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
NBPF1	55672	broad.mit.edu	37	1	16894081	16894082	+	Intron	DEL	AG	-	-	rs35523431		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16894081_16894082delAG	uc009vos.1	-						NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)														---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54871709	54871710	+	5'UTR	INS	-	CGCCGC	CGCCGC			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54871709_54871710insCGCCGC	uc001cxe.2	-	1					SSBP3_uc001cxf.2_5'UTR|SSBP3_uc001cxg.2_5'UTR	NM_145716	NP_663768			single stranded DNA binding protein 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	109051247	109051248	+	IGR	DEL	AG	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109051247_109051248delAG								NBPF6 (37988 upstream) : FAM102B (51723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	52032516	52032518	+	IGR	DEL	GTG	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52032516_52032518delGTG								NRXN1 (772842 upstream) : None (None downstream)																																			---	---	---	---
SUCLG2	8801	broad.mit.edu	37	3	67659682	67659699	+	Intron	DEL	CACCATGTGATTCCTGCA	-	-	rs71830786		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67659682_67659699delCACCATGTGATTCCTGCA	uc003dna.3	-							NM_003848	NP_003839			succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)													---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129195789	129195789	+	Intron	DEL	T	-	-	rs10575192		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129195789delT	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc011bkz.1_Intron	NM_052989	NP_443715			WD repeat domain 10 isoform 2						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																		---	---	---	---
USP13	8975	broad.mit.edu	37	3	179501649	179501649	+	Intron	DEL	A	-	-	rs72449152		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179501649delA	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)															---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54794342	54794344	+	Intron	DEL	AGC	-	-	rs61277036	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54794342_54794344delAGC	uc003haa.2	+							NM_006206	NP_006197			platelet-derived growth factor receptor alpha						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)			---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37162787	37162787	+	Intron	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37162787delT	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	78004488	78004489	+	IGR	DEL	TT	-	-	rs146198437		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78004488_78004489delTT								LHFPL2 (59840 upstream) : ARSB (68550 downstream)																																			---	---	---	---
SLC35B3	51000	broad.mit.edu	37	6	8434774	8434774	+	Intron	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8434774delT	uc010joe.2	-						uc003mye.2_5'Flank|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Intron|SLC35B3_uc011did.1_Intron|SLC35B3_uc003myd.2_Intron|SLC35B3_uc010jof.2_Intron|SLC35B3_uc011die.1_Intron	NM_001142541	NP_001136013			solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)																	---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32497712	32497713	+	Intron	INS	-	A	A	rs146725750	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									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																		---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158579538	158579538	+	Intron	DEL	A	-	-	rs111829898		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158579538delA	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)														---	---	---	---
MAP3K4	4216	broad.mit.edu	37	6	161413044	161413045	+	In_Frame_Ins	INS	-	CCG	CCG			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161413044_161413045insCCG	uc003qtn.2	+	1	223_224	c.81_82insCCG	c.(79-84)insCCG	p.36_37insP	MAP3K4_uc010kkc.1_In_Frame_Ins_p.36_37insP|MAP3K4_uc003qto.2_In_Frame_Ins_p.36_37insP|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	36_37	Poly-Pro.				activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3994080	3994081	+	Intron	INS	-	CA	CA			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3994080_3994081insCA	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						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)														---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86547640	86547641	+	Intron	DEL	AA	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86547640_86547641delAA	uc011kha.1	-						KIAA1324L_uc003uif.1_Intron|KIAA1324L_uc011kgz.1_Intron|KIAA1324L_uc003uie.2_Intron	NM_001142749	NP_001136221			hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)																	---	---	---	---
FSCN3	29999	broad.mit.edu	37	7	127234099	127234100	+	Intron	DEL	TG	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127234099_127234100delTG	uc003vmd.1	+						FSCN3_uc003vmc.1_Intron|FSCN3_uc011kog.1_Intron|FSCN3_uc011koh.1_Intron|FSCN3_uc010llc.1_Intron	NM_020369	NP_065102			fascin 3							actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68123601	68123601	+	Intron	DEL	G	-	-	rs149755855	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68123601delG	uc003xxo.1	-						ARFGEF1_uc003xxl.1_Intron|ARFGEF1_uc003xxn.1_Intron	NM_006421	NP_006412			brefeldin A-inhibited guanine						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)															---	---	---	---
RECK	8434	broad.mit.edu	37	9	36123173	36123173	+	3'UTR	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36123173delT	uc003zyv.2	+	21					RECK_uc003zyw.2_3'UTR|RECK_uc003zyx.2_RNA	NM_021111	NP_066934			RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12870642	12870643	+	Intron	INS	-	A	A	rs72066238		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12870642_12870643insA	uc001ilo.2	+							NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	95964531	95964532	+	Intron	INS	-	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95964531_95964532insA	uc001kjk.2	+						PLCE1_uc010qnx.1_Intron|PLCE1_uc001kjm.2_Intron	NM_016341	NP_057425			phospholipase C, epsilon 1 isoform 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)																---	---	---	---
TBC1D12	23232	broad.mit.edu	37	10	96163412	96163413	+	Intron	INS	-	CGGAGC	CGGAGC	rs150327271	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96163412_96163413insCGGAGC	uc001kjr.2	+							NM_015188	NP_056003			TBC1 domain family, member 12							intracellular	Rab GTPase activator activity				0		Colorectal(252;0.0429)																---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114724571	114724572	+	Intron	INS	-	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114724571_114724572insG	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128836112	128836112	+	Intron	DEL	C	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128836112delC	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16208201	16208201	+	Intron	DEL	C	-	-	rs78363793		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16208201delC	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
ITGA7	3679	broad.mit.edu	37	12	56082507	56082507	+	Intron	DEL	A	-	-	rs35887029		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56082507delA	uc001shh.2	-						ITGA7_uc001shg.2_Intron|ITGA7_uc010sps.1_Intron|ITGA7_uc001shf.2_5'Flank|ITGA7_uc009znw.2_Intron|ITGA7_uc009znx.2_Intron	NM_001144996	NP_001138468			integrin alpha 7 isoform 1 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape	integrin complex	receptor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
