MCF2_uc011mwm.1_Missense_Mutation_p.E332K|MCF2_uc011mwn.1_Missense_Mutation_p.E516K|MCF2_uc004faw.2_Missense_Mutation_p.E431K|MCF2_uc011mwo.1_Missense_Mutation_p.E431K	NM_005369	NP_005360	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	371					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138865330	138865330	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138865330T>C	uc004faz.2	-	17	1871	c.1772A>G	c.(1771-1773)AAT>AGT	p.N591S	ATP11C_uc004fay.2_RNA|ATP11C_uc004fba.2_Missense_Mutation_p.N591S	NM_173694	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C isoform a	591	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
SLITRK2	84631	broad.mit.edu	37	X	144905424	144905424	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144905424C>T	uc004fcd.2	+	5	2471	c.1481C>T	c.(1480-1482)ACG>ATG	p.T494M	SLITRK2_uc010nsp.2_Missense_Mutation_p.T494M|SLITRK2_uc010nso.2_Missense_Mutation_p.T494M|SLITRK2_uc011mwq.1_Missense_Mutation_p.T494M|SLITRK2_uc011mwr.1_Missense_Mutation_p.T494M|SLITRK2_uc011mws.1_Missense_Mutation_p.T494M|SLITRK2_uc004fcg.2_Missense_Mutation_p.T494M|SLITRK2_uc011mwt.1_Missense_Mutation_p.T494M	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	494	Extracellular (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
SLITRK2	84631	broad.mit.edu	37	X	144905693	144905693	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144905693T>A	uc004fcd.2	+	5	2740	c.1750T>A	c.(1750-1752)TTG>ATG	p.L584M	SLITRK2_uc010nsp.2_Missense_Mutation_p.L584M|SLITRK2_uc010nso.2_Missense_Mutation_p.L584M|SLITRK2_uc011mwq.1_Missense_Mutation_p.L584M|SLITRK2_uc011mwr.1_Missense_Mutation_p.L584M|SLITRK2_uc011mws.1_Missense_Mutation_p.L584M|SLITRK2_uc004fcg.2_Missense_Mutation_p.L584M|SLITRK2_uc011mwt.1_Missense_Mutation_p.L584M	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	584	Extracellular (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MIR892A	100126342	broad.mit.edu	37	X	145078239	145078239	+	RNA	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145078239C>T	hsa-mir-892a|MI0005528	-			c.23C>T			MIR890_hsa-mir-890|MI0005533_5'Flank|MIR888_hsa-mir-888|MI0005537_5'Flank																	0																		---	---	---	---
MAGEA8	4107	broad.mit.edu	37	X	149013371	149013371	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149013371C>T	uc004fdw.1	+	3	540	c.325C>T	c.(325-327)CGG>TGG	p.R109W		NM_005364	NP_005355	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	109											0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MTMR1	8776	broad.mit.edu	37	X	149931153	149931153	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149931153G>A	uc004fei.2	+	15	2084	c.1949G>A	c.(1948-1950)CGG>CAG	p.R650Q	MTMR1_uc011mya.1_Missense_Mutation_p.R556Q|MTMR1_uc004feh.1_Missense_Mutation_p.R658Q|MTMR1_uc004fej.2_RNA|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819	Q13613	MTMR1_HUMAN	myotubularin-related protein 1	650						plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PASD1	139135	broad.mit.edu	37	X	150839574	150839574	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150839574A>C	uc004fev.3	+	12	1468	c.1136A>C	c.(1135-1137)AAG>ACG	p.K379T		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	379	Potential.					nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MAGEA10	4109	broad.mit.edu	37	X	151304043	151304043	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151304043T>C	uc004ffk.2	-	5	458	c.50A>G	c.(49-51)CAA>CGA	p.Q17R	MAGEA10_uc004ffl.2_Missense_Mutation_p.Q17R	NM_001011543	NP_001011543	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	17											0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
NSDHL	50814	broad.mit.edu	37	X	152031181	152031181	+	Silent	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152031181C>T	uc004fgt.1	+	6	717	c.456C>T	c.(454-456)GGC>GGT	p.G152G	NSDHL_uc004fgs.1_Silent_p.G152G	NM_001129765	NP_001123237	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	152					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity				0	Acute lymphoblastic leukemia(192;6.56e-05)				NADH(DB00157)													---	---	---	---