RFC5	5985	broad.mit.edu	37	12	118458889	118458889	+	Intron	DEL	A	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118458889delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	81932380	81932381	+	IGR	INS	-	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81932380_81932381insT								None (None upstream) : None (None downstream)																																			---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92620656	92620657	+	Intron	INS	-	AT	AT			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92620656_92620657insAT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	28948128	28948129	+	5'Flank	INS	-	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28948128_28948129insA	uc001zcc.2	+						uc001zcd.2_5'Flank					DQ578707																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	101109346	101109346	+	IGR	DEL	G	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101109346delG								LASS3 (24421 upstream) : LINS1 (90 downstream)																																			---	---	---	---
SLC9A3R2	9351	broad.mit.edu	37	16	2077400	2077400	+	Intron	DEL	G	-	-	rs113766720		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2077400delG	uc002coi.2	+						SLC9A3R2_uc002coj.2_Intron	NM_001130012	NP_001123484			solute carrier family 9 isoform 3 regulator 2						protein complex assembly	apical plasma membrane|endomembrane system|nucleus	beta-catenin binding|phosphatase binding|protein C-terminus binding|receptor binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	32399771	32399772	+	IGR	DEL	TG	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32399771_32399772delTG								HERC2P4 (235897 upstream) : TP53TG3B (285069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	88613881	88613882	+	IGR	DEL	AG	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88613881_88613882delAG								ZFPM1 (12308 upstream) : ZC3H18 (22907 downstream)																																			---	---	---	---
SARM1	23098	broad.mit.edu	37	17	26686181	26686182	+	Intron	INS	-	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26686181_26686182insA	uc010wah.1	+						POLDIP2_uc002haz.2_5'Flank|POLDIP2_uc010wag.1_5'Flank|TMEM199_uc002hba.2_Intron	NM_152464	NP_689677			transmembrane protein 199						innate immune response	cytoplasm|intrinsic to membrane	binding|transmembrane receptor activity				0	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3013987	3013987	+	Intron	DEL	T	-	-	rs67060467		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3013987delT	uc002lww.2	-						TLE2_uc010xhb.1_Intron|TLE2_uc010dth.2_Intron|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron|TLE2_uc010xhd.1_Intron	NM_003260	NP_003251			transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				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)														---	---	---	---
DENND1C	79958	broad.mit.edu	37	19	6469735	6469736	+	Intron	INS	-	T	T	rs74772168		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6469735_6469736insT	uc002mfe.2	-						DENND1C_uc002mfb.2_Intron|DENND1C_uc002mfc.2_Intron|DENND1C_uc002mfd.2_Intron|DENND1C_uc010xje.1_Intron	NM_024898	NP_079174			DENN/MADD domain containing 1C							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1																		---	---	---	---
SEC23B	10483	broad.mit.edu	37	20	18485751	18485751	+	5'Flank	DEL	A	-	-	rs74180905		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18485751delA	uc002wqz.1	+						SEC23B_uc002wra.1_5'Flank|SEC23B_uc002wrb.1_5'Flank|SEC23B_uc010zsb.1_5'Flank|SEC23B_uc002wrc.1_5'Flank	NM_006363	NP_006354			Sec23 homolog B						ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62074838	62074843	+	Intron	DEL	CACCAT	-	-	rs111782870		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074838_62074843delCACCAT	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105			potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)													---	---	---	---
IL10RB	3588	broad.mit.edu	37	21	34660710	34660711	+	Intron	DEL	AG	-	-	rs66834406		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660710_34660711delAG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619			interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37619142	37619151	+	Intron	DEL	TTATGTTATG	-	-	rs67162183		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37619142_37619151delTTATGTTATG	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron|DOPEY2_uc002yvh.2_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CBS	875	broad.mit.edu	37	21	44476000	44476001	+	Intron	INS	-	T	T	rs79861734		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44476000_44476001insT	uc002zcu.2	-						CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron|CBS_uc002zcx.2_3'UTR	NM_000071	NP_000062			cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	6451000	6451002	+	IGR	DEL	CAC	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6451000_6451002delCAC								NLGN4X (304294 upstream) : VCX3A (658 downstream)																																			---	---	---	---
ELK1	2002	broad.mit.edu	37	X	47496205	47496207	+	3'UTR	DEL	GGT	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47496205_47496207delGGT	uc004dik.3	-	7					ELK1_uc010nhv.2_3'UTR|ELK1_uc010nhw.2_3'UTR|ELK1_uc004dil.3_RNA	NM_001114123	NP_001107595			ELK1 protein						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 transcription from RNA polymerase II promoter|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		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
TMEM52	339456	broad.mit.edu	37	1	1850628	1850636	+	In_Frame_Del	DEL	AGCGGCAGG	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1850628_1850636delAGCGGCAGG	uc001aij.2	-	1	105_113	c.69_77delCCTGCCGCT	c.(67-78)CTCCTGCCGCTG>CTG	p.23_26LLPL>L	TMEM52_uc001aii.2_5'Flank	NM_178545	NP_848640	Q8NDY8	TMM52_HUMAN	transmembrane protein 52 precursor	23_26						integral to membrane					0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8050557	8050557	+	IGR	DEL	T	-	-	rs151219071		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8050557delT								PARK7 (5216 upstream) : ERRFI1 (21223 downstream)																																			---	---	---	---
IQGAP3	128239	broad.mit.edu	37	1	156513579	156513580	+	Intron	INS	-	T	T	rs138046722	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156513579_156513580insT	uc001fpf.2	-							NM_178229	NP_839943			IQ motif containing GTPase activating protein 3						small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	200843307	200843308	+	IGR	INS	-	CCCG	CCCG	rs138315474	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200843307_200843308insCCCG								GPR25 (56 upstream) : C1orf106 (17331 downstream)																																			---	---	---	---
WDR43	23160	broad.mit.edu	37	2	29149282	29149283	+	Intron	INS	-	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29149282_29149283insT	uc002rmo.2	+						SNORD53_uc002rmq.1_5'Flank	NM_015131	NP_055946			WD repeat domain 43							nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42202061	42202061	+	Intron	DEL	G	-	-	rs59260540		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42202061delG	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc003ckz.3_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81541828	81541829	+	Intron	INS	-	TTCTCCCT	TTCTCCCT	rs149554537	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81541828_81541829insTTCTCCCT	uc003dqg.2	-							NM_000158	NP_000149			glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
CP	1356	broad.mit.edu	37	3	148899609	148899609	+	Intron	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									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)													---	---	---	---
CD38	952	broad.mit.edu	37	4	15826305	15826306	+	Intron	DEL	AC	-	-	rs3832313		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15826305_15826306delAC	uc011bxc.1	+						CD38_uc003goj.1_Intron|CD38_uc003gol.1_Intron	NM_001775	NP_001766			CD38 antigen						B cell receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of apoptosis|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of transcription, DNA-dependent|response to drug	integral to membrane|plasma membrane	binding|NAD+ nucleosidase activity|receptor activity			ovary(2)	2																		---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41699388	41699388	+	3'UTR	DEL	T	-	-	rs113753743		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41699388delT	uc003gvu.3	+	27					LIMCH1_uc003gvv.3_3'UTR|LIMCH1_uc003gvw.3_3'UTR|LIMCH1_uc003gvx.3_3'UTR|LIMCH1_uc003gwe.3_3'UTR|LIMCH1_uc003gvy.3_3'UTR|LIMCH1_uc003gwa.3_3'UTR|LIMCH1_uc003gvz.3_3'UTR|LIMCH1_uc011byu.1_3'UTR|LIMCH1_uc003gwc.3_3'UTR|LIMCH1_uc003gwd.3_3'UTR|LIMCH1_uc011byv.1_3'UTR|LIMCH1_uc011byw.1_3'UTR|LIMCH1_uc010ifv.2_RNA	NM_014988	NP_055803			LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
C4orf36	132989	broad.mit.edu	37	4	87812446	87812447	+	Intron	INS	-	AA	AA	rs34250498		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87812446_87812447insAA	uc003hqe.3	-							NM_144645	NP_653246			hypothetical protein LOC132989												0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)														---	---	---	---
SLC9A3	6550	broad.mit.edu	37	5	474775	474775	+	Intron	DEL	G	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:474775delG	uc003jbe.2	-						SLC9A3_uc011clx.1_Intron|LOC25845_uc003jbd.2_5'Flank|LOC25845_uc010itb.1_5'Flank	NM_004174	NP_004165			solute carrier family 9 (sodium/hydrogen							cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79797285	79797286	+	Intron	DEL	AA	-	-	rs34586243		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79797285_79797286delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	95170388	95170388	+	IGR	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95170388delT								GLRX (11811 upstream) : C5orf27 (17548 downstream)																																			---	---	---	---
SLC35B3	51000	broad.mit.edu	37	6	8434774	8434774	+	Intron	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8434774delT	uc010joe.2	-						uc003mye.2_5'Flank|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Intron|SLC35B3_uc011did.1_Intron|SLC35B3_uc003myd.2_Intron|SLC35B3_uc010jof.2_Intron|SLC35B3_uc011die.1_Intron	NM_001142541	NP_001136013			solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)																	---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158579538	158579538	+	Intron	DEL	A	-	-	rs111829898		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158579538delA	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)														---	---	---	---
MAP3K4	4216	broad.mit.edu	37	6	161413044	161413045	+	In_Frame_Ins	INS	-	CCG	CCG			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161413044_161413045insCCG	uc003qtn.2	+	1	223_224	c.81_82insCCG	c.(79-84)insCCG	p.36_37insP	MAP3K4_uc010kkc.1_In_Frame_Ins_p.36_37insP|MAP3K4_uc003qto.2_In_Frame_Ins_p.36_37insP|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	36_37	Poly-Pro.				activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)														---	---	---	---
SUN1	23353	broad.mit.edu	37	7	887835	887836	+	Intron	INS	-	A	A	rs74208471		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:887835_887836insA	uc011jvp.1	+						SUN1_uc003sje.1_Intron|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Intron|SUN1_uc003sjg.2_Intron|SUN1_uc011jvr.1_5'Flank|SUN1_uc003sji.2_5'Flank	NM_001130965	NP_001124437			unc-84 homolog A isoform a						cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0																		---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3994080	3994081	+	Intron	INS	-	CA	CA			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3994080_3994081insCA	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						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)														---	---	---	---
STEAP1	26872	broad.mit.edu	37	7	89791082	89791082	+	Intron	DEL	A	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89791082delA	uc003ujx.2	+						STEAP1_uc010lem.2_Intron	NM_012449	NP_036581			six transmembrane epithelial antigen of the						electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)																	---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131347294	131347294	+	Intron	DEL	C	-	-	rs11382658		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131347294delC	uc004bvl.3	+						SPTAN1_uc011mbg.1_Intron|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118			spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10																		---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18825171	18825172	+	Intron	INS	-	CTTTT	CTTTT	rs139064706	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18825171_18825172insCTTTT	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron|NSUN6_uc001iqb.2_Intron	NM_201596	NP_963890			calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	43063100	43063101	+	IGR	INS	-	A	A	rs34202394		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43063100_43063101insA								ZNF37B (14820 upstream) : ZNF33B (6532 downstream)																																			---	---	---	---
CAPRIN1	4076	broad.mit.edu	37	11	34098283	34098284	+	Intron	INS	-	T	T	rs76547269		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34098283_34098284insT	uc001mvh.1	+						CAPRIN1_uc001mvg.2_Intron|CAPRIN1_uc001mvi.2_Intron|CAPRIN1_uc001mvj.1_Intron	NM_005898	NP_005889			membrane component chromosome 11 surface marker						negative regulation of translation|positive regulation of dendrite morphogenesis|positive regulation of dendritic spine morphogenesis	cytoplasmic mRNA processing body|cytosol|dendrite|integral to plasma membrane|stress granule	protein binding|RNA binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	81932380	81932381	+	IGR	INS	-	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81932380_81932381insT								None (None upstream) : None (None downstream)																																			---	---	---	---
ABHD12B	145447	broad.mit.edu	37	14	51348148	51348148	+	Intron	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51348148delT	uc001wys.2	+						ABHD12B_uc001wyq.2_Intron|ABHD12B_uc001wyr.2_Intron|ABHD12B_uc010any.2_Intron	NM_181533	NP_853511			abhydrolase domain containing 12B isoform b								hydrolase activity			breast(1)	1	all_epithelial(31;0.00481)|Breast(41;0.148)																	---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92620656	92620657	+	Intron	INS	-	AT	AT			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92620656_92620657insAT	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)														---	---	---	---
TMEM121	80757	broad.mit.edu	37	14	105996050	105996052	+	In_Frame_Del	DEL	GCC	-	-	rs10569304		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105996050_105996052delGCC	uc001yrp.1	+	2	1030_1032	c.879_881delGCC	c.(877-882)GTGCCG>GTG	p.P299del	ADAM6_uc010tyt.1_Intron|uc001yrr.2_5'Flank	NM_025268	NP_079544	Q9BTD3	TM121_HUMAN	hole protein	299	Pro-rich.					integral to membrane					0		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.0959)|all cancers(159;0.235)														---	---	---	---
STARD5	80765	broad.mit.edu	37	15	81611436	81611436	+	Intron	DEL	A	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81611436delA	uc002bgm.2	-						STARD5_uc002bgn.2_Intron	NM_181900	NP_871629			StAR-related lipid transfer protein 5						C21-steroid hormone biosynthetic process|lipid transport	cytosol	lipid binding			ovary(1)	1																		---	---	---	---
UBE2Q2P1	388165	broad.mit.edu	37	15	85077360	85077360	+	Intron	DEL	A	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85077360delA	uc002bkn.1	-							NR_003661				Homo sapiens cDNA FLJ43276 fis, clone KIDNE2011532, moderately similar to Homo sapiens melanoma-associated chondroitin sulfate proteoglycan 4.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	101109346	101109346	+	IGR	DEL	G	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101109346delG								LASS3 (24421 upstream) : LINS1 (90 downstream)																																			---	---	---	---