ZNF275	10838	broad.mit.edu	37	X	152613218	152613218	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152613218C>T	uc004fhg.1	+	5	1154	c.977C>T	c.(976-978)CCG>CTG	p.P326L	ZNF275_uc011mym.1_Missense_Mutation_p.R359C|ZNF275_uc011myn.1_Missense_Mutation_p.R296C			A6NFS0	A6NFS0_HUMAN	SubName: Full=cDNA FLJ16723 fis, clone UTERU3004418, highly similar to Zinc finger protein 275; SubName: Full=Putative uncharacterized protein ZNF275;	326						intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ATP2B3	492	broad.mit.edu	37	X	152813346	152813346	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152813346G>A	uc004fht.1	+	7	1138	c.1012G>A	c.(1012-1014)GAG>AAG	p.E338K	ATP2B3_uc004fhs.1_Missense_Mutation_p.E338K	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	338	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ARHGAP4	393	broad.mit.edu	37	X	153184481	153184481	+	Silent	SNP	G	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153184481G>T	uc004fjk.1	-	7	879	c.837C>A	c.(835-837)GCC>GCA	p.A279A	ARHGAP4_uc011mzf.1_Silent_p.A256A|ARHGAP4_uc004fjl.1_Silent_p.A319A|ARHGAP4_uc010nup.1_RNA	NM_001666	NP_001657	P98171	RHG04_HUMAN	Rho GTPase activating protein 4 isoform 2	279					apoptosis|cytoskeleton organization|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|Rho protein signal transduction	cytosol|focal adhesion|nucleus	Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			central_nervous_system(1)	1	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ARHGAP4	393	broad.mit.edu	37	X	153184643	153184643	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153184643T>C	uc004fjk.1	-	6	818	c.776A>G	c.(775-777)AAC>AGC	p.N259S	ARHGAP4_uc011mzf.1_Missense_Mutation_p.N236S|ARHGAP4_uc004fjl.1_Missense_Mutation_p.N299S|ARHGAP4_uc010nup.1_RNA	NM_001666	NP_001657	P98171	RHG04_HUMAN	Rho GTPase activating protein 4 isoform 2	259					apoptosis|cytoskeleton organization|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|Rho protein signal transduction	cytosol|focal adhesion|nucleus	Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			central_nervous_system(1)	1	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153219884	153219884	+	Silent	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153219884G>A	uc004fjp.2	-	17	4494	c.3966C>T	c.(3964-3966)TGC>TGT	p.C1322C		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	1322	HCF repeat 6.				cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
IRAK1	3654	broad.mit.edu	37	X	153278860	153278860	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153278860G>A	uc004fjs.1	-	12	1643	c.1564C>T	c.(1564-1566)CAG>TAG	p.Q522*	IRAK1_uc004fjr.1_Intron|IRAK1_uc004fjt.1_Nonsense_Mutation_p.Q443*|IRAK1_uc010nur.2_Intron	NM_001569	NP_001560	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	522					activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|lipopolysaccharide-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein autophosphorylation|protein oligomerization|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transmembrane receptor protein serine/threonine kinase signaling pathway	cytosol|endosome membrane|interleukin-1 receptor complex	ATP binding|NF-kappaB-inducing kinase activity|protein binding|protein heterodimerization activity|protein homodimerization activity|ubiquitin-protein ligase activity			lung(5)|ovary(2)|breast(1)|central_nervous_system(1)	9	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
TKTL1	8277	broad.mit.edu	37	X	153524229	153524229	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153524229C>T	uc004fkg.2	+	1	203	c.17C>T	c.(16-18)GCG>GTG	p.A6V	TEX28_uc004fke.2_5'Flank|TEX28_uc004fkf.2_5'Flank|TEX28_uc010nut.1_5'Flank|TKTL1_uc011mzl.1_Missense_Mutation_p.A6V|TKTL1_uc011mzm.1_Missense_Mutation_p.A6V	NM_012253	NP_036385	P51854	TKTL1_HUMAN	transketolase-like 1 isoform a	6					glucose catabolic process|thiamine metabolic process	cytoplasm|nucleus	metal ion binding|transketolase activity			ovary(3)|skin(1)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
ATP6AP1	537	broad.mit.edu	37	X	153662013	153662013	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4362-01	TCGA-BR-4362-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153662013A>G	uc004flf.1	+	6	692	c.631A>G	c.(631-633)AAG>GAG	p.K211E	ATP6AP1_uc004flg.1_RNA|ATP6AP1_uc004flh.1_Missense_Mutation_p.K171E	NM_001183	NP_001174	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory	211					ATP hydrolysis coupled proton transport	integral to membrane|proton-transporting V-type ATPase, V1 domain|vacuolar membrane	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(3)|breast(1)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