CLCN7	1186	broad.mit.edu	37	16	1509323	1509324	+	Intron	DEL	AA	-	-	rs67316943		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1509323_1509324delAA	uc002clv.2	-						CLCN7_uc002clw.2_Intron	NM_001287	NP_001278			chloride channel 7 isoform a							integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Hepatocellular(780;0.0893)																---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81712240	81712241	+	Intron	INS	-	C	C	rs142187160	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81712240_81712241insC	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron|CMIP_uc002fgr.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	88226611	88226611	+	IGR	DEL	G	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88226611delG								BANP (115688 upstream) : ZNF469 (267268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	88613881	88613882	+	IGR	DEL	AG	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88613881_88613882delAG								ZFPM1 (12308 upstream) : ZC3H18 (22907 downstream)																																			---	---	---	---
AOC3	8639	broad.mit.edu	37	17	41006869	41006869	+	Intron	DEL	T	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41006869delT	uc002ibv.2	+							NM_003734	NP_003725			amine oxidase, copper containing 3 precursor						amine metabolic process|cell adhesion|inflammatory response	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)													---	---	---	---
GRIN2C	2905	broad.mit.edu	37	17	72858493	72858494	+	5'Flank	INS	-	C	C	rs150874217	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72858493_72858494insC	uc002jlt.1	-						GRIN2C_uc010wrh.1_5'Flank|GRIN2C_uc002jlu.1_5'Flank|GRIN2C_uc002jlv.1_5'Flank	NM_000835	NP_000826			N-methyl-D-aspartate receptor subunit 2C						glutamate signaling pathway	cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|N-methyl-D-aspartate selective glutamate receptor activity			ovary(2)|breast(2)	4	all_lung(278;0.172)|Lung NSC(278;0.207)				Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)											OREG0024719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	19	7440297	7440297	+	IGR	DEL	A	-	-			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7440297delA								INSR (146286 upstream) : ARHGEF18 (7423 downstream)																																			---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49845484	49845485	+	Intron	INS	-	CCACATCAGTT	CCACATCAGTT	rs149352076	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49845484_49845485insCCACATCAGTT	uc002pnj.2	-						uc002pnb.1_5'Flank|TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589			TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)														---	---	---	---
SEC23B	10483	broad.mit.edu	37	20	18485751	18485751	+	5'Flank	DEL	A	-	-	rs74180905		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18485751delA	uc002wqz.1	+						SEC23B_uc002wra.1_5'Flank|SEC23B_uc002wrb.1_5'Flank|SEC23B_uc010zsb.1_5'Flank|SEC23B_uc002wrc.1_5'Flank	NM_006363	NP_006354			Sec23 homolog B						ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
NINL	22981	broad.mit.edu	37	20	25554991	25554992	+	Intron	INS	-	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25554991_25554992insT	uc002wux.1	-						NINL_uc010gdn.1_Intron|NINL_uc010gdo.1_Intron	NM_025176	NP_079452			ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
IL10RB	3588	broad.mit.edu	37	21	34660710	34660711	+	Intron	DEL	AG	-	-	rs66834406		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660710_34660711delAG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619			interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37619142	37619151	+	Intron	DEL	TTATGTTATG	-	-	rs67162183		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37619142_37619151delTTATGTTATG	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron|DOPEY2_uc002yvh.2_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10011967	10011967	+	IGR	DEL	T	-	-	rs146357774		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10011967delT								TTTY22 (361113 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13601466	13601467	+	IGR	INS	-	T	T	rs112972965		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13601466_13601467insT								None (None upstream) : None (None downstream)																																			---	---	---	---
MTHFR	4524	broad.mit.edu	37	1	11861224	11861224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11861224G>A	uc001atc.1	-	3	653	c.469C>T	c.(469-471)CGG>TGG	p.R157W	MTHFR_uc001atb.1_Missense_Mutation_p.R180W	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	157			R -> Q (in MTHFRD).		blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	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)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)													---	---	---	---
LHX8	431707	broad.mit.edu	37	1	75602794	75602794	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75602794G>A	uc001dgo.2	+	4	779	c.115G>A	c.(115-117)GAG>AAG	p.E39K	LHX8_uc001dgq.2_5'UTR	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	39						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
FLG	2312	broad.mit.edu	37	1	152283625	152283625	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283625C>A	uc001ezu.1	-	3	3773	c.3737G>T	c.(3736-3738)AGC>ATC	p.S1246I	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1246	Ser-rich.|Filaggrin 7.				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				---	---	---	---
DCST2	127579	broad.mit.edu	37	1	154999201	154999201	+	Intron	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154999201A>G	uc001fgm.2	-						DCST2_uc009wpb.2_Intron	NM_144622	NP_653223			DC-STAMP domain containing 2							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)															---	---	---	---
OR6N1	128372	broad.mit.edu	37	1	158735950	158735950	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158735950G>C	uc010piq.1	-	1	523	c.523C>G	c.(523-525)CAG>GAG	p.Q175E		NM_001005185	NP_001005185	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N,	175	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
JMJD4	65094	broad.mit.edu	37	1	227921166	227921166	+	Silent	SNP	C	A	A	rs148217485	byFrequency	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227921166C>A	uc001hrb.2	-	4	909	c.909G>T	c.(907-909)GCG>GCT	p.A303A	SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_5'Flank|SNAP47_uc001hre.2_5'Flank|SNAP47_uc001hrf.2_5'Flank|LOC100130093_uc001hqx.3_RNA|LOC100130093_uc001hqy.3_RNA|JMJD4_uc001hrc.2_Silent_p.A303A	NM_023007	NP_075383	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4 isoform 1	303	JmjC.										0		Prostate(94;0.0885)																---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137983022	137983022	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137983022C>T	uc003esa.1	+	15	1592	c.1225C>T	c.(1225-1227)CAG>TAG	p.Q409*	TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Nonsense_Mutation_p.Q392*|ARMC8_uc011bmg.1_Nonsense_Mutation_p.Q356*|ARMC8_uc011bmh.1_Nonsense_Mutation_p.Q350*|ARMC8_uc003esb.1_Nonsense_Mutation_p.Q381*|ARMC8_uc003esc.1_Nonsense_Mutation_p.Q181*|ARMC8_uc003esf.1_5'UTR	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2	423	ARM 9.						binding				0																		---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142094635	142094635	+	Intron	SNP	C	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142094635C>G	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron	NM_019001	NP_061874			5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3																		---	---	---	---
TMPRSS11F	389208	broad.mit.edu	37	4	68934540	68934540	+	Intron	SNP	G	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68934540G>T	uc003hdt.1	-						LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron	NM_207407	NP_997290			transmembrane protease, serine 11F						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
MIER3	166968	broad.mit.edu	37	5	56234714	56234714	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56234714T>A	uc003jrd.1	-	4	336	c.311A>T	c.(310-312)GAC>GTC	p.D104V	MIER3_uc003jqz.1_Missense_Mutation_p.D41V|MIER3_uc003jra.1_Missense_Mutation_p.D104V|MIER3_uc003jrb.1_5'UTR|MIER3_uc003jrc.1_Missense_Mutation_p.D109V	NM_152622	NP_689835	Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family	104					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)														---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137485477	137485477	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137485477G>A	uc003lcf.1	-	23	3185	c.3130C>T	c.(3130-3132)CAG>TAG	p.Q1044*	BRD8_uc003lcc.1_Intron	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2	1044					cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
SPDEF	25803	broad.mit.edu	37	6	34508912	34508912	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34508912C>T	uc003ojq.1	-	3	898	c.483G>A	c.(481-483)TGG>TGA	p.W161*	SPDEF_uc011dsq.1_Nonsense_Mutation_p.W161*	NM_012391	NP_036523	O95238	SPDEF_HUMAN	SAM pointed domain containing ets transcription	161	PNT.				negative regulation of survival gene product expression|negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(3)|ovary(1)|central_nervous_system(1)	5																		---	---	---	---
TEK	7010	broad.mit.edu	37	9	27192629	27192629	+	Intron	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27192629G>A	uc003zqi.3	+						TEK_uc011lno.1_Intron|TEK_uc011lnp.1_Intron|TEK_uc003zqj.1_Intron	NM_000459	NP_000450			TEK tyrosine kinase, endothelial precursor						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)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117061471	117061471	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117061471G>A	uc001lcg.2	+	17	3122	c.2736G>A	c.(2734-2736)ACG>ACA	p.T912T	ATRNL1_uc010qsm.1_Silent_p.T87T|ATRNL1_uc010qsn.1_RNA	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	912	PSI 4.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)														---	---	---	---
MRGPRX2	117194	broad.mit.edu	37	11	19077900	19077900	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19077900C>T	uc001mph.2	-	2	138	c.50G>A	c.(49-51)GGA>GAA	p.G17E		NM_054030	NP_473371	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	17	Extracellular (Potential).				sensory perception of pain|sleep	plasma membrane	G-protein coupled receptor activity|neuropeptide binding			ovary(1)	1																		---	---	---	---
PDHX	8050	broad.mit.edu	37	11	35006231	35006231	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35006231G>C	uc001mvt.2	+	9	1664	c.1138G>C	c.(1138-1140)GAT>CAT	p.D380H	PDHX_uc010rep.1_Missense_Mutation_p.D365H|PDHX_uc010req.1_Missense_Mutation_p.D153H	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	380					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)															---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75155552	75155552	+	Intron	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75155552G>C	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc001own.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron|GDPD5_uc009yue.1_Intron	NM_030792	NP_110419			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1																		---	---	---	---
NECAP1	25977	broad.mit.edu	37	12	8242546	8242546	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8242546A>T	uc001qtx.2	+	2	188	c.110A>T	c.(109-111)AAA>ATA	p.K37I	NECAP1_uc001qty.2_5'UTR	NM_015509	NP_056324	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	37					endocytosis|protein transport	clathrin coated vesicle membrane|plasma membrane				ovary(1)	1				Kidney(36;0.0915)														---	---	---	---
STYK1	55359	broad.mit.edu	37	12	10780324	10780324	+	Splice_Site	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10780324C>A	uc001qys.2	-	7	1155	c.634_splice	c.e7-1	p.D212_splice		NM_018423	NP_060893			serine/threonine/tyrosine kinase 1							integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8															HNSCC(73;0.22)			---	---	---	---
SLC38A4	55089	broad.mit.edu	37	12	47172329	47172329	+	Silent	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47172329A>G	uc001rpi.2	-	11	1347	c.948T>C	c.(946-948)CAT>CAC	p.H316H	SLC38A4_uc001rpj.2_Silent_p.H316H	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	316	Extracellular (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Lung SC(27;0.192)|Renal(347;0.236)																	---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122967235	122967235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122967235G>A	uc001ucn.2	-	8	810	c.679C>T	c.(679-681)CCT>TCT	p.P227S	ZCCHC8_uc001ucm.2_5'UTR|ZCCHC8_uc009zxp.2_5'UTR|ZCCHC8_uc009zxq.2_5'UTR	NM_017612	NP_060082	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	227	CCHC-type.					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)														---	---	---	---
NOC4L	79050	broad.mit.edu	37	12	132636625	132636625	+	Intron	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132636625C>A	uc001ujz.1	+							NM_024078	NP_076983			nucleolar complex associated 4 homolog						rRNA processing	integral to membrane|nuclear membrane|nucleolus	protein binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)														---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108518661	108518661	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108518661T>C	uc001vql.2	-	1	800	c.284A>G	c.(283-285)CAG>CGG	p.Q95R		NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	95	Poly-Gln.					integral to membrane	binding			skin(1)	1																		---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28228486	28228486	+	Intron	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28228486C>T	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266			oculocutaneous albinism II						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				---	---	---	---
ZNF75A	7627	broad.mit.edu	37	16	3367328	3367328	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3367328T>G	uc002cut.3	+	6	876	c.350T>G	c.(349-351)TTT>TGT	p.F117C	ZNF75A_uc002cuv.3_RNA	NM_153028	NP_694573	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	117					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50258847	50258847	+	Silent	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50258847T>C	uc010vgo.1	+	10	1544	c.1509T>C	c.(1507-1509)TAT>TAC	p.Y503Y	PAPD5_uc010cbi.2_RNA|PAPD5_uc002efz.2_Silent_p.Y294Y|PAPD5_uc002ega.2_Silent_p.Y294Y	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a	424					cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)														---	---	---	---
ELAC2	60528	broad.mit.edu	37	17	12903546	12903546	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12903546C>T	uc002gnz.3	-	15	1445	c.1350G>A	c.(1348-1350)GCG>GCA	p.A450A	ELAC2_uc002gnu.3_5'UTR|ELAC2_uc002gnv.3_Silent_p.A78A|ELAC2_uc002gnw.3_Silent_p.A108A|ELAC2_uc002gnx.3_Silent_p.A210A|ELAC2_uc010vvo.1_Silent_p.A248A|ELAC2_uc010vvp.1_Silent_p.A431A|ELAC2_uc010vvq.1_Silent_p.A449A|ELAC2_uc010vvr.1_Silent_p.A410A	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	450					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0														Hereditary_Prostate_Cancer				---	---	---	---
FAM83G	644815	broad.mit.edu	37	17	18874692	18874692	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18874692G>A	uc002guw.2	-	6	2619	c.2452C>T	c.(2452-2454)CGG>TGG	p.R818W	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	818										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ZNRF4	148066	broad.mit.edu	37	19	5456633	5456633	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5456633G>A	uc002mca.3	+	1	1208	c.1131G>A	c.(1129-1131)CCG>CCA	p.P377P		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	377	Cytoplasmic (Potential).					integral to membrane	zinc ion binding	p.P377Q(1)		large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)														---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6417055	6417055	+	Silent	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6417055G>C	uc002mer.3	-	12	1235	c.1125C>G	c.(1123-1125)CCC>CCG	p.P375P		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	375	Gly-rich.|KH 3.				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																		---	---	---	---
C3	718	broad.mit.edu	37	19	6697719	6697719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6697719C>T	uc002mfm.2	-	20	2589	c.2527G>A	c.(2527-2529)GAG>AAG	p.E843K		NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	843					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)														---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17104353	17104353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17104353G>A	uc002nfb.2	-	12	1312	c.1280C>T	c.(1279-1281)ACG>ATG	p.T427M		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	380						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
TMEM143	55260	broad.mit.edu	37	19	48836573	48836573	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48836573A>G	uc002pix.1	-	8	1292	c.1283T>C	c.(1282-1284)ATG>ACG	p.M428T	TMEM143_uc002piw.1_RNA|TMEM143_uc002piy.1_Missense_Mutation_p.M393T|TMEM143_uc010xzn.1_Missense_Mutation_p.M363T|TMEM143_uc010elw.1_Missense_Mutation_p.M328T|TMEM143_uc010xzo.1_Missense_Mutation_p.M218T	NM_018273	NP_060743	Q96AN5	TM143_HUMAN	transmembrane protein 143	428						integral to membrane|mitochondrion					0		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)														---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60910072	60910072	+	Intron	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60910072C>T	uc002ycq.2	-							NM_005560	NP_005551			laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12735849	12735849	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12735849G>A	uc004cuz.1	+	16	3410	c.2904G>A	c.(2902-2904)TCG>TCA	p.S968S	FRMPD4_uc011mij.1_Silent_p.S960S	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	968					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13																		---	---	---	---
OFD1	8481	broad.mit.edu	37	X	13753462	13753462	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13753462C>T	uc004cvp.3	+	2	467	c.108C>T	c.(106-108)CTC>CTT	p.L36L	OFD1_uc004cvr.3_5'UTR|OFD1_uc011mil.1_5'UTR|OFD1_uc004cvq.3_5'UTR|OFD1_uc010nen.2_Silent_p.L35L|OFD1_uc004cvs.3_RNA|OFD1_uc004cvu.3_Silent_p.L35L|OFD1_uc004cvv.3_Silent_p.L35L|TRAPPC2_uc010nek.1_5'Flank|TRAPPC2_uc010nel.1_5'Flank|TRAPPC2_uc010nem.1_5'Flank	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	36					cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0																		---	---	---	---
ZFX	7543	broad.mit.edu	37	X	24228401	24228401	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24228401G>A	uc004dbf.2	+	9	1584	c.1326G>A	c.(1324-1326)AGG>AGA	p.R442R	ZFX_uc004dbe.2_3'UTR|ZFX_uc011mjv.1_Silent_p.R481R|ZFX_uc010nfz.2_Silent_p.R98R	NM_003410	NP_003401	P17010	ZFX_HUMAN	zinc finger protein, X-linked	442	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SLC35A2	7355	broad.mit.edu	37	X	48761971	48761971	+	Intron	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48761971C>A	uc004dlo.1	-						SLC35A2_uc011mml.1_3'UTR|SLC35A2_uc004dlp.1_3'UTR|SLC35A2_uc011mmm.1_3'UTR|SLC35A2_uc011mmn.1_3'UTR|SLC35A2_uc004dlr.1_3'UTR|SLC35A2_uc004dlq.2_Missense_Mutation_p.G209W	NM_005660	NP_005651			solute carrier family 35, member A2 isoform a						galactose metabolic process	Golgi membrane|integral to membrane|nucleus	sugar:hydrogen symporter activity|UDP-galactose transmembrane transporter activity			breast(1)	1																		---	---	---	---
MED12	9968	broad.mit.edu	37	X	70357076	70357076	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70357076C>A	uc004dyy.2	+	39	5790	c.5591C>A	c.(5590-5592)CCA>CAA	p.P1864Q	MED12_uc011mpq.1_Missense_Mutation_p.P1864Q|MED12_uc004dyz.2_Missense_Mutation_p.P1864Q|MED12_uc004dza.2_Missense_Mutation_p.P1711Q|MED12_uc010nla.2_Missense_Mutation_p.P490Q	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1864	Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)																	---	---	---	---
ZCCHC13	389874	broad.mit.edu	37	X	73524180	73524180	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73524180C>T	uc004ebs.3	+	1	156	c.79C>T	c.(79-81)CGA>TGA	p.R27*		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	27							nucleic acid binding|zinc ion binding				0																		---	---	---	---
DACH2	117154	broad.mit.edu	37	X	85969733	85969733	+	Intron	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85969733G>A	uc004eew.2	+						DACH2_uc004eex.2_Intron|DACH2_uc010nmq.2_Intron|DACH2_uc011mra.1_Intron|DACH2_uc010nmr.2_Intron|DACH2_uc004eey.2_Intron|DACH2_uc004eez.2_Intron	NM_053281	NP_444511			dachshund 2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5																		---	---	---	---
MCART6	401612	broad.mit.edu	37	X	103349655	103349655	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103349655A>T	uc004elu.2	-	2	467	c.286T>A	c.(286-288)TTT>ATT	p.F96I		NM_001012755	NP_001012773	Q5H9E4	MCAR6_HUMAN	mitochondrial carrier triple repeat 6	96	Helical; Name=2; (Potential).|Solcar 1.				transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
AMOT	154796	broad.mit.edu	37	X	112035177	112035177	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112035177C>T	uc004epr.2	-	6	1809	c.1809G>A	c.(1807-1809)GTG>GTA	p.V603V	AMOT_uc004eps.2_Silent_p.V194V	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	603	Potential.				actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117810670	117810670	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-10A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117810670G>T	uc004eqp.2	+	48	5493	c.5430G>T	c.(5428-5430)GAG>GAT	p.E1810D	DOCK11_uc004eqq.2_Missense_Mutation_p.E1589D	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1810	DHR-2.				blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
MTHFR	4524	broad.mit.edu	37	1	11861224	11861224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11861224G>A	uc001atc.1	-	3	653	c.469C>T	c.(469-471)CGG>TGG	p.R157W	MTHFR_uc001atb.1_Missense_Mutation_p.R180W	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	157			R -> Q (in MTHFRD).		blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	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)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)													---	---	---	---
LHX8	431707	broad.mit.edu	37	1	75602794	75602794	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75602794G>A	uc001dgo.2	+	4	779	c.115G>A	c.(115-117)GAG>AAG	p.E39K	LHX8_uc001dgq.2_5'UTR	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	39						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
FLG	2312	broad.mit.edu	37	1	152283625	152283625	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283625C>A	uc001ezu.1	-	3	3773	c.3737G>T	c.(3736-3738)AGC>ATC	p.S1246I	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1246	Ser-rich.|Filaggrin 7.				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				---	---	---	---
DCST2	127579	broad.mit.edu	37	1	154999201	154999201	+	Intron	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154999201A>G	uc001fgm.2	-						DCST2_uc009wpb.2_Intron	NM_144622	NP_653223			DC-STAMP domain containing 2							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)															---	---	---	---
OR6N1	128372	broad.mit.edu	37	1	158735950	158735950	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158735950G>C	uc010piq.1	-	1	523	c.523C>G	c.(523-525)CAG>GAG	p.Q175E		NM_001005185	NP_001005185	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N,	175	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
JMJD4	65094	broad.mit.edu	37	1	227921166	227921166	+	Silent	SNP	C	A	A	rs148217485	byFrequency	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227921166C>A	uc001hrb.2	-	4	909	c.909G>T	c.(907-909)GCG>GCT	p.A303A	SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_5'Flank|SNAP47_uc001hre.2_5'Flank|SNAP47_uc001hrf.2_5'Flank|LOC100130093_uc001hqx.3_RNA|LOC100130093_uc001hqy.3_RNA|JMJD4_uc001hrc.2_Silent_p.A303A	NM_023007	NP_075383	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4 isoform 1	303	JmjC.										0		Prostate(94;0.0885)																---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137983022	137983022	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137983022C>T	uc003esa.1	+	15	1592	c.1225C>T	c.(1225-1227)CAG>TAG	p.Q409*	TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Nonsense_Mutation_p.Q392*|ARMC8_uc011bmg.1_Nonsense_Mutation_p.Q356*|ARMC8_uc011bmh.1_Nonsense_Mutation_p.Q350*|ARMC8_uc003esb.1_Nonsense_Mutation_p.Q381*|ARMC8_uc003esc.1_Nonsense_Mutation_p.Q181*|ARMC8_uc003esf.1_5'UTR	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2	423	ARM 9.						binding				0																		---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142094635	142094635	+	Intron	SNP	C	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142094635C>G	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron	NM_019001	NP_061874			5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3																		---	---	---	---
TMPRSS11F	389208	broad.mit.edu	37	4	68934540	68934540	+	Intron	SNP	G	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68934540G>T	uc003hdt.1	-						LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron	NM_207407	NP_997290			transmembrane protease, serine 11F						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
MIER3	166968	broad.mit.edu	37	5	56234714	56234714	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56234714T>A	uc003jrd.1	-	4	336	c.311A>T	c.(310-312)GAC>GTC	p.D104V	MIER3_uc003jqz.1_Missense_Mutation_p.D41V|MIER3_uc003jra.1_Missense_Mutation_p.D104V|MIER3_uc003jrb.1_5'UTR|MIER3_uc003jrc.1_Missense_Mutation_p.D109V	NM_152622	NP_689835	Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family	104					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)														---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137485477	137485477	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137485477G>A	uc003lcf.1	-	23	3185	c.3130C>T	c.(3130-3132)CAG>TAG	p.Q1044*	BRD8_uc003lcc.1_Intron	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2	1044					cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
SPDEF	25803	broad.mit.edu	37	6	34508912	34508912	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34508912C>T	uc003ojq.1	-	3	898	c.483G>A	c.(481-483)TGG>TGA	p.W161*	SPDEF_uc011dsq.1_Nonsense_Mutation_p.W161*	NM_012391	NP_036523	O95238	SPDEF_HUMAN	SAM pointed domain containing ets transcription	161	PNT.				negative regulation of survival gene product expression|negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(3)|ovary(1)|central_nervous_system(1)	5																		---	---	---	---
TEK	7010	broad.mit.edu	37	9	27192629	27192629	+	Intron	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27192629G>A	uc003zqi.3	+						TEK_uc011lno.1_Intron|TEK_uc011lnp.1_Intron|TEK_uc003zqj.1_Intron	NM_000459	NP_000450			TEK tyrosine kinase, endothelial precursor						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)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117061471	117061471	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117061471G>A	uc001lcg.2	+	17	3122	c.2736G>A	c.(2734-2736)ACG>ACA	p.T912T	ATRNL1_uc010qsm.1_Silent_p.T87T|ATRNL1_uc010qsn.1_RNA	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	912	PSI 4.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)														---	---	---	---
MRGPRX2	117194	broad.mit.edu	37	11	19077900	19077900	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19077900C>T	uc001mph.2	-	2	138	c.50G>A	c.(49-51)GGA>GAA	p.G17E		NM_054030	NP_473371	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	17	Extracellular (Potential).				sensory perception of pain|sleep	plasma membrane	G-protein coupled receptor activity|neuropeptide binding			ovary(1)	1																		---	---	---	---
PDHX	8050	broad.mit.edu	37	11	35006231	35006231	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35006231G>C	uc001mvt.2	+	9	1664	c.1138G>C	c.(1138-1140)GAT>CAT	p.D380H	PDHX_uc010rep.1_Missense_Mutation_p.D365H|PDHX_uc010req.1_Missense_Mutation_p.D153H	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	380					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)															---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75155552	75155552	+	Intron	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75155552G>C	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc001own.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron|GDPD5_uc009yue.1_Intron	NM_030792	NP_110419			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1																		---	---	---	---
NECAP1	25977	broad.mit.edu	37	12	8242546	8242546	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8242546A>T	uc001qtx.2	+	2	188	c.110A>T	c.(109-111)AAA>ATA	p.K37I	NECAP1_uc001qty.2_5'UTR	NM_015509	NP_056324	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	37					endocytosis|protein transport	clathrin coated vesicle membrane|plasma membrane				ovary(1)	1				Kidney(36;0.0915)														---	---	---	---
STYK1	55359	broad.mit.edu	37	12	10780324	10780324	+	Splice_Site	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10780324C>A	uc001qys.2	-	7	1155	c.634_splice	c.e7-1	p.D212_splice		NM_018423	NP_060893			serine/threonine/tyrosine kinase 1							integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8															HNSCC(73;0.22)			---	---	---	---
SLC38A4	55089	broad.mit.edu	37	12	47172329	47172329	+	Silent	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47172329A>G	uc001rpi.2	-	11	1347	c.948T>C	c.(946-948)CAT>CAC	p.H316H	SLC38A4_uc001rpj.2_Silent_p.H316H	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	316	Extracellular (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Lung SC(27;0.192)|Renal(347;0.236)																	---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122967235	122967235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122967235G>A	uc001ucn.2	-	8	810	c.679C>T	c.(679-681)CCT>TCT	p.P227S	ZCCHC8_uc001ucm.2_5'UTR|ZCCHC8_uc009zxp.2_5'UTR|ZCCHC8_uc009zxq.2_5'UTR	NM_017612	NP_060082	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	227	CCHC-type.					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)														---	---	---	---
NOC4L	79050	broad.mit.edu	37	12	132636625	132636625	+	Intron	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132636625C>A	uc001ujz.1	+							NM_024078	NP_076983			nucleolar complex associated 4 homolog						rRNA processing	integral to membrane|nuclear membrane|nucleolus	protein binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)														---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108518661	108518661	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108518661T>C	uc001vql.2	-	1	800	c.284A>G	c.(283-285)CAG>CGG	p.Q95R		NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	95	Poly-Gln.					integral to membrane	binding			skin(1)	1																		---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28228486	28228486	+	Intron	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28228486C>T	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266			oculocutaneous albinism II						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				---	---	---	---
ZNF75A	7627	broad.mit.edu	37	16	3367328	3367328	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3367328T>G	uc002cut.3	+	6	876	c.350T>G	c.(349-351)TTT>TGT	p.F117C	ZNF75A_uc002cuv.3_RNA	NM_153028	NP_694573	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	117					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50258847	50258847	+	Silent	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50258847T>C	uc010vgo.1	+	10	1544	c.1509T>C	c.(1507-1509)TAT>TAC	p.Y503Y	PAPD5_uc010cbi.2_RNA|PAPD5_uc002efz.2_Silent_p.Y294Y|PAPD5_uc002ega.2_Silent_p.Y294Y	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a	424					cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)														---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	71054178	71054178	+	Missense_Mutation	SNP	T	C	C	rs6416709		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71054178T>C	uc002ezr.2	-	22	3357	c.3229A>G	c.(3229-3231)ATA>GTA	p.I1077V		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1077										ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
ELAC2	60528	broad.mit.edu	37	17	12903546	12903546	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12903546C>T	uc002gnz.3	-	15	1445	c.1350G>A	c.(1348-1350)GCG>GCA	p.A450A	ELAC2_uc002gnu.3_5'UTR|ELAC2_uc002gnv.3_Silent_p.A78A|ELAC2_uc002gnw.3_Silent_p.A108A|ELAC2_uc002gnx.3_Silent_p.A210A|ELAC2_uc010vvo.1_Silent_p.A248A|ELAC2_uc010vvp.1_Silent_p.A431A|ELAC2_uc010vvq.1_Silent_p.A449A|ELAC2_uc010vvr.1_Silent_p.A410A	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	450					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0														Hereditary_Prostate_Cancer				---	---	---	---
FAM83G	644815	broad.mit.edu	37	17	18874692	18874692	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18874692G>A	uc002guw.2	-	6	2619	c.2452C>T	c.(2452-2454)CGG>TGG	p.R818W	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	818										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ZNRF4	148066	broad.mit.edu	37	19	5456633	5456633	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5456633G>A	uc002mca.3	+	1	1208	c.1131G>A	c.(1129-1131)CCG>CCA	p.P377P		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	377	Cytoplasmic (Potential).					integral to membrane	zinc ion binding	p.P377Q(1)		large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)														---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6417055	6417055	+	Silent	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6417055G>C	uc002mer.3	-	12	1235	c.1125C>G	c.(1123-1125)CCC>CCG	p.P375P		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	375	Gly-rich.|KH 3.				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																		---	---	---	---
C3	718	broad.mit.edu	37	19	6697719	6697719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6697719C>T	uc002mfm.2	-	20	2589	c.2527G>A	c.(2527-2529)GAG>AAG	p.E843K		NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	843					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)														---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17104353	17104353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17104353G>A	uc002nfb.2	-	12	1312	c.1280C>T	c.(1279-1281)ACG>ATG	p.T427M		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	380						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
TMEM143	55260	broad.mit.edu	37	19	48836573	48836573	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48836573A>G	uc002pix.1	-	8	1292	c.1283T>C	c.(1282-1284)ATG>ACG	p.M428T	TMEM143_uc002piw.1_RNA|TMEM143_uc002piy.1_Missense_Mutation_p.M393T|TMEM143_uc010xzn.1_Missense_Mutation_p.M363T|TMEM143_uc010elw.1_Missense_Mutation_p.M328T|TMEM143_uc010xzo.1_Missense_Mutation_p.M218T	NM_018273	NP_060743	Q96AN5	TM143_HUMAN	transmembrane protein 143	428						integral to membrane|mitochondrion					0		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)														---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60910072	60910072	+	Intron	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60910072C>T	uc002ycq.2	-							NM_005560	NP_005551			laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
OFD1	8481	broad.mit.edu	37	X	13753462	13753462	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13753462C>T	uc004cvp.3	+	2	467	c.108C>T	c.(106-108)CTC>CTT	p.L36L	OFD1_uc004cvr.3_5'UTR|OFD1_uc011mil.1_5'UTR|OFD1_uc004cvq.3_5'UTR|OFD1_uc010nen.2_Silent_p.L35L|OFD1_uc004cvs.3_RNA|OFD1_uc004cvu.3_Silent_p.L35L|OFD1_uc004cvv.3_Silent_p.L35L|TRAPPC2_uc010nek.1_5'Flank|TRAPPC2_uc010nel.1_5'Flank|TRAPPC2_uc010nem.1_5'Flank	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	36					cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0																		---	---	---	---
ZFX	7543	broad.mit.edu	37	X	24228401	24228401	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24228401G>A	uc004dbf.2	+	9	1584	c.1326G>A	c.(1324-1326)AGG>AGA	p.R442R	ZFX_uc004dbe.2_3'UTR|ZFX_uc011mjv.1_Silent_p.R481R|ZFX_uc010nfz.2_Silent_p.R98R	NM_003410	NP_003401	P17010	ZFX_HUMAN	zinc finger protein, X-linked	442	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SLC35A2	7355	broad.mit.edu	37	X	48761971	48761971	+	Intron	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48761971C>A	uc004dlo.1	-						SLC35A2_uc011mml.1_3'UTR|SLC35A2_uc004dlp.1_3'UTR|SLC35A2_uc011mmm.1_3'UTR|SLC35A2_uc011mmn.1_3'UTR|SLC35A2_uc004dlr.1_3'UTR|SLC35A2_uc004dlq.2_Missense_Mutation_p.G209W	NM_005660	NP_005651			solute carrier family 35, member A2 isoform a						galactose metabolic process	Golgi membrane|integral to membrane|nucleus	sugar:hydrogen symporter activity|UDP-galactose transmembrane transporter activity			breast(1)	1																		---	---	---	---
MED12	9968	broad.mit.edu	37	X	70357076	70357076	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70357076C>A	uc004dyy.2	+	39	5790	c.5591C>A	c.(5590-5592)CCA>CAA	p.P1864Q	MED12_uc011mpq.1_Missense_Mutation_p.P1864Q|MED12_uc004dyz.2_Missense_Mutation_p.P1864Q|MED12_uc004dza.2_Missense_Mutation_p.P1711Q|MED12_uc010nla.2_Missense_Mutation_p.P490Q	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1864	Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)																	---	---	---	---
ZCCHC13	389874	broad.mit.edu	37	X	73524180	73524180	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73524180C>T	uc004ebs.3	+	1	156	c.79C>T	c.(79-81)CGA>TGA	p.R27*		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	27							nucleic acid binding|zinc ion binding				0																		---	---	---	---
DACH2	117154	broad.mit.edu	37	X	85969733	85969733	+	Intron	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85969733G>A	uc004eew.2	+						DACH2_uc004eex.2_Intron|DACH2_uc010nmq.2_Intron|DACH2_uc011mra.1_Intron|DACH2_uc010nmr.2_Intron|DACH2_uc004eey.2_Intron|DACH2_uc004eez.2_Intron	NM_053281	NP_444511			dachshund 2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5																		---	---	---	---
MCART6	401612	broad.mit.edu	37	X	103349655	103349655	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103349655A>T	uc004elu.2	-	2	467	c.286T>A	c.(286-288)TTT>ATT	p.F96I		NM_001012755	NP_001012773	Q5H9E4	MCAR6_HUMAN	mitochondrial carrier triple repeat 6	96	Helical; Name=2; (Potential).|Solcar 1.				transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
AMOT	154796	broad.mit.edu	37	X	112035177	112035177	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112035177C>T	uc004epr.2	-	6	1809	c.1809G>A	c.(1807-1809)GTG>GTA	p.V603V	AMOT_uc004eps.2_Silent_p.V194V	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	603	Potential.				actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117810670	117810670	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117810670G>T	uc004eqp.2	+	48	5493	c.5430G>T	c.(5428-5430)GAG>GAT	p.E1810D	DOCK11_uc004eqq.2_Missense_Mutation_p.E1589D	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1810	DHR-2.				blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
